[med-svn] [python-pbalign] 01/02: Imported Upstream version 0.2.0
Afif Elghraoui
afif-guest at moszumanska.debian.org
Wed Sep 2 03:30:28 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-pbalign.
commit b16dc6f507eb0ce8959e3895e9ad65068b7806b5
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Tue Sep 1 19:23:56 2015 -0700
Imported Upstream version 0.2.0
---
LICENSES.txt | 33 +
Makefile | 50 ++
README.md | 17 +
doc/Makefile | 153 +++++
doc/conf.py | 246 +++++++
doc/howto.rst | 353 ++++++++++
doc/index.rst | 15 +
pbalign/__init__.py | 79 +++
pbalign/alignservice/__init__.py | 34 +
pbalign/alignservice/align.py | 199 ++++++
pbalign/alignservice/blasr.py | 286 +++++++++
pbalign/alignservice/bowtie.py | 264 ++++++++
pbalign/alignservice/fastabasedalign.py | 87 +++
pbalign/alignservice/gmap.py | 307 +++++++++
pbalign/filterservice.py | 142 ++++
pbalign/forquiverservice/__init__.py | 34 +
pbalign/forquiverservice/forquiver.py | 99 +++
pbalign/forquiverservice/loadchemistry.py | 77 +++
pbalign/forquiverservice/loadpulses.py | 103 +++
pbalign/forquiverservice/repack.py | 87 +++
pbalign/forquiverservice/sort.py | 89 +++
pbalign/options.py | 522 +++++++++++++++
pbalign/pbalignfiles.py | 182 ++++++
pbalign/pbalignrunner.py | 306 +++++++++
pbalign/service.py | 73 +++
pbalign/tools/__init__.py | 36 ++
pbalign/tools/createChemistryHeader.py | 207 ++++++
pbalign/tools/extractUnmappedSubreads.py | 188 ++++++
pbalign/tools/loadChemistry.py | 78 +++
pbalign/tools/mask_aligned_reads.py | 194 ++++++
pbalign/utils/RgnH5IO.py | 295 +++++++++
pbalign/utils/__init__.py | 34 +
pbalign/utils/fileutil.py | 397 ++++++++++++
pbalign/utils/progutil.py | 69 ++
pbalign/utils/tempfileutil.py | 236 +++++++
setup.py | 26 +
tests/cram/test_mask_aligned_reads.t | 42 ++
tests/cram/test_pbalign.t | 276 ++++++++
tests/data/1.config | 25 +
tests/data/dir with spaces/reads.fasta | 5 +
tests/data/ecoli.fasta | 997 ++++++++++++++++++++++++++++
tests/data/ecoli_lp.fofn | 2 +
tests/data/example_read.fasta | 5 +
tests/data/example_ref.fasta | 62 ++
tests/data/lambda.rgn.h5 | 1 +
tests/data/lambda.sam | 21 +
tests/data/lambda_bax.fofn | 1 +
tests/data/lambda_query.fasta | 1000 +++++++++++++++++++++++++++++
tests/data/test_bas.fofn | 1 +
tests/data/test_ccs.fofn | 1 +
tests/data/test_filterAdapterOnly.fofn | 1 +
tests/data/test_leftmost_query.fasta | 50 ++
tests/data/test_leftmost_target.fasta | 301 +++++++++
tests/data/test_pulseFile.fasta | 695 ++++++++++++++++++++
tests/data/test_pulseFile.fofn | 4 +
tests/out/readme | 2 +
tests/unit/test_fileutil.py | 131 ++++
tests/unit/test_filterservice.py | 72 +++
tests/unit/test_forquiverservice.py | 47 ++
tests/unit/test_gmap.py | 54 ++
tests/unit/test_loadpulsesservice.py | 35 +
tests/unit/test_options.py | 136 ++++
tests/unit/test_pbalign.py | 56 ++
tests/unit/test_pbalignfiles.py | 83 +++
tests/unit/test_progutil.py | 19 +
tests/unit/test_referenceInfo.py | 22 +
tests/unit/test_repackservice.py | 35 +
tests/unit/test_rgnh5io.py | 119 ++++
tests/unit/test_sortservice.py | 38 ++
tests/unit/test_tmpfileutil.py | 91 +++
70 files changed, 10027 insertions(+)
diff --git a/LICENSES.txt b/LICENSES.txt
new file mode 100644
index 0000000..8aee62e
--- /dev/null
+++ b/LICENSES.txt
@@ -0,0 +1,33 @@
+Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+* Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+
+* Neither the name of Pacific Biosciences nor the names of its
+ contributors may be used to endorse or promote products derived from
+ this software without specific prior written permission.
+
+NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..83c2e54
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,50 @@
+SHELL = /bin/bash -e
+
+all: build install
+
+build:
+ python setup.py build --executable="/usr/bin/env python"
+
+bdist:
+ python setup.py build --executable="/usr/bin/env python"
+ python setup.py bdist --formats=egg
+
+install:
+ python setup.py install
+
+develop:
+ python setup.py develop
+
+test:
+ # Unit tests
+ find tests/unit -name "*.py" | xargs nosetests
+ # End-to-end tests
+ @echo pbalign cram tests require blasr installed.
+ find tests/cram -name "*.t" | xargs cram
+
+doc:
+ sphinx-apidoc -T -f -o doc src/ && cd doc && make html
+
+docs: doc
+
+doc-clean:
+ rm -f doc/*.html
+
+clean: doc-clean
+ rm -rf dist/ build/ *.egg-info
+ rm -rf doc/_build
+ find . -name "*.pyc" | xargs rm -f
+ rm -rf dist/
+ rm -f nostests.xml
+
+pip-install:
+ @which pip > /dev/null
+ @pip freeze|grep 'pbalign=='>/dev/null \
+ && ( pip uninstall -y pbalign \
+ || pip uninstall -y pbtools.pbalign ) \
+ || true
+ @pip install --no-index \
+ --install-option="--install-scripts=$(PREFIX)/bin" \
+ ./
+
+.PHONY: all build bdist install develop test doc clean
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..3c8d149
--- /dev/null
+++ b/README.md
@@ -0,0 +1,17 @@
+###pbalign maps PacBio reads to reference sequences.###
+
+
+**Q: Want to know how to install and run pbalign?**
+
+A: Please refer to [pbalign readme document](https://github.com/PacificBiosciences/pbalign/blob/master/doc/howto.rst)
+
+
+**Q: 'pbalign.py' does not work?**
+
+A: The main script has been changed from 'pbalign.py' to 'pbalign'. Please use 'pbalign' instead.
+
+
+**Q: Can pbalign handle large datasets with many movies?**
+
+A: pbalign is not designed to handle large datasets, you should follow a [divide and conquer way](https://github.com/PacificBiosciences/pbalign/wiki/Tutorial:-How-to-divide-and-conquer-large-datasets-using-pbalign) to align many movies to a reference.
+
diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 0000000..6df2701
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,153 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+BUILDDIR = _build
+
+# Internal variables.
+PAPEROPT_a4 = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo " html to make standalone HTML files"
+ @echo " dirhtml to make HTML files named index.html in directories"
+ @echo " singlehtml to make a single large HTML file"
+ @echo " pickle to make pickle files"
+ @echo " json to make JSON files"
+ @echo " htmlhelp to make HTML files and a HTML help project"
+ @echo " qthelp to make HTML files and a qthelp project"
+ @echo " devhelp to make HTML files and a Devhelp project"
+ @echo " epub to make an epub"
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+ @echo " latexpdf to make LaTeX files and run them through pdflatex"
+ @echo " text to make text files"
+ @echo " man to make manual pages"
+ @echo " texinfo to make Texinfo files"
+ @echo " info to make Texinfo files and run them through makeinfo"
+ @echo " gettext to make PO message catalogs"
+ @echo " changes to make an overview of all changed/added/deprecated items"
+ @echo " linkcheck to check all external links for integrity"
+ @echo " doctest to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+ -rm -rf $(BUILDDIR)/*
+
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+ $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+ @echo
+ @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+ ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+ @echo
+ @echo "Build finished; now you can run "qcollectiongenerator" with the" \
+ ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+ @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pbalign.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pbalign.qhc"
+
+devhelp:
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+ @echo
+ @echo "Build finished."
+ @echo "To view the help file:"
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/pbalign"
+ @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pbalign"
+ @echo "# devhelp"
+
+epub:
+ $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+ @echo
+ @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+ @echo "Run \`make' in that directory to run these through (pdf)latex" \
+ "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through pdflatex..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+ $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+ @echo
+ @echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+ $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+ @echo
+ @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo
+ @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+ @echo "Run \`make' in that directory to run these through makeinfo" \
+ "(use \`make info' here to do that automatically)."
+
+info:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo "Running Texinfo files through makeinfo..."
+ make -C $(BUILDDIR)/texinfo info
+ @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+ $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+ @echo
+ @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+ "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+ "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/doc/conf.py b/doc/conf.py
new file mode 100755
index 0000000..60c81d4
--- /dev/null
+++ b/doc/conf.py
@@ -0,0 +1,246 @@
+# -*- coding: utf-8 -*-
+#
+# pbalign documentation build configuration file, created by
+# sphinx-quickstart on Wed Jul 17 13:09:03 2013.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'pbalign'
+copyright = u'2013, 2013, pbiDevNet'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '0.5'
+# The full version, including alpha/beta/rc tags.
+release = '0.5'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'pbaligndoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+ ('index', 'pbalign.tex', u'pbalign Documentation',
+ u'2013, pbiDevNet', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ ('index', 'pbalign', u'pbalign Documentation',
+ [u'2013, pbiDevNet'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output ------------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ ('index', 'pbalign', u'pbalign Documentation',
+ u'2013, pbiDevNet', 'pbalign', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'http://docs.python.org/': None}
diff --git a/doc/howto.rst b/doc/howto.rst
new file mode 100644
index 0000000..1bbcf3e
--- /dev/null
+++ b/doc/howto.rst
@@ -0,0 +1,353 @@
+How to install and run pbalign
+==============================
+
+pbalign is a tool for aligning PacBio reads to reference sequences.
+It is part of the PacBio Bioinformatics tools, and will
+be bundled in the 2.1 release of SMRTanalysis. You may also follow the
+instructions below to install pbalign.
+
+*Note: the pseudo namespace pbtools has been removed in version 0.2.0.*
+
+*Note: program name has been changed from `pbalign.py` in version 0.1.0
+to `pbalign` in version 0.2.0.*
+
+*Note: please install this software on an isolated machine that does
+not have SMRTanalysis installed.*
+
+Background
+----------
+**pbalign** aligns PacBio reads to reference sequences, filters aligned
+reads according to user-specific filtering criteria, and converts the
+output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5)
+format. The output Compare HDF5 file will be compatible with Quiver if
+``--forQuiver`` option is specified.
+
+Required software
+-----------------
+pbalign is available through the ``pbalign`` script from the
+``pbalign`` package. To use pbalign, the following PacBio software is
+required,
+
+- ``pbalign``, containing ``pbalign``
+- ``pbcore``, a package providing access to PacBio data files
+- ``blasr``, a package of PacBio aligner blasr, containing c++ executables
+ for processing PacBio data, such as ``blasr``, ``pls2fasta``,
+ ``samFilter``, ``samtoh5`` and ``loadPulses``
+
+The following software is optionally required if ``--forQuiver`` option
+will be used to convert the output Compare HDF5 file to be compatible
+with Quiver.
+- ``pbh5tools.cmph5tools``, a PacBio Bioinformatics tools that manipulates
+Compare HDF5 files.
+- ``h5repack``, a HDF5 tool to compress and repack HDF5 files.
+
+The default aligner that pbalign uses is ``blasr``. If you want to use
+bowtie2 as aligner, then the bowtie2 package also needs to be installed.
+
+Required libraries and tools
+----------------------------
+- Python 2.7.3
+- virtualenv (builds isolated Python environments)
+- numpy 1.6.1 (required by pbcore)
+- h5py 2.0.1 (required by pbcore)
+
+If you are within PacBio, these requirements are already installed
+within the cluster environment.
+
+Otherwise, you will need to install them yourself.
+
+Data file requirements
+----------------------
+pbalign distinguishes input and output file formats by file extensions.
+
+The input PacBio reads can be in FASTA, Base HDF5, Pulse HDF5, Circular
+Consensus Sequence (CCS) HDF5 or file or file names (FOFN). The supported
+input file extensions are as follows.
+
+- FASTA : .fa or .fasta
+- PacBio BASE HDF5 : .bas.h5 or .bax.h5
+- PacBio PULSE HDF5 : .pls.h5 or .plx.h5
+- PacBio CCS HDF5 : .ccs.h5
+- File of file names : .fofn
+
+The input reference sequences can be in a FASTA file or a reference deposit
+directory created by referenceUploader (a PacBio tool for uploading
+references to the server and data preprocessing).
+
+The output file can either be a SAM file or a Compare HDF5 file. The output
+Compare HDF5 file cannot be consumed by Quiver directly unleis ``--forQuiver``
+option is specified. The supported output file extensions are as follows.
+
+- SAM : .sam
+- PacBio Compare HDF5: .cmp.h5
+
+
+Manual installation instructions
+--------------------------------
+Step 1: Set up your Python virtual environment
+```````````````````````````````````````````````````
+To install ``Python 2.7``, please visit ::
+
+ http://www.python.org/
+
+, or if you have root permission on Ubuntu, execute ::
+
+ sudo apt-get install python
+
+To install ``pip``, please visit ::
+
+ https://pypi.python.org/pypi/pip
+
+, or if you have root permission using Ubuntu, execute ::
+
+ sudo apt-get install python-pip
+
+To install ``virtualenv``, please visit ::
+
+ https://pypi.python.org/pypi/virtualenv
+
+, or execute ::
+
+ pip install virtualenv
+
+To set up a new virtualenv, do ::
+
+ $ cd; virtualenv -p python2.7 --no-site-packages my_env
+
+, and activate the virtualenv using ::
+
+ $ source ~/my_env/bin/activate
+
+
+To install ``git``, please visit ::
+
+ http://git-scm.com/.
+
+Step 2: Install required software and library
+`````````````````````````````````````````````
+To install blasr, please execute ::
+
+ $ git clone https://github.com/PacificBiosciences/blasr
+
+, and follow instructions at ::
+
+ https://github.com/PacificBiosciences/blasr/blob/master/README.md
+
+Before installing pbcore, you may need to install numpy and h5py from ::
+
+ http://www.numpy.org/
+ https://code.google.com/p/h5py/
+
+, or if you have root permission on Ubuntu, do ::
+
+ $ git install numpy
+ $ sudo apt-get install libhdf5-serial-dev
+ $ git install h5py
+
+To install pbcore, execute ::
+
+ $ pip install git+https://github.com/PacificBiosciences/pbcore
+
+
+Step 3: Install optionally required software and library
+````````````````````````````````````````````````````````
+To install pbh5tools, execute ::
+
+ $ pip install git+https://github.com/PacificBiosciences/pbh5tools
+
+To install ``HDF5 tools``, visit ::
+
+ http://www.hdfgroup.org/products/hdf5_tools/
+
+, or if you have root permission on Ubuntu, do ::
+
+ $ sudo apt-get install hdf5-tools
+
+
+Step 4: Install pbalign
+```````````````````````
+To *uninstall* pbalign, execute ::
+
+ $ pip uninstall pbalign
+
+
+To install pbalign, execute ::
+
+ $ pip install git+https://github.com/PacificBiosciences/pbalign
+
+, or to download the whole pbalign package with examples ::
+
+ $ git clone https://github.com/PacificBiosciences/pbalign.git
+ $ cd pbalign
+ $ pip install .
+
+
+Examples
+--------
+
+(1) Basic usage of pbalign.
+
+- Example (1.1) ::
+
+ $ pbalign tests/data/example_read.fasta \
+ tests/data/example_ref.fasta \
+ example.sam
+
+- Example (1.2) ::
+
+ $ pbalign tests/data/example_read.fasta \
+ tests/data/example_ref.fasta \
+ example.cmp.h5
+
+- Example (1.3) - with optional arguments ::
+
+ $ pbalign --maxHits 10 --hitPolicy all \
+ tests/data/example_read.fasta \
+ tests/data/example_ref.fasta \
+ example.sam
+
+
+(2) Advanced usage of pbalign.
+
+- Example (2.1) - Import pre-defined options from a config File ::
+
+ $ pbalign --configFile=tests/data/1.config \
+ tests/data/example_read.fasta \
+ tests/data/example_ref.fasta \
+ example.sam
+
+- Example (2.2) - Pass options through to aligner ::
+
+ $ pbalign --algorithmOptions='-nCandidates 10 -sdpTupleSize 12' \
+ tests/data/example_read.fasta \
+ tests/data/example_ref.fasta \
+ example.sam
+
+
+- Example (2.3) - Create a cmp.h5 file with --forQuiver option ::
+
+ # The output cmp.h5 file will loaded with quality values (pulses)
+ # from the input bas/bax.h5 file, sorted and repacked, and therefore
+ # can be consumed by Quiver directly, (Note that in order to use
+ # --forQuiver option, cmph5tools and h5repack are required.)
+
+ $ pbalign --forQuiver your_movie.bas.h5 your_reference.fasta out.cmp.h5
+
+
+
+(3) Use pbalign as a library through Python API.
+
+- Example (3.1) ::
+
+ $ python
+ >>> from pbalign.pbalignrunner import PBAlignRunner
+ >>> # Specify arguments in a list.
+ >>> args = ['--maxHits', '20', 'tests/data/example_read.fasta',\
+ ... 'tests/data/example_ref.fasta', 'example.sam']
+ >>> # Create a PBAlignRunner object.
+ >>> a = PBAlignRunner(args)
+ >>> # Execute.
+ >>> exitCode = a.start()
+ >>> # Show all files used.
+ >>> print a.fileNames
+
+
+Usage
+-----
+::
+
+ usage: pbalign [-h] [--verbose] [--version] [--profile] [--debug]
+ [--regionTable REGIONTABLE] [--configFile CONFIGFILE]
+ [--algorithm {blasr,bowtie}] [--maxHits MAXHITS]
+ [--minAnchorSize MINANCHORSIZE]
+ [--useccs {useccs,useccsall,useccsdenovo}]
+ [--noSplitSubreads] [--nproc NPROC]
+ [--algorithmOptions ALGORITHMOPTIONS]
+ [--maxDivergence MAXDIVERGENCE] [--minAccuracy MINACCURACY]
+ [--minLength MINLENGTH]
+ [--scoreFunction {alignerscore,editdist,blasrscore}]
+ [--scoreCutoff SCORECUTOFF]
+ [--hitPolicy {randombest,allbest,random,all}] [--forQuiver]
+ [--seed SEED] [--tmpDir TMPDIR]
+ inputFileName referencePath outputFileName
+
+ Mapping PacBio sequences to references using an algorithm
+ selected from a selection of supported command-line alignment
+ algorithms. Input can be a fasta, pls.h5, bas.h5 or ccs.h5
+ file or a fofn (file of file names). Output is in either
+ cmp.h5 or sam format.
+
+ positional arguments:
+ inputFileName The input file can be a fasta, pls.h5, bas.h5, ccs.h5
+ file or a fofn.
+ referencePath Either a reference fasta file or a reference repository.
+ outputFileName The output cmp.h5 or sam file.
+
+ optional arguments:
+ -h, --help show this help message and exit
+ --verbose, -v Set the verbosity level
+ --version show program's version number and exit
+ --profile Print runtime profile at exit
+ --debug Run within a debugger session
+ --regionTable REGIONTABLE
+ Specify a region table for filtering reads.
+ --configFile CONFIGFILE
+ Specify a set of user-defined argument values.
+ --algorithm {blasr,bowtie}
+ Select an aligorithm from ('blasr', 'bowtie').
+ Default algorithm is blasr.
+ --maxHits MAXHITS The maximum number of matches of each read to the
+ reference sequence that will be evaluated. Default
+ value is 10.
+ --minAnchorSize MINANCHORSIZE
+ The minimum anchor size defines the length of the read
+ that must match against the reference sequence. Default
+ value is 12.
+ --useccs {useccs,useccsall,useccsdenovo}
+ Map the ccsSequence to the genome first, then align
+ subreads to the interval that the CCS reads mapped to.
+ useccs: only maps subreads that span the length of
+ the template.
+ useccsall: maps all subreads.
+ useccsdenovo: maps ccs only.
+ --noSplitSubreads Do not split reads into subreads even if subread
+ regions are available.
+ Default value is False.
+ --nproc NPROC Number of threads. Default value is 8.
+ --algorithmOptions ALGORITHMOPTIONS
+ Pass alignment options through.
+ --maxDivergence MAXDIVERGENCE
+ The maximum allowed percentage divergence of a read
+ from the reference sequence. Default value is 30.
+ --minAccuracy MINACCURACY
+ The minimum percentage accuracy of alignments that
+ will be evaluated. Default value is 70.
+ --minLength MINLENGTH
+ The minimum aligned read length of alignments that
+ will be evaluated. Default value is 50.
+ --scoreFunction {alignerscore,editdist,blasrscore}
+ Specify a score function for evaluating alignments.
+ alignerscore : aligner's score in the SAM tag 'as'.
+ editdist : edit distance between read and reference.
+ blasrscore : blasr's default score function.
+ Default value is alignerscore.
+ --scoreCutoff SCORECUTOFF
+ The worst score to output an alignment.
+ --hitPolicy {randombest,allbest,random,all}
+ Specify a policy for how to treat multiple hit
+ random : selects a random hit.
+ all : selects all hits.
+ allbest : selects all the best score hits.
+ randombest: selects a random hit from all best
+ alignment score hits.
+ Default value is randombest.
+ --forQuiver The output cmp.h5 file which will be sorted, loaded
+ with pulse information, and repacked, so that it
+ can be consumed by quiver directly. This requires
+ the input file to be in PacBio bas/pls.h5 format.
+ Default value is False.
+ --seed SEED Initialize the random number generator with a none-zero
+ integer. Zero means that current system time is used.
+ Default value is 1.
+ --tmpDir TMPDIR Specify a directory for saving temporary files.
+ Default is /scratch.
diff --git a/doc/index.rst b/doc/index.rst
new file mode 100644
index 0000000..00bbafb
--- /dev/null
+++ b/doc/index.rst
@@ -0,0 +1,15 @@
+.. pbalign documentation master file, created by
+ sphinx-quickstart on Wed Jul 17 13:09:03 2013.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+pbalign
+=======
+
+Contents:
+
+.. toctree::
+ :maxdepth: 3
+
+ howto
+
diff --git a/pbalign/__init__.py b/pbalign/__init__.py
new file mode 100755
index 0000000..76a6c57
--- /dev/null
+++ b/pbalign/__init__.py
@@ -0,0 +1,79 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+# Author: Yuan Li
+"""Initialization."""
+
+from __future__ import absolute_import
+
+_changelist = "$Change: 141024 $"
+
+
+def _get_changelist(perforce_str):
+ """Extract change list from p4 str"""
+ import re
+ rx = re.compile(r'Change: (\d+)')
+ match = rx.search(perforce_str)
+ if match is None:
+ v = 'UnknownChangelist'
+ else:
+ try:
+ v = int(match.group(1))
+ except (TypeError, IndexError):
+ v = "UnknownChangelist"
+ return v
+
+
+def get_changelist():
+ """Return changelist"""
+ return _get_changelist(_changelist)
+
+def get_dir():
+ """Return lib directory."""
+ return op.dirname(op.realpath(__file__))
+
+VERSION = (0, 2, 0, get_changelist())
+
+
+def get_version():
+ """Return the version as a string. "O.7"
+
+ This uses a major.minor
+
+ Each python module of the system (e.g, butler, detective, siv_butler.py)
+ will use this version + individual changelist. This allows top level
+ versioning, and sub-component to be versioned based on a p4 changelist.
+
+ .. note:: This should be improved to be compliant with PEP 386.
+ """
+ return ".".join([str(i) for i in VERSION])
+
+
diff --git a/pbalign/alignservice/__init__.py b/pbalign/alignservice/__init__.py
new file mode 100755
index 0000000..175bd6a
--- /dev/null
+++ b/pbalign/alignservice/__init__.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+# Author: Yuan Li
+"""Initialization."""
+from __future__ import absolute_import
diff --git a/pbalign/alignservice/align.py b/pbalign/alignservice/align.py
new file mode 100755
index 0000000..eb39eb2
--- /dev/null
+++ b/pbalign/alignservice/align.py
@@ -0,0 +1,199 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+# Author: Yuan Li
+"""This script defines class AlignService."""
+
+from __future__ import absolute_import
+import logging
+from copy import copy
+from pbalign.options import importDefaultOptions
+from pbalign.utils.tempfileutil import TempFileManager
+from pbalign.service import Service
+
+
+class AlignService (Service):
+ """Super class for all alignment services.
+
+ AlignService takes argument options as input and generates a SAM file
+ as output.
+ Non-abstract subclasses should define the following properties.
+ name : name of the subclass align service
+ availability: availability of the subclass align service
+ scoreSign : score sign of the subclass align service
+ Subclasses should override the following virtual methods.
+ _preProcess :
+ _toCmd()
+ _postProcesss()
+ If --algorithmOptions needs to be supported by a subclass, override
+ _resolveAlgorithmOptions().
+
+ """
+ @property
+ def scoreSign(self):
+ """Align service score sign can be -1 or 1.
+ -1: negative scores are better than positive ones.
+ 1: positive scores are better than negative ones.
+ """
+ raise NotImplementedError(
+ "Virtual property scoreSign() for AlignService must be " +
+ "overwritten.")
+
+ def _resolveAlgorithmOptions(self, options, fileNames):
+ """A virtual method to resolve options specified within
+ --algorithmOptions and options parsed from the command-line
+ (including the config file).
+ Input:
+ options: options parsed from a command-line and a config file.
+ fileNames: an PBAlignFiles object.
+ Output: new options
+ """
+ if options.algorithmOptions is None or options.algorithmOptions == "":
+ return copy(options)
+
+ raise NotImplementedError(
+ "_resolveAlgorithmOptions() method for AlignService must be " +
+ "overridden if --algorithmOptions is specified.")
+
+ def __init__(self, options, fileNames, tempFileManager=None):
+ """Initialize an AlignSerivce object.
+ Need to resolve options specified within algorithmOptions;
+ patch default options if not specified by the user
+ inherit or initialize a tempory file manager
+ Input:
+ options : options parsed from (a list of arguments and
+ a config file if --configFile is specified).
+ fileNames : an object of PBAlignFiles
+ tempFileManager: a temporary file manager. If it is None,
+ create a new temporary file manager.
+ """
+ self._options = options
+
+ # Verify and assign input & output files.
+ self._fileNames = fileNames
+ self._fileNames.SetInOutFiles(self._options.inputFileName,
+ self._options.referencePath,
+ self._options.outputFileName,
+ self._options.regionTable,
+ self._options.pulseFile)
+
+ # Resolve options specified within --algorithmOptions with
+ # options parsed from the argument list (e.g. the command-line)
+ # or a config file.
+ self._options = self._resolveAlgorithmOptions(self._options,
+ self._fileNames)
+
+ # Patch PBalign default options if they havn't been specified yet.
+ self._options = importDefaultOptions(self._options)[0]
+
+ if tempFileManager is None:
+ self._tempFileManager = TempFileManager(self._options.tmpDir)
+ else:
+ self._tempFileManager = tempFileManager
+ self._tempFileManager.SetRootDir(self._options.tmpDir)
+ # self.args is finalized.
+ logging.debug("Parsed arguments considering configFile and " +
+ "algorithmOptions: " + str(self._options))
+
+ @property
+ def cmd(self):
+ """String of a command line to align reads."""
+ return self._toCmd(self._options,
+ self._fileNames,
+ self._tempFileManager)
+
+ def _toCmd(self, options, fileNames, tempFileManager):
+ """A virtual method to generate a command line string.
+
+ Generate a command line of the aligner to use in bash based on
+ options and PBAlignFiles.
+ Input:
+ options : arguments parsed from the command-line, the
+ config file and --algorithmOptions.
+ fileNames: an PBAlignFiles object.
+ tempFileManager: temporary file manager.
+ Output:
+ a command-line string which can be used in bash.
+
+ """
+ raise NotImplementedError(
+ "_toCmd() method for AlignService must be overridden")
+
+ def _preProcess(self, inputFileName, referenceFile, regionTable,
+ noSplitSubreads, tempFileManager, isWithinRepository):
+ """A virtual method to prepare inputs for the aligner.
+
+ Input:
+ inputFileName : a PacBio BASE/PULSE/FOFN file.
+ referenceFile : a FASTA reference file.
+ regionTable : a region table RGN.H5/FOFN file.
+ noSplitSubreads: whether to split subreads or not.
+ tempFileManager: temporary file manager.
+ isWithinRepository: whether or not the reference is within
+ a refererence repository.
+ Output:
+ String, a FASTA file which can be used by the aligner.
+
+ """
+ raise NotImplementedError(
+ "_preProcess() method for AlignService must be overridden")
+
+ def _postProcess(self):
+ """A virtual method to post process the generated output file. """
+ raise NotImplementedError(
+ "_postProcess() method for AlignService must be overridden")
+
+ def run(self):
+ """AlignService starts to run. """
+ logging.info(self.name + ": Align reads to references using " +
+ "{prog}.".format(prog=self.progName))
+ # Prepare inputs for the aligner.
+ self._fileNames.queryFileName = self._preProcess(
+ self._fileNames.inputFileName,
+ self._fileNames.targetFileName,
+ self._fileNames.regionTable,
+ self._options.noSplitSubreads,
+ self._tempFileManager,
+ self._fileNames.isWithinRepository)
+
+ self._fileNames.alignerSamOut = self._tempFileManager.\
+ RegisterNewTmpFile(suffix=".sam")
+
+ # Generate and execute cmd.
+ try:
+ output, errCode, errMsg = self._execute()
+ except RuntimeError as e:
+ raise RuntimeError(str(e))
+
+ # Post process the results.
+ self._postProcess()
+
+ return output, errCode, errMsg
diff --git a/pbalign/alignservice/blasr.py b/pbalign/alignservice/blasr.py
new file mode 100755
index 0000000..3ec94af
--- /dev/null
+++ b/pbalign/alignservice/blasr.py
@@ -0,0 +1,286 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+"""This script defines class BalserService which calls blasr to align reads."""
+
+# Author: Yuan Li
+
+from __future__ import absolute_import
+from pbalign.alignservice.align import AlignService
+from pbalign.utils.fileutil import FILE_FORMATS, real_upath
+import logging
+
+
+class BlasrService(AlignService):
+ """Class BlasrService calls blasr to align reads."""
+
+ @property
+ def name(self):
+ """Blasr Service name."""
+ return "BlasrService"
+
+ @property
+ def progName(self):
+ """Program to call."""
+ return "blasr"
+
+ @property
+ def scoreSign(self):
+ """score sign for blasr is -1, the lower the better."""
+ return -1
+
+ def __parseAlgorithmOptionItems(self, optionstr):
+ """Given a string of algorithm options, reconstruct option items.
+ First, split the string by white space, then reconstruct path with
+ white spaces.
+ """
+ items = optionstr.split(' ')
+ ret = []
+ for index, item in enumerate(items):
+ if item.endswith('\\'):
+ item = '{x} '.format(x=item)
+ if index > 0 and items[index-1].endswith('\\'):
+ ret[-1] = "{x}{y}".format(x=ret[-1], y=item)
+ else:
+ ret.append(item)
+ return ret
+
+ def _resolveAlgorithmOptions(self, options, fileNames):
+ """ Resolve options specified within --algorithmOptions with
+ options parsed from the command-line or the config file.
+ Return updated options.
+ If find conflicting values of the following options, error out.
+ (1) --maxHits and blasr -bestn
+ (2) --maxAnchorSize and blasr -minMatch
+ (3) --useccs and blasr -useccs/-useccsall/useccsdenovo
+ If find conflicting values of sawriter, regionTable and nproc,
+ it does not matter which value is used.
+ Input:
+ options : the original pbalign options from argumentList
+ and configFile.
+ fileNames: an PBAlignFiles object
+ Output:
+ new options by resolving options specified within
+ --algorithmOptions and the original pbalign options
+ """
+ if options.algorithmOptions is None:
+ return options
+
+ ignoredBinaryOptions = ['-m', '-out', '-V']
+ ignoredUnitaryOptions = ['-h', '--help', '--version',
+ '-v', '-vv', '-sam']
+
+ items = self.__parseAlgorithmOptionItems(options.algorithmOptions)
+ i = 0
+ try:
+ while i < len(items):
+ infoMsg, errMsg, item = "", "", items[i]
+ if item == "-sa":
+ val = real_upath(items[i+1])
+ if fileNames.sawriterFileName != val:
+ infoMsg = "Over write sa file with {0}".format(val)
+ fileNames.sawriterFileName = val
+ elif item == "-regionTable":
+ val = real_upath(items[i+1])
+ if fileNames.regionTable != val:
+ infoMsg = "Over write regionTable with {0}.\n"\
+ .format(val)
+ fileNames.regionTable = val
+ elif item == "-bestn":
+ val = int(items[i+1])
+ if options.maxHits is not None and \
+ int(options.maxHits) != val:
+ errMsg = "blasr -bestn specified within " + \
+ "--algorithmOptions is equivalent to " + \
+ "--maxHits. Conflicting values of " + \
+ "--algorithmOptions '-bestn' and " +\
+ "--maxHits have been found."
+ else:
+ options.maxHits = val
+ elif item == "-minMatch":
+ val = int(items[i+1])
+ if options.minAnchorSize is not None and \
+ int(options.minAnchorSize) != val:
+ errMsg = "blasr -minMatch specified within " + \
+ "--algorithmOptions is equivalent to " + \
+ "--minAnchorSize. Conflicting values " + \
+ "of --algorithmOptions '-minMatch' and " + \
+ "--minAnchorSize have been found."
+ else:
+ options.minAnchorSize = val
+ elif item == "-nproc":
+ val = int(items[i+1])
+ # The number of threads is not critical.
+ if options.nproc is None or \
+ int(options.nproc) != val:
+ infoMsg = "Over write nproc with {n}.".format(n=val)
+ options.nproc = val
+ elif item == "-noSplitSubreads":
+ if not options.noSplitSubreads:
+ infoMsg = "Over write noSplitSubreads with True."
+ logging.info(self.name +
+ ": Resolve algorithmOptions. " + infoMsg)
+ options.noSplitSubreads = True
+ del items[i]
+ continue
+ elif item == "-concordant":
+ if not options.concordant:
+ infoMsg = "Over writer concordant with True."
+ logging.info(self.name +
+ ": Resolve algorithmOptions. " + infoMsg)
+ options.concordant = True
+ del items[i]
+ elif "-useccs" in item: # -useccs, -useccsall, -useccsdenovo
+ val = item.lstrip('-')
+ if options.useccs != val and options.useccs is not None:
+ errMsg = "Found conflicting options in " + \
+ "--algorithmOptions '{v}' \nand --useccs={u}"\
+ .format(v=item, u=options.useccs)
+ else:
+ options.useccs = val
+ elif item == "-seed" or item == "-randomSeed":
+ val = int(items[i+1])
+ if options.seed is None or int(options.seed) != val:
+ infoMsg = "Overwrite random seed with {0}.".format(val)
+ options.seed = val
+ elif item in ignoredBinaryOptions:
+ pass
+ elif item in ignoredUnitaryOptions:
+ del items[i:i+1]
+ continue
+ else:
+ i += 1
+ continue
+
+ if errMsg != "":
+ logging.error(errMsg)
+ raise ValueError(errMsg)
+
+ if infoMsg != "":
+ logging.info(self.name + ": Resolve algorithmOptions. " +
+ infoMsg)
+
+ del items[i:i+2]
+ except Exception as e:
+ errMsg = "An error occured during parsing algorithmOptions " + \
+ "'{ao}': ".format(ao=options.algorithmOptions)
+ logging.error(errMsg + str(e))
+ raise ValueError(errMsg + str(e))
+
+ # Update algorithmOptions when resolve is done
+ options.algorithmOptions = " ".join(items)
+ return options
+
+ def _toCmd(self, options, fileNames, tempFileManager):
+ """ Generate a command line for blasr based on options and
+ PBAlignFiles, and return a command-line string which can
+ be used in bash.
+ Input:
+ options : arguments parsed from the command-line, the
+ config file and --algorithmOptions.
+ fileNames: an PBAlignFiles object.
+ tempFileManager: temporary file manager.
+ Output:
+ a command-line string which can be used in bash.
+ """
+ cmdStr = "blasr {queryFile} {targetFile} -sam -out {outFile} ".format(
+ queryFile=fileNames.queryFileName,
+ targetFile=fileNames.targetFileName,
+ outFile=fileNames.alignerSamOut)
+
+ if ((fileNames.sawriterFileName is not None) and
+ (fileNames.sawriterFileName != "")):
+ cmdStr += " -sa {sawriter} ".format(
+ sawriter=fileNames.sawriterFileName)
+
+ if ((fileNames.regionTable != "") and
+ (fileNames.regionTable is not None)):
+ cmdStr += " -regionTable {regionTable} ".format(
+ regionTable=fileNames.regionTable)
+
+ if options.maxHits is not None and options.maxHits != "":
+ cmdStr += " -bestn {n}".format(n=options.maxHits)
+
+ if (options.minAnchorSize is not None and
+ options.minAnchorSize != ""):
+ cmdStr += " -minMatch {0} ".format(options.minAnchorSize)
+
+ if options.nproc is not None and options.nproc != "":
+ cmdStr += " -nproc {0} ".format(options.nproc)
+
+ if options.minLength is not None:
+ cmdStr += " -minSubreadLength {n} -minReadLength {n} ".\
+ format(n=options.minLength)
+
+ if options.noSplitSubreads:
+ cmdStr += " -noSplitSubreads "
+
+ if options.concordant:
+ cmdStr += " -concordant "
+
+ if options.seed is not None and options.seed != 0:
+ cmdStr += " -randomSeed {0} ".format(options.seed)
+
+ if options.hitPolicy == "randombest":
+ cmdStr += " -placeRepeatsRandomly "
+
+ if options.useccs is not None and options.useccs != "":
+ cmdStr += " -{0} ".format(options.useccs)
+
+ # When input is a FASTA file, blasr -clipping = soft
+ if fileNames.inputFileFormat == FILE_FORMATS.FASTA:
+ cmdStr += " -clipping soft "
+
+ if options.algorithmOptions is not None:
+ cmdStr += " {0} ".format(options.algorithmOptions)
+
+ return cmdStr
+
+ def _preProcess(self, inputFileName, referenceFile=None,
+ regionTable=None, noSplitSubreads=None,
+ tempFileManager=None, isWithinRepository=None):
+ """Preprocess input files.
+ Input:
+ inputFilieName : a PacBio BASE/PULSE/FOFN file.
+ referenceFile : a FASTA reference file.
+ regionTable : a region table RGN.H5/FOFN file.
+ noSplitSubreads: whether to split subreads or not.
+ tempFileManager: temporary file manager.
+ Output:
+ string, a file which can be used by blasr.
+ """
+ # For blasr, nothing needs to be done, return the input PacBio
+ # PULSE/BASE/FOFN reads directly.
+ return inputFileName
+
+ def _postProcess(self):
+ """ Postprocess after alignment is done. """
+ logging.debug(self.name + ": Postprocess after alignment is done. ")
diff --git a/pbalign/alignservice/bowtie.py b/pbalign/alignservice/bowtie.py
new file mode 100755
index 0000000..24ed2a5
--- /dev/null
+++ b/pbalign/alignservice/bowtie.py
@@ -0,0 +1,264 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+"""This script defines class BowtieSerive, which uses bowtie to align reads."""
+
+# Author: Yuan Li
+
+from __future__ import absolute_import
+from pbalign.alignservice.fastabasedalign import FastaBasedAlignService
+from os import path
+from pbcore.util.Process import backticks
+import logging
+
+
+def bt2BaseName(tempDir, refFile):
+ """Return basename of bowtie2 index files.
+
+ Input:
+ tempDir: a temporary directory for saving bowtie2
+ index files.
+ refFile: the reference sequence file.
+ Output:
+ string, the basename of bowtie2 index files.
+
+ """
+ return path.join(tempDir, path.splitext(path.basename(refFile))[0])
+
+
+def bt2IndexFiles(baseName):
+ """Return a tuple of bowtie2 index files.
+
+ Input:
+ baseName: the base name of bowtie2 index files.
+ Output:
+ list of strings, bowtie2 index files.
+
+ """
+ exts = ['1.bt2', '2.bt2', '3.bt2', '4.bt2',
+ 'rev.1.bt2', 'rev.2.bt2']
+ return [".".join([baseName, ext]) for ext in exts]
+
+
+class BowtieService(FastaBasedAlignService):
+ """BowtieService calls bowtie to align reads."""
+ @property
+ def name(self):
+ """Name of the service."""
+ return "BowtieService"
+
+ @property
+ def progName(self):
+ """Program name."""
+ return "bowtie2"
+
+ @property
+ def scoreSign(self):
+ """Score sign for bowtie2 is 1, the larger the better."""
+ return 1
+
+ def _resolveAlgorithmOptions(self, options, fileNames):
+ """Resolve options specified within --algorithmOptions with
+ options parsed from the command-line or the config file, and
+ return updated options.
+
+ Input:
+ options : the original pbalign options from argumentList
+ and configFile.
+ fileNames: an PBAlignFiles object
+ Output:
+ new options built by resolving options specified within
+ --algorithmOptions and the original pbalign options
+
+ """
+ if options.algorithmOptions is None:
+ return options
+
+ ignoredBinaryOptions = ['-x', '-S', # Needs to be computed.
+ '-1', '-2', '-U', # No paired-end input.
+ '-r', '-q', '--qseq', # Only accepts FASTA.
+ '--seed']
+ ignoredUnitaryOptions = ['--version', '--help']
+
+ items = options.algorithmOptions.split(' ')
+ i = 0
+ try:
+ while i < len(items):
+ infoMsg, errMsg, item = "", "", items[i]
+ if item == "-k":
+ val = int(items[i+1])
+ if options.maxHits is not None and \
+ int(options.maxHits) != val:
+ errMsg = "bowtie2 -k specified within " + \
+ "--algorithmOptions is equivalent to " + \
+ "--maxHits. Conflicting values of " + \
+ "--algorithmOptions '-k' and " +\
+ "--maxHits have been found."
+ elif item == "-L":
+ val = int(items[i+1])
+ if options.minAnchorSize is not None and \
+ int(options.minAnchorSize) != val:
+ errMsg = "bowtie2 -L specified within " + \
+ "--algorithmOptions is equivalent to " + \
+ "--minAnchorSize. Conflicting values " + \
+ "of --algorithmOptions '-L' and " + \
+ "--minAnchorSize have been found."
+ elif item == "-p":
+ val = int(items[i+1])
+ # The number of threads is not critical.
+ if options.nproc is None or \
+ int(options.npoc) != val:
+ infoMsg = "Over write nproc with {n}.".format(n=val)
+ options.nproc = val
+ elif item in ignoredBinaryOptions:
+ pass
+ elif item in ignoredUnitaryOptions:
+ del items[i:i+1]
+ continue
+ else:
+ i += 1
+ continue
+
+ if errMsg != "":
+ logging.error(errMsg)
+ raise ValueError(errMsg)
+
+ if infoMsg != "":
+ logging.info(self.name + ": Resolve algorithmOptions. " +
+ infoMsg)
+
+ del items[i:i+2]
+ except Exception as e:
+ errMsg = "An error occured during parsing algorithmOptions '{ao}'"\
+ .format(ao=options.algorithmOptions) + str(e)
+ logging.error(errMsg)
+ raise ValueError(errMsg)
+
+ # Update algorithmOptions when resolve is done
+ options.algorithmOptions = " ".join(items)
+
+ return options
+
+ def _bt2BuildIndex(self, tempDir, referenceFile):
+ """Build bt2 index files.
+
+ Input:
+ tempDir : a temporary directory for saving bowtie2
+ index files.
+ referenceFile: the reference sequence file.
+ Output:
+ list of strings, bowtie2 index files.
+
+ """
+ refBaseName = bt2BaseName(tempDir, referenceFile)
+ cmdStr = "bowtie2-build -q -f {0} {1}".\
+ format(referenceFile, refBaseName)
+
+ logging.info(self.name + ": Build bowtie2 index files.")
+ logging.debug(self.name + ": Call {0}".format(cmdStr))
+
+ _output, errCode, errMsg = backticks(cmdStr)
+ if (errCode != 0):
+ logging.error(self.name + ": Failed to build bowtie2 " +
+ "index files.\n" + errMsg)
+ raise RuntimeError(errMsg)
+
+ return bt2IndexFiles(refBaseName)
+
+ def _preProcess(self, inputFileName, referenceFile, regionTable,
+ noSplitSubreads, tempFileManager, isWithinRepository):
+ """Preprocess inputs and pre-build reference index files for bowtie2.
+
+ For bowtie2, we need to
+ (1) index the reference sequences,
+ (2) convert the input PULSE/BASE/FOFN file to FASTA.
+ Input:
+ inputFilieName : a PacBio BASE/PULSE/FOFN file.
+ referenceFile : a FASTA reference file.
+ regionTable : a region table RGN.H5/FOFN file.
+ noSplitSubreads: whether to split subreads or not.
+ tempFileManager: temporary file manager.
+ isWithinRepository: whether or not the reference is within
+ a reference repository.
+ Output:
+ String, a FASTA file which can be used by bowtie2.
+
+ """
+ # Build bt2 index files and return files that have been built.
+ indexFiles = self._bt2BuildIndex(tempFileManager.defaultRootDir,
+ referenceFile)
+
+ # Register bt2 index files in the temporary file manager.
+ for indexFile in indexFiles:
+ tempFileManager.RegisterExistingTmpFile(indexFile, own=True)
+
+ # Return a FASTA file that can be used by bowtie2 directly.
+ return self._pls2fasta(inputFileName, regionTable, noSplitSubreads)
+
+ def _toCmd(self, options, fileNames, tempFileManager):
+ """Return a bowtie2 command line to run in bash.
+
+ Generate a bowtie2 command line based on options and PBAlignFiles.
+ Input:
+ options : arguments parsed from the command-line, the
+ config file and --algorithmOptions.
+ fileNames: an PBAlignFiles object.
+ tempFileManager: temporary file manager.
+ Output:
+ a command-line string which can be used in bash.
+
+ """
+ cmdStr = "bowtie2 "
+
+ if options.maxHits is not None and options.maxHits != "":
+ cmdStr += " -k {maxHits}".format(maxHits=options.maxHits)
+
+ if options.nproc is not None and options.nproc != "":
+ cmdStr += " -p {nproc}".format(nproc=options.nproc)
+
+ if options.algorithmOptions is not None:
+ cmdStr += " {opts} ".format(opts=options.algorithmOptions)
+
+ if options.seed is not None and options.seed != "":
+ cmdStr += " --seed {seed} ".format(seed=options.seed)
+
+ refBaseName = bt2BaseName(tempFileManager.defaultRootDir,
+ fileNames.targetFileName)
+ cmdStr += "-x {refBase} -f {queryFile} -S {outFile} ".\
+ format(refBase=refBaseName,
+ queryFile=fileNames.queryFileName,
+ outFile=fileNames.alignerSamOut)
+
+ return cmdStr
+
+ def _postProcess(self):
+ """Postprocess after alignment is done."""
+ logging.debug("Preprocess after alignment is done. ")
diff --git a/pbalign/alignservice/fastabasedalign.py b/pbalign/alignservice/fastabasedalign.py
new file mode 100755
index 0000000..1e30a19
--- /dev/null
+++ b/pbalign/alignservice/fastabasedalign.py
@@ -0,0 +1,87 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+"""This script defines FastaBasedAlignService, a subclass of AlignService,
+which converts PacBio reads in BASE/PULSE/FOFN formats into FASTA format before
+align."""
+
+# Author: Yuan Li
+from __future__ import absolute_import
+from pbalign.alignservice.align import AlignService
+from pbalign.utils.fileutil import getFileFormat, FILE_FORMATS
+from pbcore.util.Process import backticks
+import logging
+
+
+class FastaBasedAlignService(AlignService):
+ """An abstract class for aligners that do not support PacBio reads in
+ BASE/PULSE/FOFN formats. All subclasses need to call _pls2fasta in
+ preprocess to convert input PacBio reads to FASTA."""
+
+ def _pls2fasta(self, inputFileName, regionTable, noSplitSubreads):
+ """ Call pls2fasta to convert a PacBio BASE/PULSe/FOFN file to FASTA.
+ Input:
+ inputFilieName : a PacBio BASE/PULSE/FOFN file.
+ regionTable : a region table RGN.H5/FOFN file.
+ noSplitSubreads: whether to split subreads or not.
+ Output:
+ a FASTA file which can be used as an input by an aligner.
+ """
+ # If the incoming file is a FASTA file, no conversion is needed.
+ if getFileFormat(inputFileName) == FILE_FORMATS.FASTA:
+ return inputFileName
+
+ # Otherwise, create a temporary FASTA file to write.
+ outFastaFile = self._tempFileManager.RegisterNewTmpFile(
+ suffix=".fasta")
+
+ cmdStr = "pls2fasta {plsFile} {fastaFile} ".format(
+ plsFile=inputFileName, fastaFile=outFastaFile)
+
+ if regionTable is not None and regionTable != "":
+ cmdStr += " -regionTable {rt} ".format(rt=regionTable)
+
+ if noSplitSubreads:
+ cmdStr += " -noSplitSubreads "
+
+ logging.info(self.name + ": Convert {inFile} to FASTA format.".
+ format(inFile=inputFileName))
+ logging.debug(self.name + ": Call \"{cmd}\"".format(cmd=cmdStr))
+
+ _output, errCode, errMsg = backticks(cmdStr)
+ if errCode != 0:
+ errMsg += "Failed to convert {i} to {o}.".format(
+ i=inputFileName, o=outFastaFile)
+ logging.error(errMsg)
+ raise RuntimeError(errMsg)
+
+ # Return the converted FASTA file which can be used by an aligner.
+ return outFastaFile
diff --git a/pbalign/alignservice/gmap.py b/pbalign/alignservice/gmap.py
new file mode 100755
index 0000000..759c271
--- /dev/null
+++ b/pbalign/alignservice/gmap.py
@@ -0,0 +1,307 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+"""This script defines class GMAPService which calls GMAP to align reads."""
+
+# Author: Yuan Li
+
+from __future__ import absolute_import
+from os import path
+from pbalign.alignservice.fastabasedalign import FastaBasedAlignService
+from pbalign.utils.fileutil import isExist
+from pbcore.util.Process import backticks
+from time import sleep
+from random import randint
+import logging
+
+
+class GMAPService(FastaBasedAlignService):
+ """Class GMAPService calls gmap to align reads."""
+ def __init__(self, options, fileNames, tempFileManager=None):
+ super(GMAPService, self).__init__(options, fileNames, tempFileManager)
+ self.dbRoot = None
+ # If a GMAP DB is within a PacBio reference repository, its name should
+ # always be 'gmap_db'. However, if it is not within a repository, its
+ # name should be randomized. Otherwise, if multiple calls of
+ # 'gmap_build' running simultaneously will fail.
+ self.dbName = "gmap_db"
+
+ @property
+ def name(self):
+ """GMAP Service name."""
+ return "GMAPService"
+
+ @property
+ def progName(self):
+ """Program to call."""
+ return "gmap"
+
+ @property
+ def scoreSign(self):
+ """Using edit distance as align score for GMAP, the lower the better.
+ """
+ return -1
+
+ def _resolveAlgorithmOptions(self, options, fileNames):
+ """ Resolve options specified within --algorithmOptions with
+ options parsed from the command-line or the config file.
+ Return updated options.
+ If find conflicting values of the following options, error out.
+ (1) --maxHits and gmap -n
+ (2) --maxAnchorSize and gmap -k
+ Input:
+ options : the original pbalign options from argumentList
+ and configFile.
+ fileNames: an PBAlignFiles object
+ Output:
+ new options by resolving options specified within
+ --algorithmOptions and the original pbalign options
+ """
+ if options.algorithmOptions is None:
+ return options
+
+ unsupportedOptions = ['-1', '--selfalign', '-2', '--pairalign',
+ '--cmdline', '--cmetdir', '--atoidir',
+ '-v', '--use-snps',
+ '-V', '--snpsdir']
+ # Ignore options to specify the input database
+ ignoredBinaryOptions = ['-D', '-d']
+
+ # Ignore options to specify output types, and always output in SAM
+ # with full headers and the 'sam-use-0M' option.
+ # Ignore --kmer, --nthreads, and --npaths
+ # Ignore help and version.
+ ignoredUnitaryOptions = ['-S', '-A', '-3', '-4', '-Z', '-E',
+ '-P', '-Q', '-5', '--no-sam-headers',
+ '-f', '--sam-use-0M', '--dir', '--db',
+ '--kmer', '--nthreads', '--npaths',
+ '--help', '--version']
+
+ items = options.algorithmOptions.split(' ')
+ i = 0
+ try:
+ while i < len(items):
+ infoMsg, errMsg, item = "", "", items[i].split("=")[0]
+ if item in unsupportedOptions:
+ raise ValueError("Unsupported option: {i}".format(i=item))
+ elif item in ignoredUnitaryOptions:
+ infoMsg = "Ignore option: {i}".format(i=item)
+ del items[i:i+1]
+ elif item in ignoredBinaryOptions:
+ infoMsg = "Ignore option: {i}".format(i=item)
+ del items[i:i+2]
+ elif item == "-k": # kmer size
+ val = int(items[i+1])
+ if options.minAnchorSize == val:
+ del items[i:i+2]
+ else:
+ errMsg = "Found conflicting options: " + \
+ "--algorithmOptions '-k={k}'".format(k=val) +\
+ "and --minAnchorSize={v}.".format(
+ v=options.minAnchorSize)
+ elif item == "-t":
+ val = int(items[i+1])
+ # The number of threads is not critical.
+ if options.nproc is None or \
+ int(options.nproc) != val:
+ infoMsg = "Over write nproc with {n}.".format(n=val)
+ options.nproc = val
+ del items[i:i+2]
+ elif item == "-n":
+ val = int(items[i+1])
+ if options.maxHits == val:
+ del items[i:i+2]
+ else:
+ errMsg = "Found conflicting options: " + \
+ "--algorithmsOptions '-n={n}' and " + \
+ "--maxHits={v}.".format(v=options.maxHits)
+
+ if errMsg != "":
+ logging.error(errMsg)
+ raise ValueError(errMsg)
+
+ if infoMsg != "":
+ logging.info(self.name + ": Resolve algorithmOptions. " +
+ infoMsg)
+
+ except Exception as e:
+ errMsg = "An error occured during parsing algorithmOptions " + \
+ "'{ao}': ".format(ao=options.algorithmOptions)
+ logging.error(errMsg + str(e))
+ raise ValueError(errMsg + str(e))
+
+ # Update algorithmOptions when resolve is done
+ options.algorithmOptions = " ".join(items)
+ return options
+
+ def _toCmd(self, options, fileNames, tempFileManager):
+ """ Generate a command line for GMAP based on options and
+ PBAlignFiles, and return a command-line string which can
+ be used in bash.
+ Input:
+ options : arguments parsed from the command-line, the
+ config file and --algorithmOptions.
+ fileNames: an PBAlignFiles object.
+ tempFileManager: temporary file manager.
+ Output:
+ a command-line string which can be used in bash.
+ """
+ cmdStr = "gmap -D {dbRoot} ".format(dbRoot=self.dbRoot) + \
+ "-d {dbName} -f samse ".format(dbName=self.dbName) + \
+ "--sam-use-0M {inFa} ".format(inFa=fileNames.queryFileName)
+
+ if options.maxHits is not None and options.maxHits != "":
+ cmdStr += "-n {n} ".format(n=options.maxHits)
+
+ if (options.minAnchorSize is not None and
+ options.minAnchorSize != ""):
+ cmdStr += "-k {0} ".format(options.minAnchorSize)
+
+ if options.nproc is not None and options.nproc != "":
+ cmdStr += "-t {0} ".format(options.nproc)
+
+ if options.algorithmOptions is not None:
+ cmdStr += "{0} ".format(options.algorithmOptions)
+
+ cmdStr += "> {outSam} ".format(outSam=fileNames.alignerSamOut)
+
+ return cmdStr
+
+ def _releaseLock(self, dbLock):
+ """Release dbLock."""
+ _o, errCode, _m = backticks("rm -f {dbLock}".format(dbLock=dbLock))
+ if errCode == 0:
+ logging.debug(self.name + ": Release the lock for DB creation.")
+ else:
+ raise RuntimeError(self.name + ": Failed to release lock " +
+ dbLock + ". Please delete the lock manually.")
+
+ def _gmapCreateDB(self, referenceFile, isWithinRepository, tempRootDir):
+ """
+ Create gmap database for reference sequences if no DB exists.
+ Wait for gmap DB to be created if gmap_db.lock exists.
+ return (gmap_DB_root_path, gmap_DB_name).
+ """
+ # Determine dbRoot according to whether the reference file is wihtin
+ # a reference repository.
+ if isWithinRepository:
+ # If the reference file is within a reference repository, create
+ # gmap_db under the root of the repository, then the gmap DB root
+ # is the repo root, and gmap DB name is 'gmap_db', e.g.,
+ # refrepo/
+ # --------sequence/
+ # --------gmap_db/
+ # --------reference.info.xml
+ dbRoot = path.split(path.dirname(referenceFile))[0]
+ dbName = "gmap_db"
+ else: # Otherwise, create gmap_db under the tempRootDir, and give the
+ # gmap DB a random name
+ dbRoot = tempRootDir
+ dbName = "gmap_db_{sfx}".format(sfx=randint(100000, 1000000))
+
+ dbPath = path.join(dbRoot, dbName)
+ dbLock = dbPath + ".lock"
+ # Check if DB already exists
+ if isExist(dbPath) and not isExist(dbLock):
+ # gmap_db already exists
+ logging.info(self.name + ": GMAP database {dbPath} found".format(
+ dbPath=dbPath))
+ return (dbRoot, dbName)
+
+ # Check if DB is being created by other pbalign calls
+ while isExist(dbLock):
+ logging.info(self.name + ": Waiting for GMAP database to be " + \
+ "created for {inFa}".format(inFa=referenceFile))
+ sleep(10)
+
+ # Create DB if it does not exist
+ if not isExist(dbPath):
+ # Touch the lock file
+ _output, errCode, errMsg = backticks("touch {dbLock}".format(
+ dbLock=dbLock))
+ logging.debug(self.name + ": Create a lock when GMAP DB is " +
+ "being built.")
+ if (errCode != 0):
+ logging.error(self.name + ": Failed to create {dbLock}.\n" +
+ errMsg)
+ self._releaseLock(dbLock)
+ raise RuntimeError(errMsg)
+
+ logging.info(self.name + ": Create GMAP DB for {inFa}.".format(
+ inFa=referenceFile))
+ cmdStr = "gmap_build -k 12 --db={dbName} --dir={dbRoot} {inFa}".\
+ format(dbName=dbName, dbRoot=dbRoot, inFa=referenceFile)
+ _output, errCode, errMsg = backticks(cmdStr)
+ logging.debug(self.name + ": Call {cmdStr}".format(cmdStr=cmdStr))
+ if (errCode != 0):
+ logging.error(self.name + ": Failed to build GMAP db.\n" +
+ errMsg)
+ self._releaseLock(dbLock)
+ raise RuntimeError(errMsg)
+
+ # Delete the lock file to notify others pbalign who are waiting
+ # for this DB to be created.
+ self._releaseLock(dbLock)
+
+ return (dbRoot, dbName)
+
+ def _preProcess(self, inputFileName, referenceFile, regionTable,
+ noSplitSubreads, tempFileManager, isWithinRepository):
+ """Preprocess inputs and pre-build reference index files for gmap.
+
+ For gmap, we need to
+ (1) create indices for reference sequences,
+ (2) convert the input PULSE/BASE/FOFN file to FASTA.
+ Input:
+ inputFileName : a PacBio BASE/PULSE/FOFN file.
+ referenceFile : a FASTA reference file.
+ regionTable : a region table RGN.H5/FOFN file.
+ noSplitSubreads: whether to split subreads or not.
+ tempFileManager: temporary file manager.
+ Output:
+ String, a FASTA read file which can be used by gmap.
+ """
+ # Create a gmap database, update gmap DB root path and db name.
+ (self.dbRoot, self.dbName) = self._gmapCreateDB(referenceFile,
+ isWithinRepository, tempFileManager.defaultRootDir)
+
+ # DO NOT delete gmap_db if it is within a reference repository;
+ # otherwise, delete it.
+ if not isWithinRepository:
+ tempFileManager.RegisterExistingTmpFile(path.join(self.dbRoot,
+ self.dbName), own=True, isDir=True)
+
+ # Return a FASTA file that can be used by gmap as query directly.
+ return self._pls2fasta(inputFileName, regionTable, noSplitSubreads)
+
+ def _postProcess(self):
+ """ Postprocess after alignment is done. """
+ logging.debug(self.name + ": Postprocess after alignment is done. ")
diff --git a/pbalign/filterservice.py b/pbalign/filterservice.py
new file mode 100755
index 0000000..9d23215
--- /dev/null
+++ b/pbalign/filterservice.py
@@ -0,0 +1,142 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+"""This script defines FilterService, which calls samFilter to remove aligments
+in an input SAM file according to filtering criteria."""
+
+# Author: Yuan Li
+
+from __future__ import absolute_import
+import logging
+from pbalign.service import Service
+from pbalign.utils.fileutil import isExist
+
+
+class FilterService(Service):
+ """ Call samFilter to filter low quality hits and apply multiple hits
+ policy. """
+ @property
+ def name(self):
+ """Name of filter service."""
+ return "FilterService"
+
+ @property
+ def progName(self):
+ """Program to call."""
+ return "samFilter"
+
+ def __init__(self, inSamFile, refFile, outSamFile,
+ alnServiceName, scoreSign, options,
+ adapterGffFile=None):
+ """Initialize a FilterService object.
+ Input:
+ inSamFile: an input SAM file
+ refFile : the reference FASTA file
+ outSAM : an output SAM file
+ alnServiceName: the name of the align service
+ scoreSign: score sign of the aligner, can be -1 or 1
+ options : pbalign options
+ adapterGffFile: a GFF file storing all the adapters
+ """
+ self.inSamFile = inSamFile
+ self.refFile = refFile
+ self.outSamFile = outSamFile
+ self.alnServiceName = alnServiceName
+ self.scoreSign = scoreSign
+ self.options = options
+ self.adapterGffFile = adapterGffFile
+
+ @property
+ def cmd(self):
+ """String of a command-line to execute."""
+ return self._toCmd(self.inSamFile, self.refFile,
+ self.outSamFile, self.alnServiceName,
+ self.scoreSign, self.options,
+ self.adapterGffFile)
+
+ def _toCmd(self, inSamFile, refFile, outSamFile,
+ alnServiceName, scoreSign, options, adapterGffFile):
+ """ Generate a samFilter command line from options.
+ Input:
+ inSamFile : the input SAM file
+ refFile : the reference FASTA file
+ outSamFile: the output SAM file
+ alnServiceName: aligner service name
+ scoreSign : score sign, can be -1 or 1
+ options : argument options
+ Output:
+ a command-line string
+ """
+ cmdStr = self.progName + \
+ " {inSamFile} {refFile} {outSamFile} ".format(
+ inSamFile=inSamFile,
+ refFile=refFile,
+ outSamFile=outSamFile)
+
+ if options.maxDivergence is not None:
+ maxDivergence = int(options.maxDivergence if options.maxDivergence
+ > 1.0 else (options.maxDivergence * 100))
+ cmdStr += " -minPctSimilarity {0}".format(100 - maxDivergence)
+
+ if options.minAccuracy is not None:
+ minAccuracy = int(options.minAccuracy if options.minAccuracy > 1.0
+ else (options.minAccuracy * 100))
+ cmdStr += " -minAccuracy {0}".format(minAccuracy)
+
+ if options.minLength is not None:
+ cmdStr += " -minLength {0}".format(options.minLength)
+
+ if options.seed is not None:
+ cmdStr += " -seed {0}".format(options.seed)
+
+ if scoreSign in [1, -1]:
+ cmdStr += " -scoreSign {0}".format(scoreSign)
+ else:
+ logging.error("{0}'s score sign is neither 1 nor -1.".format(
+ alnServiceName))
+
+ if options.scoreCutoff is not None:
+ cmdStr += " -scoreCutoff {0}".format(options.scoreCutoff)
+
+ if options.hitPolicy is not None:
+ cmdStr += " -hitPolicy {0}".format(options.hitPolicy)
+
+ if options.filterAdapterOnly is True and \
+ isExist(adapterGffFile):
+ cmdStr += " -filterAdapterOnly {gffFile}".format(
+ gffFile=adapterGffFile)
+ return cmdStr
+
+ def run(self):
+ """ Run the filter service. """
+ logging.info(self.name + ": Filter alignments using {0}.".
+ format(self.progName))
+ return self._execute()
diff --git a/pbalign/forquiverservice/__init__.py b/pbalign/forquiverservice/__init__.py
new file mode 100755
index 0000000..175bd6a
--- /dev/null
+++ b/pbalign/forquiverservice/__init__.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+# Author: Yuan Li
+"""Initialization."""
+from __future__ import absolute_import
diff --git a/pbalign/forquiverservice/forquiver.py b/pbalign/forquiverservice/forquiver.py
new file mode 100755
index 0000000..e478daa
--- /dev/null
+++ b/pbalign/forquiverservice/forquiver.py
@@ -0,0 +1,99 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+"""This script defines ForQuiverService, which post-processes a cmp.h5 file so
+that it can be used by quiver directly. ForQuiverService sorts the file, loads
+pulse information to it and finally repacks it.."""
+
+# Author: Yuan Li
+
+from __future__ import absolute_import
+import logging
+from pbalign.forquiverservice.sort import SortService
+from pbalign.forquiverservice.loadpulses import LoadPulsesService
+from pbalign.forquiverservice.loadchemistry import LoadChemistryService
+from pbalign.forquiverservice.repack import RepackService
+
+
+class ForQuiverService(object):
+ """
+ Uses SortService, LoadPulsesService, LoadChemistryService,
+ RepackService to post process a cmp.h5 file so that the file can
+ be used by quiver directly.
+ """
+ @property
+ def name(self):
+ """Name of ForQuiverService."""
+ return "ForQuiverService"
+
+ def __init__(self, fileNames, options):
+ """Initialize a ForQuiverService object.
+
+ Input:
+ fileNames : pbalign file names
+ options : pbalign options
+
+ """
+ self.fileNames = fileNames
+ self.options = options
+ self._loadpulsesService = LoadPulsesService(
+ self.fileNames.pulseFileName,
+ self.fileNames.outputFileName,
+ self.options)
+ self._loadchemistryService = LoadChemistryService(
+ self.fileNames.pulseFileName,
+ self.fileNames.outputFileName,
+ self.options)
+ self._sortService = SortService(
+ self.fileNames.outputFileName,
+ self.options)
+ self._repackService = RepackService(
+ self.fileNames.outputFileName,
+ self.fileNames.outputFileName + ".TMP")
+
+ def run(self):
+ """ Run the ForQuiver service."""
+ logging.info(self.name + ": Sort.")
+
+ self._sortService.checkAvailability()
+ self._sortService.run()
+
+ logging.info(self.name + ": LoadPulses.")
+ self._loadpulsesService.checkAvailability()
+ self._loadpulsesService.run()
+
+ logging.info(self.name + ": LoadChemistry.")
+ self._loadchemistryService.checkAvailability()
+ self._loadchemistryService.run()
+
+ logging.info(self.name + ": Repack.")
+ self._repackService.checkAvailability()
+ self._repackService.run()
diff --git a/pbalign/forquiverservice/loadchemistry.py b/pbalign/forquiverservice/loadchemistry.py
new file mode 100755
index 0000000..5f6516f
--- /dev/null
+++ b/pbalign/forquiverservice/loadchemistry.py
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+from __future__ import absolute_import
+import logging
+from pbalign.service import Service
+
+class LoadChemistryService(Service):
+ @property
+ def name(self):
+ return "LoadChemistryService"
+
+ @property
+ def progName(self):
+ return "loadChemistry.py"
+
+ # Quiver only uses the following five metrics.
+
+ def __init__(self, basFofnFile, cmpFile, options):
+ """
+ Input:
+ basFofnFile: the input BASE.H5 (or fofn) files
+ cmpFile : an input CMP.H5 file
+ options : pbalign options
+ """
+ self.basFofnFile = basFofnFile
+ self.cmpFile = cmpFile
+ self.options = options
+
+ @property
+ def cmd(self):
+ """String of a command-line to execute."""
+ return self._toCmd(self.basFofnFile, self.cmpFile)
+
+ def _toCmd(self, basFofnFile, cmpFile):
+ """
+ Generate a loadChemistry command line.
+ """
+ cmdStr = self.progName + \
+ " {basFofnFile} {cmpFile} ".format(
+ basFofnFile=basFofnFile, cmpFile=cmpFile)
+
+ return cmdStr
+
+ def run(self):
+ """Run the loadChemistry service."""
+ logging.info(self.name + ": Load pulses using {progName}.".
+ format(progName=self.progName))
+ return self._execute()
diff --git a/pbalign/forquiverservice/loadpulses.py b/pbalign/forquiverservice/loadpulses.py
new file mode 100755
index 0000000..98c71b8
--- /dev/null
+++ b/pbalign/forquiverservice/loadpulses.py
@@ -0,0 +1,103 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+"""Define LoadPulseService class, which calls loadPulses to load PacBio
+pulse metrics to a cmp.h5 file. Five metrics, inclduing DeletionQV,
+DeletionTag, InsertionQV, MergeQV, and SubstitutionQV, are loaded by default
+unless --metrics is specified."""
+
+# Author: Yuan Li
+
+from __future__ import absolute_import
+import logging
+from pbalign.service import Service
+
+
+class LoadPulsesService(Service):
+ """
+ LoadPulsesService calls loadPulses to load PacBio pulse information to a
+ cmp.h5 file.
+ """
+ @property
+ def name(self):
+ """Name of LoadPulsesService."""
+ return "LoadPulsesService"
+
+ @property
+ def progName(self):
+ """Program to call."""
+ return "loadPulses"
+
+ # Quiver only uses the following five metrics.
+
+ def __init__(self, basFofnFile, cmpFile, options):
+ """Initialize a LoadPulsesService object.
+ Input:
+ basFofnFile: the input BASE.H5 (or fofn) files
+ cmpFile : an input CMP.H5 file
+ options : pbalign options
+ """
+ self.basFofnFile = basFofnFile
+ self.cmpFile = cmpFile
+ self.options = options
+
+ @property
+ def cmd(self):
+ """String of a command-line to execute."""
+ return self._toCmd(self.basFofnFile, self.cmpFile)
+
+ def _toCmd(self, basFofnFile, cmpFile):
+ """Generate a loadPulses command line.
+
+ Input:
+ basFofnFile: a BAX/PLX.H5 (or fofn) file with pulses
+ cmpFile : an input CMP.H5 file
+ Output:
+ a command-line string
+
+ """
+ cmdStr = self.progName + \
+ " {basFofnFile} {cmpFile} ".format(
+ basFofnFile=basFofnFile, cmpFile=cmpFile)
+
+ metrics = self.options.metrics.replace(" ", "")
+ cmdStr += " -metrics {metrics} ".format(metrics=metrics)
+
+ if self.options.byread:
+ cmdStr += " -byread "
+
+ return cmdStr
+
+ def run(self):
+ """Run the loadPulses service."""
+ logging.info(self.name + ": Load pulses using {progName}.".
+ format(progName=self.progName))
+ return self._execute()
diff --git a/pbalign/forquiverservice/repack.py b/pbalign/forquiverservice/repack.py
new file mode 100755
index 0000000..5c0f210
--- /dev/null
+++ b/pbalign/forquiverservice/repack.py
@@ -0,0 +1,87 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+"""Define RepackService class, which calls h5repack to repack a cmp.h5 file."""
+
+# Author: Yuan Li
+
+from __future__ import absolute_import
+import logging
+from pbalign.service import Service
+
+
+class RepackService(Service):
+ """RepackService calls h5repack to repack a PacBio cmp.h5 file."""
+ @property
+ def name(self):
+ """Name of RepackService."""
+ return "RepackService"
+
+ @property
+ def progName(self):
+ """Program to call."""
+ return "h5repack"
+
+ def __init__(self, cmpFile, tmpcmpFile):
+ """Initialize a RepackService object.
+
+ Input:
+ cmpFile : an input CMP.H5 file
+ tmpcmpFile : a temporary CMP.H5 file
+
+ """
+ self.cmpFile = cmpFile
+ self.tmpcmpFile = tmpcmpFile
+
+ @property
+ def cmd(self):
+ """String of a command-line to execute."""
+ return self._toCmd(self.cmpFile, self.tmpcmpFile)
+
+ def _toCmd(self, cmpFile, tmpcmpFile):
+ """Generate a h5repack command line.
+
+ Input:
+ cmpFile : an input CMP.H5 file
+ options : pbalign options
+ Output:
+ a command-line string
+
+ """
+ cmdStr = self.progName + " -f GZIP=1 {i} {o} && mv {o} {i}".\
+ format(i=cmpFile, o=tmpcmpFile)
+ return cmdStr
+
+ def run(self):
+ """Run the Repack service."""
+ logging.info(self.name + ": Repack a cmp.h5 file using {progName}.".
+ format(progName=self.progName))
+ return self._execute()
diff --git a/pbalign/forquiverservice/sort.py b/pbalign/forquiverservice/sort.py
new file mode 100755
index 0000000..750601e
--- /dev/null
+++ b/pbalign/forquiverservice/sort.py
@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+"""This script defines SortService, which calls cmph5tools.py sort to sort a
+cmp.h5 file."""
+
+# Author: Yuan Li
+
+from __future__ import absolute_import
+import logging
+from pbalign.service import Service
+
+
+class SortService(Service):
+ """Call cmph5tools.py sort to sort a PacBio cmp.h5 file."""
+ @property
+ def name(self):
+ """Name of SortService."""
+ return "SortService"
+
+ @property
+ def progName(self):
+ """Program to call."""
+ return "cmph5tools.py"
+
+ def __init__(self, cmpFile, options):
+ """Initialize a SortService object.
+ Input:
+ cmpFile : an input CMP.H5 file
+ options : pbalign options
+ """
+ self.cmpFile = cmpFile
+ self.options = options
+
+ @property
+ def cmd(self):
+ """String of a command-line to execute."""
+ return self._toCmd(self.cmpFile, self.options)
+
+ def _toCmd(self, cmpFile, options):
+ """Generate a cmph5tools.py sort command line.
+
+ Input:
+ cmpFile : an input CMP.H5 file
+ options : pbalign options
+ Output:
+ a command-line string
+
+ """
+ cmdStr = self.progName
+ if options.verbosity > 1:
+ cmdStr += " -vv "
+
+ cmdStr += " sort --deep --inPlace {cmpFile} ".format(cmpFile=cmpFile)
+ return cmdStr
+
+ def run(self):
+ """Run the sort service."""
+ logging.info(self.name + ": Sort a cmp.h5 file using {progName}.".
+ format(progName=self.progName))
+ return self._execute()
diff --git a/pbalign/options.py b/pbalign/options.py
new file mode 100755
index 0000000..9cb1e81
--- /dev/null
+++ b/pbalign/options.py
@@ -0,0 +1,522 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+# Author:Yuan Li
+"""This scripts defines functions for parsing PBAlignRunner options."""
+
+from __future__ import absolute_import
+import argparse
+from copy import copy
+
+# The first candidate 'blasr' is the default.
+ALGORITHM_CANDIDATES = ('blasr', 'bowtie', 'gmap')
+
+# The first candidate 'randombest' is the default.
+HITPOLICY_CANDIDATES = ('randombest', 'allbest', 'random', 'all', 'leftmost')
+
+# The first candidate 'aligner' is the default.
+SCOREFUNCTION_CANDIDATES = ('alignerscore', 'editdist',
+ #'blasrscore', 'userscore')
+ 'blasrscore')
+DEFAULT_METRICS = ("DeletionQV", "DeletionTag", "InsertionQV",
+ "MergeQV", "SubstitutionQV")
+
+# Default values of arguments
+DEFAULT_OPTIONS = {"regionTable": None,
+ "configFile": None,
+ # Choose an aligner
+ "algorithm": ALGORITHM_CANDIDATES[0],
+ # Aligner options
+ "maxHits": 10,
+ "minAnchorSize": 12,
+ "noSplitSubreads": False,
+ "concordant": False,
+ "algorithmOptions": None,
+ "useccs": None,
+ # Filter options
+ "maxDivergence": 30,
+ "minAccuracy": 70,
+ "minLength": 50,
+ "scoreFunction": SCOREFUNCTION_CANDIDATES[0],
+ "scoreCutoff": None,
+ "hitPolicy": HITPOLICY_CANDIDATES[0],
+ "filterAdapterOnly": False,
+ # Cmp.h5 writer options
+ "readType": "standard",
+ "forQuiver": False,
+ "loadQVs": False,
+ "byread": False,
+ "metrics": str(",".join(DEFAULT_METRICS)),
+ # Miscellaneous options
+ "nproc": 8,
+ "seed": 1,
+ "tmpDir": "/scratch"}
+
+
+def constructOptionParser(parser=None):
+ """Constrct and return an argument parser.
+
+ If a parser is specified, use it. Otherwise, create a parser instead.
+ Add PBAlignRunner arguments to construct the parser, and finally
+ return it.
+
+ """
+ desc = "Mapping PacBio sequences to references using an algorithm \n"
+ desc += "selected from a selection of supported command-line alignment\n"
+ desc += "algorithms. Input can be a fasta, pls.h5, bas.h5 or ccs.h5\n"
+ desc += "file or a fofn (file of file names). Output is in either\n"
+ desc += "cmp.h5 or sam format.\n"
+
+ if (parser is None):
+ parser = argparse.ArgumentParser()
+
+ parser.description = desc
+ parser.argument_default = argparse.SUPPRESS
+ parser.formatter_class = argparse.RawTextHelpFormatter
+
+ # Optional input.
+ parser.add_argument("--regionTable",
+ dest="regionTable",
+ type=str,
+ default=None,
+ action="store",
+ help="Specify a region table for filtering reads.")
+
+ parser.add_argument("--configFile",
+ dest="configFile",
+ default=None,
+ type=str,
+ action="store",
+ help="Specify a set of user-defined argument values.")
+
+ helpstr = "When input reads are in fasta format and output is a cmp.h5\n" + \
+ "this option can specify pls.h5 or bas.h5 or \n" + \
+ "FOFN files from which pulse metrics can be loaded for Quiver."
+ parser.add_argument("--pulseFile",
+ dest="pulseFile",
+ default=None,
+ type=str,
+ action="store",
+ help=helpstr)
+
+ # Chose an aligner.
+ helpstr = "Select an aligorithm from {0}.\n".format(ALGORITHM_CANDIDATES)
+ helpstr += "Default algorithm is {0}.".format(DEFAULT_OPTIONS["algorithm"])
+ parser.add_argument("--algorithm",
+ dest="algorithm",
+ type=str,
+ action="store",
+ choices=ALGORITHM_CANDIDATES,
+ default=ALGORITHM_CANDIDATES[0],
+ help=helpstr)
+
+ # Aligner options.
+ helpstr = "The maximum number of matches of each read to the \n" + \
+ "reference sequence that will be evaluated. Default\n" + \
+ "value is {0}.".format(DEFAULT_OPTIONS["maxHits"])
+ parser.add_argument("--maxHits",
+ dest="maxHits",
+ type=int,
+ default=None, # Set as None instead of a real number.
+ action="store",
+ help=helpstr)
+
+ helpstr = "The minimum anchor size defines the length of the read\n" + \
+ "that must match against the reference sequence. Default\n" + \
+ "value is {0}.".format(DEFAULT_OPTIONS["minAnchorSize"])
+ parser.add_argument("--minAnchorSize",
+ dest="minAnchorSize",
+ type=int,
+ default=None, # Set as None to avoid conflicts with
+ # --algorithmOptions
+ action="store",
+ help=helpstr)
+
+ # Aligner options: Use ccs or not?
+ helpstr = "Map the ccsSequence to the genome first, then align\n" + \
+ "subreads to the interval that the CCS reads mapped to.\n" + \
+ " useccs: only maps subreads that span the length of\n" + \
+ " the template.\n" + \
+ " useccsall: maps all subreads.\n" + \
+ " useccsdenovo: maps ccs only."
+ parser.add_argument("--useccs",
+ type=str,
+ choices=["useccs", "useccsall", "useccsdenovo"],
+ action="store",
+ default=None,
+ help=helpstr)
+
+ helpstr = "Do not split reads into subreads even if subread \n" + \
+ "regions are available. Default value is {0}."\
+ .format(DEFAULT_OPTIONS["noSplitSubreads"])
+ parser.add_argument("--noSplitSubreads",
+ dest="noSplitSubreads",
+ default=DEFAULT_OPTIONS["noSplitSubreads"],
+ action="store_true",
+ help=helpstr)
+
+ helpstr = "Map subreads of a ZMW to the same genomic location.\n"
+ parser.add_argument("--concordant",
+ dest="concordant",
+ default=DEFAULT_OPTIONS["concordant"],
+ action="store_true",
+ help=helpstr)
+
+ helpstr = "Number of threads. Default value is {v}."\
+ .format(v=DEFAULT_OPTIONS["nproc"])
+ parser.add_argument("--nproc",
+ type=int,
+ dest="nproc",
+ default=DEFAULT_OPTIONS["nproc"],
+ #default=15,
+ action="store",
+ help=helpstr)
+
+ parser.add_argument("--algorithmOptions",
+ type=str,
+ dest="algorithmOptions",
+ default=None,
+ action="append",
+ help="Pass alignment options through.")
+
+ # Filtering criteria and hit policy.
+ helpstr = "The maximum allowed percentage divergence of a read \n" + \
+ "from the reference sequence. Default value is {0}." \
+ .format(DEFAULT_OPTIONS["maxDivergence"])
+ parser.add_argument("--maxDivergence",
+ dest="maxDivergence",
+ type=float,
+ default=DEFAULT_OPTIONS["maxDivergence"],
+ #default=30,
+ action="store",
+ help=helpstr)
+
+ helpstr = "The minimum percentage accuracy of alignments that\n" + \
+ "will be evaluated. Default value is {v}." \
+ .format(v=DEFAULT_OPTIONS["minAccuracy"])
+ parser.add_argument("--minAccuracy",
+ dest="minAccuracy",
+ type=float,
+ default=DEFAULT_OPTIONS["minAccuracy"],
+ #default=70,
+ action="store",
+ help=helpstr)
+
+ helpstr = "The minimum aligned read length of alignments that\n" + \
+ "will be evaluated. Default value is {v}." \
+ .format(v=DEFAULT_OPTIONS["minLength"])
+ parser.add_argument("--minLength",
+ dest="minLength",
+ type=int,
+ default=DEFAULT_OPTIONS["minLength"],
+ action="store",
+ help=helpstr)
+
+ helpstr = "Specify a score function for evaluating alignments.\n"
+ helpstr += " alignerscore : aligner's score in the SAM tag 'as'.\n"
+ helpstr += " editdist : edit distance between read and reference.\n"
+ helpstr += " blasrscore : blasr's default score function.\n"
+ helpstr += "Default value is {0}.".format(DEFAULT_OPTIONS["scoreFunction"])
+ parser.add_argument("--scoreFunction",
+ dest="scoreFunction",
+ type=str,
+ choices=SCOREFUNCTION_CANDIDATES,
+ default=DEFAULT_OPTIONS["scoreFunction"],
+ action="store",
+ help=helpstr)
+ #" userscore : user-defined score matrix (by -scoreMatrix).\n")
+ #parser.add_argument("--scoreMatrix",
+ # dest="scoreMatrix",
+ # type=str,
+ # default=None,
+ # help=
+ # "Specify a user-defined score matrix for "
+ # "scoring reads.The matrix\n"+\
+ # "is in the format\n"
+ # " ACGTN\n"
+ # " A abcde\n"
+ # " C fghij\n"
+ # " G klmno\n"
+ # " T pqrst\n"
+ # " N uvwxy\n"
+ # ". The values a...y should be input as a "
+ # "quoted space separated\n"
+ # "string: "a b c ... y". Lower scores are better,"
+ # "so matches\n"
+ # "should be less than mismatches e.g. a,g,m,s "
+ # "= -5 (match),\n"
+ # "mismatch = 6.\n")
+
+ parser.add_argument("--scoreCutoff",
+ dest="scoreCutoff",
+ type=int,
+ default=None,
+ action="store",
+ help="The worst score to output an alignment.\n")
+
+ helpstr = "Specify a policy for how to treat multiple hit\n" + \
+ " random : selects a random hit.\n" + \
+ " all : selects all hits.\n" + \
+ " allbest : selects all the best score hits.\n" + \
+ " randombest: selects a random hit from all best score hits.\n" + \
+ " leftmost : selects a hit which has the best score and the\n" + \
+ " smallest mapping coordinate in any reference.\n" + \
+ "Default value is {v}.".format(v=DEFAULT_OPTIONS["hitPolicy"])
+ parser.add_argument("--hitPolicy",
+ dest="hitPolicy",
+ type=str,
+ choices=HITPOLICY_CANDIDATES,
+ default=DEFAULT_OPTIONS["hitPolicy"],
+ action="store",
+ help=helpstr)
+
+ helpstr = "If specified, do not report adapter-only hits using\n" + \
+ "annotations with the reference entry."
+ parser.add_argument("--filterAdapterOnly",
+ dest="filterAdapterOnly",
+ default=DEFAULT_OPTIONS["filterAdapterOnly"],
+ action="store_true",
+ help=helpstr)
+
+ # Output.
+ helpstr = "Specify the ReadType attribute in the cmp.h5 output.\n" + \
+ "Default value is {v}.".format(v=DEFAULT_OPTIONS["readType"])
+ parser.add_argument("--readType",
+ dest="readType",
+ type=str,
+ action="store",
+ default=DEFAULT_OPTIONS["readType"],
+ help=argparse.SUPPRESS)
+ #help=helpstr)
+
+ helpstr = "The output cmp.h5 file which will be sorted, loaded\n" + \
+ "with pulse QV information, and repacked, so that it \n" + \
+ "can be consumed by quiver directly. This requires\n" + \
+ "the input file to be in PacBio bas/pls.h5 format,\n" + \
+ "and --useccs must be None. Default value is False."
+ parser.add_argument("--forQuiver",
+ dest="forQuiver",
+ action="store_true",
+ default=DEFAULT_OPTIONS["forQuiver"],
+ help=helpstr)
+
+ helpstr = "Similar to --forQuiver, the only difference is that \n" + \
+ "--useccs can be specified. Default value is False."
+ parser.add_argument("--loadQVs",
+ dest="loadQVs",
+ action="store_true",
+ default=DEFAULT_OPTIONS["loadQVs"],
+ help=helpstr)
+
+ helpstr = "Load pulse information using -byread option instead\n" + \
+ "of -bymetric. Only works when --forQuiver or \n" + \
+ "--loadQVs are set. Default value is False."
+ parser.add_argument("--byread",
+ dest="byread",
+ action="store_true",
+ default=DEFAULT_OPTIONS["byread"],
+ help=helpstr)
+
+ helpstr = "Load the specified (comma-delimited list of) metrics\n" + \
+ "instead of the default metrics required by quiver.\n" + \
+ "This option only works when --forQuiver or \n" + \
+ "--loadQVs are set. Default: {m}".\
+ format(m=DEFAULT_OPTIONS["metrics"])
+ parser.add_argument("--metrics",
+ dest="metrics",
+ type=str,
+ action="store",
+ default=DEFAULT_OPTIONS["metrics"],
+ help=helpstr)
+
+ # Miscellaneous.
+ helpstr = "Initialize the random number generator with a none-zero \n" + \
+ "integer. Zero means that current system time is used.\n" + \
+ "Default value is {v}.".format(v=DEFAULT_OPTIONS["seed"])
+ parser.add_argument("--seed",
+ dest="seed",
+ type=int,
+ default=DEFAULT_OPTIONS["seed"],
+ action="store",
+ help=helpstr)
+
+ helpstr = "Specify a directory for saving temporary files.\n" + \
+ "Default is {v}.".format(v=DEFAULT_OPTIONS["tmpDir"])
+ parser.add_argument("--tmpDir",
+ dest="tmpDir",
+ type=str,
+ action="store",
+ default=DEFAULT_OPTIONS["tmpDir"],
+ help=helpstr)
+
+ # Keep all temporary & intermediate files.
+ parser.add_argument("--keepTmpFiles",
+ dest="keepTmpFiles",
+ action="store_true",
+ default=False,
+ help=argparse.SUPPRESS)
+
+ # Required options: inputs and outputs.
+ helpstr = "The input file can be a fasta, plx.h5, bax.h5, ccs.h5\n" + \
+ "file or a fofn."
+ parser.add_argument("inputFileName",
+ type=str,
+ action="store",
+ help=helpstr)
+
+ helpstr = "Either a reference fasta file or a reference repository."
+ parser.add_argument("referencePath",
+ type=str,
+ action="store",
+ help=helpstr)
+
+ parser.add_argument("outputFileName",
+ type=str,
+ action="store",
+ help="The output cmp.h5 or sam file.")
+
+ return parser
+
+
+def importConfigOptions(options):
+ """
+ Import options from options.configFile if the file exists, and
+ overwrite a copy of the incoming options with options imported
+ from the config file. Finally, return the new options and an
+ info message.
+ """
+ newOptions = copy(options)
+ # No config file exists.
+ if 'configFile' not in options or options.configFile is None:
+ return newOptions, ""
+
+ # There exists a config file
+ optionsDictView = vars(newOptions)
+ configFile = options.configFile
+ infoMsg = "ConfigParser: Import options from a config file {0}: "\
+ .format(configFile)
+ # The following arguments are defined in PBToolRunner, and may
+ # not exist in the input options (if the input options is parsed
+ # by a parser created in constructOptionParser).
+ specialArguments = ("--version", "--configFile", "--verbose",
+ "--debug", "--profile", "-v", "-vv", "-vvv",
+ "--keepTmpFiles")
+ try:
+ with open(configFile, 'r') as cf:
+ for line in cf:
+ line = line.strip()
+ errMsg = ""
+ # First parse special arguments and comments
+ if (line.startswith("#") or line == "" or
+ line in specialArguments):
+ pass
+ else: # Parse binary arguments
+ try:
+ k, v = line.split("=")
+ k = k.lstrip().lstrip('-').strip()
+ v = v.strip().strip('\"').strip('\'')
+ except ValueError as e:
+ errMsg = "ConfigParser: could not find '=' when " + \
+ "parsing {0}.".format(line)
+ raise ValueError(errMsg)
+ # Always use options' values from the configFile.
+ if k not in optionsDictView:
+ errMsg = "{k} is an invalid option.".format(k=k)
+ raise ValueError(errMsg)
+ else:
+ infoMsg += "{k}={v}, ".format(k=k, v=v)
+ optionsDictView[k] = v
+ except IOError as e:
+ errMsg = "ConfigParser: Could not open a config file {0}.\n".\
+ format(configFile)
+ raise IOError(errMsg + str(e))
+ return newOptions, infoMsg
+
+
+def importDefaultOptions(parsedOptions, additionalDefaults=DEFAULT_OPTIONS):
+ """Import default options and return (update_options, an_info_message).
+
+ After parsing the arguments and resolving algorithmOptions, we need
+ to patch the default pbalign options, if they have not been overwritten
+ on the command-line nor in the config file nor within algorithmOptions.
+
+ """
+ newOptions = copy(parsedOptions)
+ infoMsg = "Importing default options: "
+ optionsDictView = vars(newOptions)
+ for k, v in additionalDefaults.iteritems():
+ if (k not in optionsDictView) or (optionsDictView[k] is None):
+ infoMsg += "{k}={v}, ".format(k=optionsDictView[k], v=v)
+ optionsDictView[k] = v
+ return newOptions, infoMsg.rstrip(', ')
+
+
+def parseOptions(argumentList, parser=None):
+ """Parse a list of arguments, return options and an info message.
+
+ If a parser is not specified, create a new parser, otherwise, use
+ the specifed parser. If there exists a config file, import options
+ from the config file and finally overwrite these options with
+ options from the argument list.
+
+ """
+ # Obtain a constructed argument parser.
+ parser = constructOptionParser(parser)
+
+ # Parse argumentList for the first time in order to
+ # get a config file.
+ options = parser.parse_args(args=argumentList)
+
+ # Import options from the specified config file, if it exists.
+ configOptions, infoMsg = importConfigOptions(options)
+
+ # Parse argumentList for the second time in order to
+ # overwrite config options with options in argumentList.
+ newOptions = copy(configOptions)
+ newOptions.algorithmOptions = None
+ newOptions = parser.parse_args(namespace=newOptions, args=argumentList)
+
+ # Overwrite config algorithmOptions if it is specified in argumentList
+ if newOptions.algorithmOptions is None:
+ if configOptions.algorithmOptions is not None:
+ newOptions.algorithmOptions = configOptions.algorithmOptions
+ else:
+ newOptions.algorithmOptions = \
+ " ".join(newOptions.algorithmOptions)
+
+ # Return the updated options and an info message.
+ return parser, newOptions, infoMsg
+
+#if __name__ == "__main__":
+# import sys
+# parser = argparse.ArgumentParser()
+# parser, options, info = parseOptions(argumentList = sys.argv[1:],
+# parser=parser)
diff --git a/pbalign/pbalignfiles.py b/pbalign/pbalignfiles.py
new file mode 100755
index 0000000..9bf4ad9
--- /dev/null
+++ b/pbalign/pbalignfiles.py
@@ -0,0 +1,182 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+# Author: Yuan Li
+"""This script defines class PBALignFiles."""
+
+from __future__ import absolute_import
+import logging
+from pbalign.utils.fileutil import checkInputFile, getRealFileFormat, \
+ checkOutputFile, checkReferencePath, checkRegionTableFile, \
+ getFileFormat, FILE_FORMATS
+
+
+class PBAlignFiles:
+ """PBAlignFiles contains files that will be used by pbalign."""
+ def __init__(self, inputFileName=None, referencePath=None,
+ outputFileName=None, regionTable=None,
+ pulseFileName=None):
+ """ Initialize an instance of PBAlignFiles.
+ Input:
+ inputFileName : The user-specified input PacBio read file
+ can be in FASTA/BASE/PULSE/FOFN format.
+ referencePath : The user-specified reference path or file.
+ outputFileName: The user-specified output file in CMP.H5 or
+ SAM format.
+ regionTable : The user-specified region table. It can
+ be None if region table is not specified.
+ """
+ self.inputFileName = None # The input PacBio read files.
+ self.referencePath = None # The reference file or repository.
+ self.outputFileName = None # The output CMP.H5 or SAM file.
+ self.regionTable = None # The region table.
+
+ # The query file that will be used by an aligner. queryFileName
+ # and inputFileName can be different, because PacBio BASE/PULSE/FOFN
+ # files need to be converted to FASTA for aligners that do not accept
+ # PacBio reads.
+ self.queryFileName = None
+
+ # Load pulses from the pulse file. When input reads are in
+ # BASE/PULSE/CCS.H5 files, pulseFileName=inputFileName;
+ # otherwise, use '--pulseFile'.
+ self.pulseFileName = None
+
+ # File format of inputFileName if it is not a FOFN; otherwise,
+ # file format of the first file in FOFN: FASTA/BAS.H5/PLS.H5/CCS.H5.
+ self.inputFileFormat = None
+
+ # The target (reference) file that will be used by an aligner.
+ # referencePath can be a directory but targetFileName should always
+ # be a FASTA file.
+ self.targetFileName = None
+ self.sawriterFileName = None
+ self.isWithinRepository = False
+ self.alignerSamOut = None # The sam output file by an aligner
+ self.filteredSam = None # The filtered sam file.
+
+ # There might be an adapter file in the reference repository in
+ # directory 'annotations', which can be used by the
+ # 11k_Unrolled_Resequencing protocol to filter reads that
+ # only map to adapter regions.
+ self.adapterGffFileName = None
+
+ # Verify and assign the input & output files.
+ self.SetInOutFiles(inputFileName, referencePath,
+ outputFileName, regionTable, pulseFileName)
+
+ def SetInputFile(self, inputFileName):
+ """Verify and assign input file name and input file format."""
+ # Validate the user-specified input PacBio read file and get
+ # the absolute and expanded path. Validate file format.
+ if inputFileName is not None and inputFileName != "":
+ self.inputFileName = checkInputFile(inputFileName)
+ self.inputFileFormat = getRealFileFormat(inputFileName)
+
+ def SetPulseFileName(self, inputFileName, pulseFileName):
+ """Verify and assign the pulse file from which pulses can be
+ extracted. When inputFileName is a Base/Pulse/CCS.H5 file or a
+ fofn of Base/Pulse/CCS.H5, pulse file is inputFileName. Otherwise,
+ pulse file is pulseFileName."""
+ self.pulseFileName = None
+ if inputFileName is not None and inputFileName != "":
+ inputFormat = getRealFileFormat(inputFileName)
+ if inputFormat in [FILE_FORMATS.BAS, FILE_FORMATS.BAX,
+ FILE_FORMATS.PLS, FILE_FORMATS.PLX, FILE_FORMATS.CCS]:
+ self.pulseFileName = checkInputFile(inputFileName)
+
+ if self.pulseFileName is None:
+ if pulseFileName is not None and pulseFileName != "":
+ self.pulseFileName = checkInputFile(pulseFileName)
+
+ def SetReferencePath(self, referencePath):
+ """Validate the user-specified referencePath and get the absolute
+ and expanded path for referencePath, targetFileName and
+ sawriterFileName. targetFileName is the target reference FASTA
+ file to be used by an aligner. sawriterFileName is the reference
+ sawriter file that can be used by an aligner (e.g. blasr), its
+ value can be None if absent.
+ """
+ if referencePath is not None and referencePath != "":
+ (self.referencePath, self.targetFileName,
+ self.sawriterFileName, self.isWithinRepository,
+ self.adapterGffFileName) = \
+ checkReferencePath(referencePath)
+
+ def SetOutputFileName(self, outputFileName):
+ """Validate the user-specified output file and get the absolute and
+ expanded path.
+ """
+ if outputFileName is not None and outputFileName != "":
+ self.outputFileName = checkOutputFile(outputFileName)
+
+ def SetRegionTable(self, regionTable):
+ """Validate the user-specified region table and get the absolute and
+ expanded path. The value can be None if regionTable is not given.
+ """
+ if regionTable is not None and regionTable != "":
+ self.regionTable = checkRegionTableFile(regionTable)
+
+ def SetInOutFiles(self, inputFileName, referencePath,
+ outputFileName, regionTable, pulseFileName=None):
+ """Verify and assign the input & output files."""
+ self.SetInputFile(inputFileName)
+
+ self.SetReferencePath(referencePath)
+
+ self.SetOutputFileName(outputFileName)
+
+ self.SetRegionTable(regionTable)
+
+ self.SetPulseFileName(inputFileName, pulseFileName)
+
+ def __repr__(self):
+ """ Represent PBAlignFiles."""
+ desc = "Input file : {i}\n".format(i=self.inputFileName)
+ desc += "Reference path: {r} ".format(r=self.referencePath)
+ desc += "is {res}within a reference repository.\n".format(
+ res="" if self.isWithinRepository else "not ")
+ desc += "Output file: {o}\n".format(o=self.outputFileName)
+ desc += "Query file : {q}\n".format(q=self.queryFileName)
+ desc += "Target file: {t}\n".format(t=self.targetFileName)
+ desc += "Suffix array file: {s}\n".format(s=self.sawriterFileName)
+ desc += "regionTable:{s}\n".format(s=self.regionTable)
+ if self.pulseFileName is not None:
+ desc += "Pulse files: {s}\n".format(s=self.pulseFileName)
+ desc += "Aligner's SAM out: {t}\n".format(t=self.alignerSamOut)
+ desc += "Filtered SAM file: {t}\n".format(t=self.filteredSam)
+ if self.adapterGffFileName is not None:
+ desc += "Adapter GFF file: {t}\n".format(
+ t=self.adapterGffFileName)
+ return desc
+
+#if __name__ == "__main__":
+# p = PBAlignFiles("lambda.fasta", "lambda_ref.fasta", "tmp.sam")
diff --git a/pbalign/pbalignrunner.py b/pbalign/pbalignrunner.py
new file mode 100755
index 0000000..afd2a18
--- /dev/null
+++ b/pbalign/pbalignrunner.py
@@ -0,0 +1,306 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+"""This script defines class PBAlignRunner.
+
+PBAlignRunner uses AlignService to align PacBio reads in FASTA/BASE/PULSE/FOFN
+formats to reference sequences, then uses FilterServices to filter out
+alignments that do not satisfy filtering criteria, and finally generates a SAM
+or CMP.H5 file.
+
+"""
+
+# Author: Yuan Li
+
+import logging
+import time
+import sys
+import shutil
+
+from pbalign.__init__ import get_version
+from pbalign.options import parseOptions, ALGORITHM_CANDIDATES
+from pbalign.alignservice.blasr import BlasrService
+from pbalign.alignservice.bowtie import BowtieService
+from pbalign.alignservice.gmap import GMAPService
+from pbalign.utils.fileutil import getFileFormat, FILE_FORMATS, real_ppath
+from pbalign.utils.tempfileutil import TempFileManager
+from pbalign.pbalignfiles import PBAlignFiles
+from pbalign.filterservice import FilterService
+from pbalign.forquiverservice.forquiver import ForQuiverService
+from pbcore.util.Process import backticks
+from pbcore.util.ToolRunner import PBToolRunner
+
+
+class PBAlignRunner(PBToolRunner):
+ """Tool runner."""
+
+ def __init__(self, argumentList):
+ """Initialize a PBAlignRunner object.
+ argumentList is a list of arguments, such as:
+ ['--debug', '--maxHits', '10', 'in.fasta', 'ref.fasta', 'out.sam']
+ """
+ desc = "Utilities for aligning PacBio reads to reference sequences."
+ super(PBAlignRunner, self).__init__(desc)
+ self._argumentList = argumentList
+ self._alnService = None
+ self._filterService = None
+ self.fileNames = PBAlignFiles()
+ self._tempFileManager = TempFileManager()
+
+ self.parser, self.args, _infoMsg = parseOptions(
+ argumentList=self._argumentList, parser=self.parser)
+ # args.verbosity is computed by counting # of 'v's in '-vv...'.
+ # However in parseOptions, arguments are parsed twice to import config
+ # options and then overwrite them with argumentList (e.g. command-line)
+ # options.
+ self.args.verbosity = 0 if (self.args.verbosity is None) else \
+ int(self.args.verbosity) / 2
+
+ def getVersion(self):
+ """Return version."""
+ return get_version()
+
+ def _createAlignService(self, name, args, fileNames, tempFileManager):
+ """
+ Create and return an AlignService by algorithm name.
+ Input:
+ name : an algorithm name such as blasr
+ fileNames : an PBAlignFiles object
+ args : pbalign options
+ tempFileManager: a temporary file manager
+ Output:
+ an object of AlignService subclass (such as BlasrService).
+ """
+ if name not in ALGORITHM_CANDIDATES:
+ errMsg = "ERROR: unrecognized algorithm {algo}".format(algo=name)
+ logging.error(errMsg)
+ raise ValueError(errMsg)
+
+ service = None
+ if name == "blasr":
+ service = BlasrService(args, fileNames, tempFileManager)
+ elif name == "bowtie":
+ service = BowtieService(args, fileNames, tempFileManager)
+ elif name == "gmap":
+ service = GMAPService(args, fileNames, tempFileManager)
+ else:
+ errMsg = "Service for {algo} is not implemented.".\
+ format(algo=name)
+ logging.error(errMsg)
+ raise ValueError(errMsg)
+
+ service.checkAvailability()
+ return service
+
+ def _makeSane(self, args, fileNames):
+ """
+ Check whether the input arguments make sense or not.
+ """
+ errMsg = ""
+ if args.useccs == "useccsdenovo":
+ args.readType = "CCS"
+
+ if fileNames.inputFileFormat == FILE_FORMATS.CCS:
+ args.readType = "CCS"
+
+ if args.forQuiver:
+ if args.useccs is not None:
+ errMsg = "Options --forQuiver and --useccs should not " + \
+ "be used together, since Quiver is not designed to " + \
+ "polish ccs reads. if you want to align ccs reads" + \
+ "in cmp.h5 format with pulse QVs loaded, use " + \
+ "--loadQVs with --useccs instead."
+ raise ValueError(errMsg)
+ args.loadQVs = True
+
+ if args.loadQVs:
+ if fileNames.pulseFileName is None:
+ errMsg = "The input file has to be in bas/pls/ccs.h5 " + \
+ "format, or --pulseFile needs to be specified, "
+ if getFileFormat(fileNames.outputFileName) != FILE_FORMATS.CMP:
+ errMsg = "The output file has to be in cmp.h5 format, "
+ if errMsg != "":
+ errMsg += "in order to load pulse QVs."
+ logging.error(errMsg)
+ raise ValueError(errMsg)
+
+ def _parseArgs(self):
+ """Overwrite ToolRunner.parseArgs(self).
+ Parse PBAlignRunner arguments considering both args in argumentList and
+ args in a config file (specified by --configFile).
+ """
+ pass
+
+ def _output(self, inSam, refFile, outFile, readType=None, smrtTitle=False):
+ """Generate a sam or a cmp.h5 file.
+ Input:
+ inSam : an input SAM file. (e.g. fileName.filteredSam)
+ refFile : the reference file. (e.g. fileName.targetFileName)
+ outFile : the output SAM or CMP.H5 file.
+ (i.e. fileName.outputFileName)
+ readType: standard or cDNA or CCS (can be None if not specified)
+ Output:
+ output, errCode, errMsg
+ """
+ output, errCode, errMsg = "", 0, ""
+
+ if getFileFormat(outFile) == FILE_FORMATS.SAM:
+ #`mv inSam outFile`
+ logging.info("OutputService: Genearte the output SAM file.")
+ logging.debug("OutputService: Move {src} as {dst}".format(
+ src=inSam, dst=outFile))
+ try:
+ shutil.move(real_ppath(inSam), real_ppath(outFile))
+ except shutil.Error as e:
+ output, errCode, errMsg = "", 1, str(e)
+ elif getFileFormat(outFile) == FILE_FORMATS.CMP:
+ #`samtoh5 inSam outFile -readType readType
+ logging.info("OutputService: Genearte the output CMP.H5 " +
+ "file using samtoh5.")
+ prog = "samtoh5"
+ cmd = "samtoh5 {samFile} {refFile} {outFile}".format(
+ samFile=inSam, refFile=refFile, outFile=outFile)
+ if readType is not None:
+ cmd += " -readType {0} ".format(readType)
+ if smrtTitle:
+ cmd += " -smrtTitle "
+ # Execute the command line
+ logging.debug("OutputService: Call \"{0}\"".format(cmd))
+ output, errCode, errMsg = backticks(cmd)
+
+ if errCode != 0:
+ errMsg = prog + " returned a non-zero exit status." + errMsg
+ logging.error(errMsg)
+ raise RuntimeError(errMsg)
+ return output, errCode, errMsg
+
+ def _cleanUp(self, realDelete=False):
+ """ Clean up temporary files and intermediate results. """
+ logging.debug("Clean up temporary files and directories.")
+ self._tempFileManager.CleanUp(realDelete)
+
+# def _setupLogging(self):
+# LOG_FORMAT = "%(asctime)s [%(levelname)s] %(message)s"
+# if self.args.verbosity >= 2:
+# print "logLevel = debug"
+# logLevel = logging.DEBUG
+# elif self.args.verbosity == 1:
+# print "logLevel = info"
+# logLevel = logging.INFO
+# else:
+# print "logLevel = warn"
+# logLevel = logging.WARN
+# logging.basicConfig(level=logLevel, format=LOG_FORMAT)
+
+ def run(self):
+ """
+ The main function, it is called by PBToolRunner.start().
+ """
+ startTime = time.time()
+ logging.info("pbalign version: {version}".format(version=get_version()))
+ logging.debug("Original arguments: " + str(self._argumentList))
+
+ # Create an AlignService by algorithm name.
+ self._alnService = self._createAlignService(self.args.algorithm,
+ self.args,
+ self.fileNames,
+ self._tempFileManager)
+
+ # Make sane.
+ self._makeSane(self.args, self.fileNames)
+
+ # Run align service.
+ try:
+ self._alnService.run()
+ except RuntimeError:
+ return 1
+
+ # Create a temporary filtered SAM file as output for FilterService.
+ self.fileNames.filteredSam = self._tempFileManager.\
+ RegisterNewTmpFile(suffix=".sam")
+
+ # Call filter service.
+ self._filterService = FilterService(self.fileNames.alignerSamOut,
+ self.fileNames.targetFileName,
+ self.fileNames.filteredSam,
+ self._alnService.name,
+ self._alnService.scoreSign,
+ self.args,
+ self.fileNames.adapterGffFileName)
+ try:
+ self._filterService.run()
+ except RuntimeError:
+ return 1
+
+ # Output all hits either in SAM or CMP.H5.
+ try:
+ useSmrtTitle = False
+ if (self.args.algorithm != "blasr" or
+ self.fileNames.inputFileFormat == FILE_FORMATS.FASTA):
+ useSmrtTitle = True
+
+ self._output(
+ self.fileNames.filteredSam,
+ self.fileNames.targetFileName,
+ self.fileNames.outputFileName,
+ self.args.readType,
+ useSmrtTitle)
+ except RuntimeError:
+ return 1
+
+ # Call post service for quiver.
+ if self.args.forQuiver or self.args.loadQVs:
+ postService = ForQuiverService(self.fileNames,
+ self.args)
+ try:
+ postService.run()
+ except RuntimeError:
+ return 1
+
+ # Delete temporay files anyway to make
+ self._cleanUp(False if (hasattr(self.args, "keepTmpFiles") and
+ self.args.keepTmpFiles is True) else True)
+
+ endTime = time.time()
+ logging.info("Total time: {:.2f} s.".format(float(endTime - startTime)))
+ return 0
+
+
+def main():
+ pbobj = PBAlignRunner(sys.argv[1:])
+ return pbobj.start()
+
+
+if __name__ == "__main__":
+ # For testing PBAlignRunner.
+ # PBAlignRunner inherits PBToolRunner. So PBAlignRunner.start() parses args,
+ # sets up logging and finally returns run().
+ sys.exit(main())
diff --git a/pbalign/service.py b/pbalign/service.py
new file mode 100755
index 0000000..e0da72d
--- /dev/null
+++ b/pbalign/service.py
@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+"""This script defines a virtual class Service."""
+from __future__ import absolute_import
+from pbalign.utils.progutil import Availability, \
+ CheckAvailability, Execute
+
+
+class Service(object):
+ """A Service object class."""
+ @property
+ def name(self):
+ """Service name."""
+ raise NotImplementedError(
+ "Virtual property name() for {0} must be overwritten.".
+ format(type(self)))
+
+ @property
+ def progName(self):
+ """Program to call."""
+ raise NotImplementedError(
+ "Virtual property progName() for {0} must be overwritten.".
+ format(type(self)))
+
+ @property
+ def availability(self):
+ """Return True if self.progName is available, otherwise false."""
+ return Availability(self.progName)
+
+ @property
+ def cmd(self):
+ """Command to execute for this service."""
+ raise NotImplementedError(
+ "Virtual property progName() for {0} must be overwritten.".
+ format(type(self)))
+
+ def checkAvailability(self):
+ """Raise a runtime error if program for this service is not
+ available."""
+ CheckAvailability(self.progName)
+
+ def _execute(self):
+ """Execute a command (self.cmd)."""
+ return Execute(self.name, self.cmd)
diff --git a/pbalign/tools/__init__.py b/pbalign/tools/__init__.py
new file mode 100755
index 0000000..4e1e00a
--- /dev/null
+++ b/pbalign/tools/__init__.py
@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+# Author: Yuan Li
+"""Migrate pbpy scripts to bioinformatics."""
+
+from __future__ import absolute_import
+
diff --git a/pbalign/tools/createChemistryHeader.py b/pbalign/tools/createChemistryHeader.py
new file mode 100755
index 0000000..434d98c
--- /dev/null
+++ b/pbalign/tools/createChemistryHeader.py
@@ -0,0 +1,207 @@
+#!/usr/bin/env python
+"""createChemistryHeader.py gets chemistry triple information for movies in
+a BLASR-produced SAM file. It writes a new SAM header file that contains the
+chemisty information. This header can be used with samtools reheader. Most
+of the work is actually done by BasH5Reader.
+"""
+import argparse
+import copy
+import logging
+import sys
+
+import pysam
+
+from pbcore.io import BasH5IO, FofnIO
+
+log = logging.getLogger('main')
+
+MOVIENAME_TAG = 'PU'
+
+class ChemistryLoadingException(Exception):
+ """Exception when chemistry lookup fails."""
+ pass
+
+def format_rgds_entries(rgds_entries):
+ """Turn the RG DS dictionary into a list of strings that
+ can be placed into a header object.
+ """
+
+ rgds_strings = {}
+ for rg_id in rgds_entries:
+ rgds_string = ("BINDINGKIT:{b};SEQUENCINGKIT:{s};"
+ "SOFTWAREVERSION:{v}"
+ .format(b=rgds_entries[rg_id][0],
+ s=rgds_entries[rg_id][1],
+ v=rgds_entries[rg_id][2]))
+ rgds_strings[rg_id] = rgds_string
+ return rgds_strings
+
+def extend_header(old_header, new_rgds_strings):
+ """Create a new SAM/BAM header, adding the RG descriptions to the
+ old_header.
+ """
+
+ new_header = copy.deepcopy(old_header)
+
+ for rg_entry in new_header['RG']:
+ try:
+ new_ds_string = new_rgds_strings[rg_entry['ID']]
+ except KeyError:
+ continue
+
+ if 'DS' in rg_entry:
+ rg_entry['DS'] += ';' + new_ds_string
+ else:
+ rg_entry['DS'] = new_ds_string
+
+ return new_header
+
+def get_chemistry_info(sam_header, input_filenames, fail_on_missing=False):
+ """Get chemistry triple information for movies referenced in a SAM
+ header.
+
+ Args:
+ sam_header: a pysam.Samfile.header, which is a multi-level dictionary.
+ Movie names are read from RG tags in this header.
+ input_filenames: a list of bas, bax, or fofn filenames.
+ fail_on_missing: if True, raise an exception if the chemistry
+ information for a movie in the header cannot be
+ found. If False, just log a warning.
+ Returns:
+ a list of strings that can be written as DS tags to RG entries in the
+ header of a new SAM or BAM file. For example,
+ ['BINDINGKIT:xxxx;SEQUENCINGKIT:yyyy;SOFTWAREVERSION:2.0']
+
+ Raises:
+ ChemistryLoadingException if chemistry information cannot be found
+ for a movie in the header and fail_on_missing is True.
+ """
+
+ # First get the full list of ba[sx] files, reading through any fofn or xml
+ # inputs
+ bas_filenames = []
+ for filename in input_filenames:
+ bas_filenames.extend(FofnIO.enumeratePulseFiles(filename))
+
+ # Then get the chemistry triple for each movie in the list of bas files
+ triple_dict = {}
+ for bas_filename in bas_filenames:
+ bas_file = BasH5IO.BasH5Reader(bas_filename)
+ movie_name = bas_file.movieName
+ chem_triple = bas_file.chemistryBarcodeTriple
+ triple_dict[movie_name] = chem_triple
+
+ # Finally, find the movie names that appear in the header and create CO
+ # lines with the chemistry triple
+ if 'RG' not in sam_header:
+ return []
+ rgds_entries = {}
+ for rg_entry in sam_header['RG']:
+ rg_id = rg_entry['ID']
+ rg_movie_name = rg_entry[MOVIENAME_TAG]
+
+ try:
+ rg_chem_triple = triple_dict[rg_movie_name]
+ rgds_entries[rg_id] = rg_chem_triple
+ except KeyError:
+ err_msg = ("Cannot find chemistry information for movie {m}."
+ .format(m=rg_movie_name))
+ if fail_on_missing:
+ raise ChemistryLoadingException(err_msg)
+ else:
+ log.warning(err_msg)
+
+ rgds_strings = format_rgds_entries(rgds_entries)
+
+ return rgds_strings
+
+def get_parser():
+ """Return an ArgumentParser for pbcompress options."""
+
+ desc = ("createChemistryHeader creates a SAM header that contains the "
+ "chemistry information used by Quiver.")
+
+ parser = argparse.ArgumentParser(
+ prog='getChemistryHeader.py', description=desc,
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+ parser.add_argument("--debug", help="Output detailed log information.",
+ action='store_true')
+
+ def sam_or_bam_filename(val):
+ """Check that val names a SAM or BAM file."""
+ if not (val.endswith(".bam") or val.endswith(".sam")):
+ raise argparse.ArgumentTypeError(
+ "File must end with .sam or .bam. {f} doesn't "
+ "end with either of those."
+ .format(f=val))
+ return val
+
+ parser.add_argument(
+ "input_alignment_file",
+ help="A SAM or BAM file produced by BLASR.",
+ type=sam_or_bam_filename)
+
+ parser.add_argument(
+ "output_header_file",
+ help=("Name of the SAM or BAM header file that will be created with "
+ "chemistry information loaded."),
+ type=sam_or_bam_filename)
+
+ parser.add_argument(
+ "--bas_files",
+ help=("The bas or bax files containing the reads that were aligned in "
+ "the input_alignment_file. Also can be a fofn of bas or bax "
+ "files."),
+ nargs='+',
+ required=True)
+
+ return parser
+
+def setup_log(alog, file_name=None, level=logging.DEBUG, str_formatter=None):
+ """Util function for setting up logging."""
+
+ if file_name is None:
+ handler = logging.StreamHandler(sys.stderr)
+ else:
+ handler = logging.FileHandler(file_name)
+
+ if str_formatter is None:
+ str_formatter = ('[%(levelname)s] %(asctime)-15s '
+ '[%(name)s %(funcName)s %(lineno)d] %(message)s')
+
+ formatter = logging.Formatter(str_formatter)
+ handler.setFormatter(formatter)
+ alog.addHandler(handler)
+ alog.setLevel(level)
+
+def main():
+ """Entry point."""
+ parser = get_parser()
+ args = parser.parse_args()
+
+ if args.debug:
+ setup_log(log, level=logging.DEBUG)
+ else:
+ setup_log(log, level=logging.INFO)
+
+ input_file = pysam.Samfile(args.input_alignment_file, 'r')
+ input_header = input_file.header
+ log.debug("Read header from {f}.".format(f=input_file.filename))
+
+ chemistry_rgds_strings = get_chemistry_info(
+ input_header, args.bas_files)
+
+ new_header = extend_header(input_header, chemistry_rgds_strings)
+
+ if args.output_header_file.endswith('.bam'):
+ output_file = pysam.Samfile(args.output_header_file, 'wb',
+ header=new_header)
+ elif args.output_header_file.endswith('.sam'):
+ output_file = pysam.Samfile(args.output_header_file, 'wh',
+ header=new_header)
+
+ output_file.close()
+
+if __name__ == '__main__':
+ main()
diff --git a/pbalign/tools/extractUnmappedSubreads.py b/pbalign/tools/extractUnmappedSubreads.py
new file mode 100755
index 0000000..a862cb9
--- /dev/null
+++ b/pbalign/tools/extractUnmappedSubreads.py
@@ -0,0 +1,188 @@
+#!/usr/bin/env python
+"""
+Starts with the filtered_reads.fa file. Reads in the control.cmp.h5 and
+reference.cmp.h5, removing any subreads that map. Writes resulting fasta
+entries to stdout.
+"""
+
+import sys
+import logging
+import os.path as op
+import re
+import h5py
+from pbcore.io import FastaReader
+from pbcore.util.ToolRunner import PBToolRunner
+
+__version__ = "0.1.0.133504"
+
+
+class ExtractRunner(PBToolRunner):
+ """ExtractUnmappedReads Runner."""
+ def __init__(self):
+ """Handle command line argument parsing"""
+ desc = "Extract unmapped subreads from a fasta file."
+ PBToolRunner.__init__(self, desc)
+ self.set_parser(self.parser)
+ self.fastaFN = None
+ self.cmpH5FNs = []
+
+ def set_parser(self, parser):
+ """Set parser."""
+ parser.add_argument("fasta", type=str,
+ help="a fasta file containing all subreads.")
+ parser.add_argument("cmph5", metavar="cmp.h5", nargs="+",
+ help="input cmp.h5 files.")
+ return parser
+
+ def getVersion(self):
+ """Get version string."""
+ return __version__
+
+ def _getFastaReadsInfo(self, fastaReads):
+ """ Get reads' info (not including alignments) from the fasta. """
+ pattern = re.compile(r"(m.+)\/(\d+)\/(\d+)_(\d+)")
+ #for entry in FastaIO.SimpleFastaReader(self.fastaFN):
+ with FastaReader(self.fastaFN) as reader:
+ for entry in reader:
+ match = pattern.search( entry.name.strip() )
+ if not match:
+ continue
+ movie, holeNumber, srStart, srEnd = match.groups()
+ holeNumber, srStart, srEnd = \
+ int(holeNumber), int(srStart), int(srEnd)
+ fastaReads.setdefault(movie, {})
+ fastaReads[movie].setdefault(holeNumber, [])
+ fastaReads[movie][holeNumber].append((srStart, srEnd))
+
+ def _loadMappedSubreads(self, subreads, cmpH5FN):
+ """Loads all subreads from the specified cmpH5 into the
+ subread data structure."""
+ cmpFile = h5py.File(cmpH5FN, 'r')
+ movieInfo = cmpFile["/MovieInfo"]
+ movieDict = dict(zip(movieInfo["ID"], movieInfo["Name"]))
+
+ numAln = cmpFile["/AlnInfo/AlnIndex"].shape[0]
+ movieIdIdx, holeIdx, startIdx, endIdx = 2, 7, 11, 12
+
+ if numAln != 0:
+ for row in cmpFile["/AlnInfo/AlnIndex"].value:
+ movie = movieDict[row[movieIdIdx]]
+ subreads.setdefault(movie, {})
+ subreads[movie].setdefault(row[holeIdx], [])
+ subreads[movie][row[holeIdx]].append(
+ (row[startIdx], row[endIdx]))
+ logging.info("Loaded {n} subreads from {f}".format(n=numAln, f=cmpH5FN))
+ cmpFile.close()
+
+ def _rmMappedReads( self, fastaReadsPos, cmpReadsPos):
+ """ Remove fasta reads that are mapped. """
+ # For a read of a hole, the number of subreads that can map to reference
+ # is usually small (e.g. 1 or 2). Actually, it is not profitable at all
+ # to "sort and binary search for mapped subreads" based on experiments.
+ i = 0
+ while i < len(fastaReadsPos):
+ fStart, fEnd = fastaReadsPos[i]
+ for cStart, cEnd in cmpReadsPos:
+ if cStart >= fStart and cEnd <= fEnd:
+ logging.debug("{0} {1} in {2} {3} ?".\
+ format(cStart, cEnd, fStart, fEnd))
+ fastaReadsPos.pop(i)
+ i -= 1
+ break
+ i += 1
+
+ def _printUnMappedReads(self, fastaReads):
+ """Print unmapped subreads."""
+ pattern = re.compile(r"(m.+)\/(\d+)\/(\d+)_(\d+)")
+ with FastaReader(self.fastaFN) as reader:
+ for entry in reader:
+ match = pattern.search( entry.name.strip() )
+ if not match:
+ continue
+ movie, holeNumber, srStart, srEnd = match.groups()
+ holeNumber, srStart, srEnd = \
+ int(holeNumber), int(srStart), int(srEnd)
+ if movie in fastaReads and \
+ holeNumber in fastaReads[movie] and \
+ (srStart, srEnd) in fastaReads[movie][holeNumber]:
+ entry.COLUMNS=70
+ print str(entry)
+
+ def run(self):
+ """Executes the body of the script."""
+ logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
+ v=self.getVersion))
+ args = self.args
+ logging.info("Extracting unmapped reads from a fasta file.")
+
+ self.fastaFN = args.fasta
+ self.cmpH5FNs = args.cmph5
+ logging.debug("Input fasta is {f}.".format(f=self.fastaFN))
+ logging.debug("Input fasta is {f}.".format(f=self.cmpH5FNs))
+
+ fastaReads = {}
+ self._getFastaReadsInfo(fastaReads)
+
+ subreads = {}
+ for cmpH5FN in self.cmpH5FNs:
+ subreads = { }
+ self._loadMappedSubreads(subreads, cmpH5FN)
+
+ for movie in subreads:
+ for holeNumber in subreads[movie]:
+ logging.debug("Movie: {m}".format(m=movie))
+ if movie not in fastaReads:
+ break
+ elif holeNumber not in fastaReads[movie]:
+ continue
+ # Remove mapped reads from fastaReads[movie][holeNumber]
+ self._rmMappedReads(fastaReads[movie][holeNumber],
+ subreads[movie][holeNumber])
+
+ # Print unmapped reads
+ self._printUnMappedReads(fastaReads)
+
+
+# The following code can cut the memory used in half (if there is only
+# one cmpH5FN) at the expense of increased running time
+# (by 80% ~ 100% if there are multiple movies).
+# def run( self ):
+# """Executes the body of the script."""
+#
+# logging.info("Log level set to INFO")
+# logging.debug("Log Level set to DEBUG")
+#
+# subreads = { }
+# for cmpH5FN in self.cmpH5FNs:
+# self._loadMappedSubreads( subreads, cmpH5FN )
+#
+# subreadId = re.compile("(m.+)\/(\d+)\/(\d+)_(\d+)")
+# for entry in FastaIO.SimpleFastaReader( self.fastaFN ):
+# match = subreadId.search( entry.name.strip() )
+# if not match:
+# continue
+# movie, read, srStart, srEnd = [match.group(i) for i in range(1,5)]
+# read, srStart, srEnd = int(read), int(srStart), int(srEnd)
+# mapped = False
+# if movie in subreads and read in subreads[ movie ]:
+# ids = subreads[ movie ][ read ]
+# logging.debug("Movie: %s" % movie)
+# for id in ids:
+# logging.debug("%s inside %s?" %
+# ( str(id), "(%s,%s)" % ( srStart, srEnd)))
+# if id[0] >= srStart and id[1] <= srEnd:
+# mapped = True
+# break
+# if not mapped:
+# print str(entry)
+#
+# return 0
+
+def main():
+ """Main entry"""
+ runner = ExtractRunner()
+ return runner.start()
+
+
+if __name__ == "__main__":
+ sys.exit(main())
diff --git a/pbalign/tools/loadChemistry.py b/pbalign/tools/loadChemistry.py
new file mode 100755
index 0000000..78d05d4
--- /dev/null
+++ b/pbalign/tools/loadChemistry.py
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+
+USAGE = \
+"""
+loadChemistry.py
+
+ Load chemistry info into a cmp.h5, just copying the triple. Note
+ that there is no attempt to "decode" chemistry barcodes here---this
+ is a dumb pipe.
+
+ usage:
+ % loadChemistry [input.fofn | list of input.ba[sx].h5] aligned_reads.cmp.h5
+"""
+
+import sys, h5py, numpy as np
+from pbcore.io import *
+
+class ChemistryLoadingException(BaseException): pass
+
+STRING_DTYPE = h5py.special_dtype(vlen=bytes)
+
+def safeDelete(group, dsName):
+ if dsName in group:
+ del group[dsName]
+
+def writeTriples(movieInfoGroup, triplesByMovieName):
+ movieNamesInCmpH5 = list(movieInfoGroup["Name"])
+ if not set(movieNamesInCmpH5).issubset(set(triplesByMovieName.keys())):
+ raise ChemistryLoadingException, "Mismatch between movies in input.fofn and cmp.h5 movies"
+
+ safeDelete(movieInfoGroup, "BindingKit")
+ safeDelete(movieInfoGroup, "SequencingKit")
+ safeDelete(movieInfoGroup, "SoftwareVersion")
+
+ shape = movieInfoGroup["Name"].shape
+ bindingKit = movieInfoGroup.create_dataset("BindingKit" , shape=shape, dtype=STRING_DTYPE, maxshape=(None,))
+ sequencingKit = movieInfoGroup.create_dataset("SequencingKit" , shape=shape, dtype=STRING_DTYPE, maxshape=(None,))
+ softwareVersion = movieInfoGroup.create_dataset("SoftwareVersion", shape=shape, dtype=STRING_DTYPE, maxshape=(None,))
+
+ for (movieName, triple) in triplesByMovieName.items():
+ if movieName in movieNamesInCmpH5:
+ idx = movieNamesInCmpH5.index(movieName)
+ bindingKit[idx] = triple[0]
+ sequencingKit[idx] = triple[1]
+ softwareVersion[idx] = triple[2]
+
+ assert all(bindingKit.value != "")
+ assert all(sequencingKit.value != "")
+ assert all(softwareVersion.value != "")
+
+
+def main():
+ if len(sys.argv) < 3:
+ print USAGE
+ return -1
+
+ inputFilenames = sys.argv[1:-1]
+ cmpFname = sys.argv[-1]
+
+ if len(inputFilenames) == 1 and inputFilenames[0].endswith(".fofn"):
+ basFnames = list(enumeratePulseFiles(inputFilenames[0]))
+ else:
+ basFnames = inputFilenames
+
+ f = h5py.File(cmpFname, "r+")
+ movieInfoGroup = f["MovieInfo"]
+
+ triples = {}
+ for basFname in basFnames:
+ bas = BasH5Reader(basFname)
+ movieName = bas.movieName
+ chemTriple = bas.chemistryBarcodeTriple
+ triples[movieName] = chemTriple
+
+ writeTriples(movieInfoGroup, triples)
+
+if __name__ == '__main__':
+ main()
diff --git a/pbalign/tools/mask_aligned_reads.py b/pbalign/tools/mask_aligned_reads.py
new file mode 100755
index 0000000..591cf0c
--- /dev/null
+++ b/pbalign/tools/mask_aligned_reads.py
@@ -0,0 +1,194 @@
+#!/usr/bin/env python
+"""Takes in a rgn.fofn and corresponding cmp.h5. Uses the
+alignments from the cmp.h5 to mask corresponding regions of
+the rgn.h5s. Writes output to a new rgn.fofn."""
+
+import os
+import sys
+import logging
+import argparse
+import re
+
+from pbcore.io import CmpH5Reader, EmptyCmpH5Error
+import traceback
+from pbalign.utils.RgnH5IO import RgnH5Reader, RgnH5Writer
+
+__VERSION__ = "0.3"
+
+
+class AlignedReadsMasker(object):
+ """Mask aligned reads in a region table.
+ Input: inCmpFile - a cmp.h5 file with alignments.
+ inRgnFofn - a input fofn of region table files.
+ Output: outRgnFofn - a output fofn of region table files.
+ Generate new rgn.h5 files, which mask aligned reads in `inRgnFofn`
+ by overwritting their corresponding HQ regions to (0, 0). The
+ generated new rgn.h5 files have to be stored in the same directory
+ as `outRgnFofn`.
+ """
+ def __init__(self, inCmpFile, inRgnFofn, outRgnFofn):
+ self.inCmpFile = inCmpFile
+ self.inRgnFofn = inRgnFofn
+ self.outRgnFofn = outRgnFofn
+
+ def maskAlignedReads(self):
+ """Mask aligned zmws in region tables."""
+ logging.info("Log level set to INFO")
+ logging.debug("Log Level set to DEBUG")
+
+ alignedReads = self._extractAlignedReads()
+ nreads = sum([len(v) for v in alignedReads.values()])
+ logging.info("Extracted {r} reads ({m} movies) from {f}".format(
+ r=nreads, m=len(alignedReads), f=self.inCmpFile))
+
+ outDir = os.path.splitext(self.outRgnFofn)[0]
+
+ if not os.path.exists(outDir):
+ os.mkdir(outDir)
+
+ outRgnFofn = open(self.outRgnFofn, 'w')
+
+ # Check for new format generated from bax files.
+ # m130226_022844_...131362_s1_p0.3.rgn.h5
+ rx = re.compile(r'\.[0-9].rgn\.h5')
+
+ for rgnH5FN in [line.strip() for line in open(self.inRgnFofn, 'r')]:
+ if not rgnH5FN.endswith("rgn.h5"):
+ logging.error("Region table file " +
+ "{0} should be a rgn.h5 file.".format(rgnH5FN))
+ return 1
+ rgnReader = RgnH5Reader(rgnH5FN)
+
+ basename = os.path.basename(rgnH5FN)
+ # Default movie name
+ movieName = rgnReader.movieName
+
+ # 'movieId' is used to write the file compatible with bax style.
+ # m130226_022844_ethan_c100471672550000001823071906131362_s1_p0.3
+ if rx.search(basename):
+ movieId = re.split(r'.rgn\.h5', basename)[0]
+ else:
+ # old format
+ # m130226_022844_....131362_s1_p0.rgn.h5
+ movieId = movieName
+
+ outH5FN = os.path.abspath(os.path.join(outDir,
+ movieId + ".rgn.h5"))
+ outRgnFofn.write("{o}\n".format(o=outH5FN))
+ rgnWriter = RgnH5Writer(outH5FN)
+ rgnWriter.writeScanDataGroup(rgnReader.scanDataGroup)
+
+ logging.info("Processing {f}...".format(f=rgnH5FN))
+ for rt in rgnReader:
+ if movieName in alignedReads and \
+ rt.holeNumber in alignedReads[movieName]:
+ rt.setHQRegion(0, 0)
+ rgnWriter.addRegionTable(rt)
+
+ rgnReader.close()
+ rgnWriter.close()
+
+ outRgnFofn.close()
+ return 0
+
+ def _extractAlignedReads(self):
+ """Grab a mapping of all movie names of aligned reads to hole numbers.
+ and return { Movie: [HoleNumbers ...] }.
+ """
+ alignedReads = {}
+
+ try:
+ reader = CmpH5Reader(self.inCmpFile)
+
+ for movie in reader.movieInfoTable.Name:
+ alignedReads.setdefault(movie, set())
+
+ for i in reader:
+ alignedReads[i.movieInfo.Name].add(i.HoleNumber)
+ reader.close()
+ except (IndexError, EmptyCmpH5Error):
+ msg = "No aligned reads found in {x}".format(x=self.inCmpFile)
+ sys.stderr.write(msg + "\n")
+ logging.warn(msg)
+
+ return alignedReads
+
+
+def getParser():
+ """Add arguments to an argument parser and return it.
+ usage = "%prog [--help] [options] cmp.h5 rgn.fofn rgn_out.fofn"
+ """
+
+ desc = "Use in.cmp.h5 to mask corresponing regions of files in " + \
+ "in.rgn.h5, write output to a new rgn.fofn."
+ parser = argparse.ArgumentParser(
+ description=desc,
+ version=__VERSION__,
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+ parser.add_argument(
+ "-l", "--logFile", default=None,
+ help="Specify a file to log to. Defaults to stderr.")
+ parser.add_argument(
+ "-d", "--debug", default=False, action="store_true",
+ help="Increases verbosity of logging")
+ parser.add_argument(
+ "-i", "--info", default=False, action="store_true",
+ help="Display informative log entries")
+ parser.add_argument(
+ "inCmpFile", type=str,
+ help="An input cmp.h5 file.")
+ parser.add_argument(
+ "inRgnFofn", type=str,
+ help="A fofn of input region table files.")
+ parser.add_argument(
+ "outRgnFofn", type=str,
+ help="A fofn of output region table files.")
+ return parser
+
+
+def configLog(isInfo, isDebug, logFile):
+ """Sets up logging based on command line arguments.
+ Allows for three levels of logging:
+ logging.error( ): always emitted
+ logging.info( ): emitted with --info or --debug
+ logging.debug( ): only with --debug
+ """
+ logLevel = logging.DEBUG if isDebug else \
+ logging.INFO if isInfo else logging.ERROR
+ logFormat = "%(asctime)s [%(levelname)s] %(message)s"
+
+ if logFile is not None:
+ logging.basicConfig(filename=logFile, level=logLevel,
+ format=logFormat)
+ else:
+ logging.basicConfig(stream=sys.stderr, level=logLevel,
+ format=logFormat)
+
+
+def run(inCmpFile, inRgnFofn, outRgnFofn):
+ """Main function to run mask aligned reads()."""
+
+ masker = AlignedReadsMasker(inCmpFile, inRgnFofn, outRgnFofn)
+ try:
+ masker.maskAlignedReads()
+ except Exception as e:
+ logging.error(e, exc_info=True)
+ traceback.print_exc(file=sys.stderr)
+ return 1
+ return 0
+
+
+def main():
+ """Main function."""
+ parser = getParser()
+ args = parser.parse_args()
+ configLog(args.debug, args.info, args.logFile)
+
+ rcode = run(args.inCmpFile, args.inRgnFofn, args.outRgnFofn)
+ logging.info("Exiting {f} {v} with rturn code {r}.".format(
+ r=rcode, f=os.path.basename(__file__), v=__VERSION__))
+ return rcode
+
+if __name__ == "__main__":
+ sys.exit(main())
diff --git a/pbalign/utils/RgnH5IO.py b/pbalign/utils/RgnH5IO.py
new file mode 100755
index 0000000..c3185b8
--- /dev/null
+++ b/pbalign/utils/RgnH5IO.py
@@ -0,0 +1,295 @@
+#!/usr/bin/env python
+# Author: Yuan Li
+"""
+Region table reader and writer.
+"""
+__all__ = ["RgnH5Reader",
+ "RgnH5Writer"]
+import h5py
+import os.path as op
+import numpy as np
+from pbcore.io.BasH5IO import ADAPTER_REGION, INSERT_REGION, HQ_REGION, \
+ REGION_TABLE_DTYPE, toRecArray, _makeRegionTableIndex
+
+__version__ = "1.0"
+REGION_COLUMN_NAMES = (
+ "HoleNumber",
+ "TypeIndex",
+ "Start",
+ "End",
+ "Score"
+ )
+REGION_TYPES = (
+ "Adapter",
+ "Insert",
+ "HQRegion"
+ )
+REGION_SOURCES = (
+ "AdapterFinding",
+ "AdapterFinding",
+ "PulseToBase Region classifer"
+ )
+REGION_DESCRIPTIONS = (
+ "Adapter Hit", "Insert Region",
+ "High Quality bases region. Score is 1000 * predicted accuracy, " +
+ "where predicted accuary is 0 to 1.0"
+ )
+
+
+class Region(object):
+ """
+ A `Region` represents a row in /PulseData/Regions, including five fields:
+ HoleNumber, TypeIndex, Start, End and Score.
+ """
+ __slots__ = ['holeNumber', 'typeIndex', 'start', 'end', 'score']
+
+ def __init__(self, l):
+ self.holeNumber = np.int32(l[0])
+ self.typeIndex = np.int32(l[1])
+ self.start = np.int32(l[2])
+ self.end = np.int32(l[3])
+ self.score = np.int32(l[4])
+
+ def __repr__(self):
+ return "ZMW=%r, %r, start=%r, end=%r, score=%r\n" % (
+ self.holeNumber, REGION_TYPES[self.typeIndex],
+ self.start, self.end, self.score)
+
+ def toTuple(self):
+ """Convert a Region object to a tuple."""
+ return (self.holeNumber, self.typeIndex,
+ self.start, self.end, self.score)
+
+ def setStartAndEnd(self, newStart, newEnd):
+ """Reset start and end."""
+ self.start = newStart
+ self.end = newEnd
+
+ @property
+ def isHqRegion(self):
+ """Is this a HQ region?"""
+ return self.typeIndex == HQ_REGION
+
+ @property
+ def isAdapter(self):
+ """Is this an adapter?"""
+ return self.typeIndex == ADAPTER_REGION
+
+ @property
+ def isInsert(self):
+ """Is this an insert region?"""
+ return self.typeIndex == INSERT_REGION
+
+
+class RegionTable(object):
+ """
+ A `RegionTable` represents a list of all regions of a ZMW.
+ """
+
+ def __init__(self, holeNumber, regions):
+ self.holeNumber = holeNumber
+ for r in regions:
+ assert self.holeNumber == r.holeNumber, \
+ "RegionTable instantiated with holeNumber %i != " \
+ "region holeNumber %i" % (self.holeNumber, r.holeNumber)
+ self.regions = regions
+
+ def __str__(self):
+ ret = "ZMW: %s, regions are:\n" % self.holeNumber
+ for r in self.regions:
+ ret += " (%s, %s, %s, %s)" % (REGION_TYPES[r.typeIndex],
+ r.start, r.end, r.score)
+ return ret
+
+ def setHQRegion(self, newHQStart, newHQEnd):
+ """
+ If a HQ region exists, reset HQ region; otherwise add one.
+ """
+ hqRegionsFound = 0
+ for r in self.regions:
+ if r.isHqRegion:
+ r.setStartAndEnd(newHQStart, newHQEnd)
+ hqRegionsFound += 1
+ if hqRegionsFound == 0:
+ # No HQ Region exists in the region table, add one to the table.
+ self.regions.append(
+ Region([self.holeNumber, HQ_REGION, newHQStart, newHQEnd, 0]))
+ elif hqRegionsFound > 1:
+ # If more than one HQ region exists, give a warning.
+ print "WARNING: Found more than one HQ region in ZMW %s." % \
+ self.holeNumber
+
+ def __len__(self):
+ return self.regions.__len__()
+
+ def __getitem__(self, key):
+ return self.regions.__getitem__(key)
+
+ def __delitem__(self, key):
+ return self.regions.__delitem__(key)
+
+ def __setitem__(self, key, value):
+ return self.regions.__setitem__(key, value)
+
+ @property
+ def numRegions(self):
+ """Return the number of regions in a ZMW's region table."""
+ return len(self.regions)
+
+ def toList(self):
+ """Return a list of regions."""
+ return [r.toTuple() for r in self.regions]
+
+
+class RgnH5Reader(object):
+ """
+ The `RgnH5Reader` class provides access to rgn.h5 files.
+
+ Region tables are usually small (e.g. a few MB), so we can cache all data.
+
+ To use RgnH5Reader and RgnH5Writer:
+ reader = RgnH5Reader(inFileName)
+ writer = RgnH5Reader(outFileName)
+ writer.writeScanDataGroup(reader.scanDataGroup)
+ for rt in reader:
+ writer.addRegionTable(rt)
+ reader.close()
+ writer.close()
+ """
+
+ def __init__(self, filename):
+ self.filename = op.abspath(op.expanduser(filename))
+ self.file = h5py.File(self.filename, 'r')
+ if "Regions" in self.file["/PulseData"]:
+ self._regionsGroup = self.file["/PulseData/Regions"]
+ else:
+ raise TypeError("Unsupported region table which does not " +
+ "contain /PulseData/Regions: %s " % self.filename)
+ self._regionsData = toRecArray(
+ REGION_TABLE_DTYPE, self._regionsGroup.value)
+
+ self._regionTableIndex = _makeRegionTableIndex(
+ self._regionsData.holeNumber)
+ self.holeNumbers = set(self._regionsData.holeNumber)
+
+ def __iter__(self):
+ for holeNumber in self.holeNumbers:
+ startRow, endRow = self._regionTableIndex[holeNumber]
+ yield RegionTable(
+ holeNumber,
+ [Region(r) for r in self._regionsData[startRow:endRow]])
+
+ def __enter__(self):
+ return self
+
+ def __exit__(self, exc_type, exc_value, traceback):
+ self.close()
+
+ @property
+ def movieName(self):
+ """Copied from BasH5Reader, written by David Alexander."""
+ movieNameAttr = self.file["/ScanData/RunInfo"].attrs["MovieName"]
+
+ # In old bas.h5 files, attributes of ScanData/RunInfo are stored as
+ # strings in arrays of length one.
+ if (isinstance(movieNameAttr, (np.ndarray, list)) and
+ len(movieNameAttr) == 1):
+ movieNameString = movieNameAttr[0]
+ else:
+ movieNameString = movieNameAttr
+
+ if not isinstance(movieNameString, basestring):
+ raise TypeError("Unsupported movieName {m} of type {t}."
+ .format(m=movieNameString,
+ t=type(movieNameString)))
+ return movieNameString
+
+ @property
+ def numZMWs(self):
+ """Return the number of ZMWs in the region table."""
+ return len(self.holeNumbers)
+
+ @property
+ def scanDataGroup(self):
+ """Return /ScanData Group."""
+ return self.file["/ScanData"]
+
+ def close(self):
+ """Close the file."""
+ if hasattr(self, "file") and self.file is not None:
+ self.file.close()
+ self.file = None
+
+
+def addStrListAttr(obj, attrName, attrList):
+ """Add a string list as an attribute to a hdf5 object."""
+ obj.attrs[attrName] = np.array(attrList, dtype=h5py.new_vlen(str))
+
+
+class RgnH5Writer(object):
+ """Region table writer."""
+
+ def __init__(self, filename):
+ self.filename = op.abspath(op.expanduser(filename))
+ if not self.filename.endswith("rgn.h5"):
+ raise TypeError("File extension of region table: " +
+ "%s should be rgn.h5" % self.filename)
+ self.file = h5py.File(self.filename, 'w')
+ self.regions = []
+
+ def _addVersion(self):
+ """Add version to file."""
+ self.file.attrs['Version'] = __version__
+
+ def _addRegionsDataset(self):
+ """Add /PulseData/Regions dataset."""
+ # Create /PulseData group.
+ pulseDataGroup = self.file.create_group("PulseData")
+ # Get the total number of regions in region table.
+ numRegions = len(self.regions)
+ shape = (max(1, numRegions), len(REGION_COLUMN_NAMES))
+ # Add /PulseData/Regions dataset.
+ # The datatype is int32 instead of uint32 because scores can be -1.
+ regionsDataset = pulseDataGroup.create_dataset(
+ "Regions", shape, np.int32,
+ maxshape=(None, len(REGION_COLUMN_NAMES)))
+ # Add attributes to Regions.
+ addStrListAttr(regionsDataset, "ColumnNames", REGION_COLUMN_NAMES)
+ addStrListAttr(regionsDataset, "RegionTypes", REGION_TYPES)
+ addStrListAttr(regionsDataset, "RegionDescriptions",
+ REGION_DESCRIPTIONS)
+ addStrListAttr(regionsDataset, "RegionSources", REGION_SOURCES)
+
+ # Fill Regions dataset.
+ if len(self.regions) == 0:
+ self.regions = [(0, 0, 0, 0, 0)]
+ regionsDataset[:] = np.array(self.regions)
+
+ def writeScanDataGroup(self, scanDataGroup=None):
+ """Copy /ScanData group if not None."""
+ if scanDataGroup is not None:
+ self.file.copy(scanDataGroup, "/ScanData")
+
+ def addRegionTable(self, regionTable):
+ """Add a ZMW's region table to the writer's region table list."""
+ self.regions.extend(regionTable.toList())
+
+ def write(self):
+ """Write the region table list to file."""
+ # ensure the output is sorted by hole number, de facto "spec" for rgn.h5
+ self.regions.sort(key=lambda x:x[0])
+ self._addVersion()
+ self._addRegionsDataset()
+
+ def close(self):
+ """Close the file."""
+ if hasattr(self, "file") and self.file is not None:
+ self.write()
+ self.file.close()
+ self.file = None
+
+ def __enter__(self):
+ return self
+
+ def __exit__(self, exc_type, exc_value, traceback):
+ self.close()
diff --git a/pbalign/utils/__init__.py b/pbalign/utils/__init__.py
new file mode 100755
index 0000000..b88e9dc
--- /dev/null
+++ b/pbalign/utils/__init__.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+# Author: Yuan Li
+
+from __future__ import absolute_import
diff --git a/pbalign/utils/fileutil.py b/pbalign/utils/fileutil.py
new file mode 100755
index 0000000..02afbb4
--- /dev/null
+++ b/pbalign/utils/fileutil.py
@@ -0,0 +1,397 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+
+# Author: Yuan Li
+
+"""This scripts defines functions for handling input and output files."""
+
+from __future__ import absolute_import
+import os.path as op
+import logging
+from xml.etree import ElementTree as ET
+from pbcore.util.Process import backticks
+
+def enum(**enums):
+ """Simulate enum."""
+ return type('Enum', (), enums)
+
+FILE_FORMATS = enum(FASTA="FASTA", PLS="PLS_H5", PLX="PLX_H5",
+ BAS="BAS_H5", BAX="BAX_H5", FOFN="FOFN",
+ SAM="SAM", CMP="CMP_H5", RGN="RGN_H5",
+ SA="SA", XML="XML", UNKNOWN="UNKNOWN",
+ CCS="CCS_H5")
+
+VALID_INPUT_FORMATS = (FILE_FORMATS.FASTA, FILE_FORMATS.PLS,
+ FILE_FORMATS.PLX, FILE_FORMATS.BAS,
+ FILE_FORMATS.BAX, FILE_FORMATS.FOFN,
+ FILE_FORMATS.CCS)
+
+VALID_REGIONTABLE_FORMATS = (FILE_FORMATS.RGN, FILE_FORMATS.FOFN)
+
+VALID_OUTPUT_FORMATS = (FILE_FORMATS.CMP, FILE_FORMATS.SAM)
+
+def real_ppath(fn):
+ """Return real 'python-style' path of a file.
+ Consider files with white spaces in their paths, such as
+ 'res\ with\ space/out.sam' or 'res with space/out.sam',
+ 'res\ with\ space/out.sam' is unix-style file path.
+ 'res with space/out.sam' is python style file path.
+
+ We need to convert all '\_' in path to ' ' so that python
+ can handle files with space correctly, which means that
+ 'res\ with\ space/out.sam' will be converted to
+ 'res with space/out.sam'.
+ """
+ return op.abspath(op.expanduser(fn)).replace(r'\ ', ' ')
+
+
+def real_upath(fn):
+ """Return real 'unix-style' path of a file.
+ Consider files with white spaces in their paths, such as
+ 'res\ with\ space/out.sam' or 'res with space/out.sam',
+ 'res\ with\ space/out.sam' is unix-style file path.
+ 'res with space/out.sam' is python style file path.
+
+ We need to convert all ' ' to '\ ' so that unix can handle
+ files with space correctly, which means that
+ 'res with space/out.sam' will be converted to
+ 'res\ with\ space/out.sam'.
+ """
+ return real_ppath(fn).replace(' ', r'\ ')
+
+
+def isExist(ff):
+ """Return whether a file or a dir ff exists or not.
+ Call ls instead of python os.path.exists to eliminate NFS errors.
+ """
+ if ff is None:
+ return False
+ cmd = "ls %s" % real_upath(ff)
+ _output, errCode, _errMsg = backticks(cmd)
+ return (errCode == 0)
+
+def isValidInputFormat(ff):
+ """Return True if ff is a valid input file format."""
+ return ff in VALID_INPUT_FORMATS
+
+
+def isValidOutputFormat(ff):
+ """Return True if ff is a valid output file format."""
+ return ff in VALID_OUTPUT_FORMATS
+
+
+def isValidRegionTableFormat(ff):
+ """Return true if ff is a valid region table file format."""
+ return ff in VALID_REGIONTABLE_FORMATS
+
+
+def getFileFormat(filename):
+ """Verify and return a file's format.
+
+ If a file format is supported, return the format. Otherwise,
+ return FILE_FORMATS.UNKOWN.
+
+ """
+ base, ext = op.splitext(filename)
+ ext = ext.lower()
+ if ext in [".fa", ".fasta", ".fsta", ".fna"]:
+ return FILE_FORMATS.FASTA
+ elif ext in [".sam"]:
+ return FILE_FORMATS.SAM
+ elif ext in [".sa"]:
+ return FILE_FORMATS.SA
+ elif ext in [".fofn"]:
+ return FILE_FORMATS.FOFN
+ elif ext in [".xml"]:
+ return FILE_FORMATS.XML
+ elif ext in [".h5"]:
+ ext = op.splitext(base)[1].lower()
+ if ext in [".pls"]:
+ return FILE_FORMATS.PLS
+ elif ext in [".plx"]:
+ return FILE_FORMATS.PLX
+ elif ext in [".bas"]:
+ return FILE_FORMATS.BAX
+ elif ext in [".bax"]:
+ return FILE_FORMATS.BAX
+ elif ext in [".cmp"]:
+ return FILE_FORMATS.CMP
+ elif ext in [".rgn"]:
+ return FILE_FORMATS.RGN
+ elif ext in [".ccs"]:
+ return FILE_FORMATS.CCS
+ return FILE_FORMATS.UNKNOWN
+
+
+def getFilesFromFOFN(fofnname):
+ """
+ Given a fofn file, return a list of absolute path of
+ all files in fofn.
+ """
+ lines = []
+ with open(real_ppath(fofnname), 'r') as f:
+ lines = f.readlines()
+
+ lines.sort()
+ return [real_upath(l.strip()) for l in lines]
+
+
+def getFileFormatsFromFOFN(fofnname):
+ """
+ Given a fofn file, return a list of file formats of
+ all files in this fofn.
+ """
+ fs = getFilesFromFOFN(fofnname)
+ return [getFileFormat(f) for f in fs]
+
+
+def checkInputFile(filename, validFormats=VALID_INPUT_FORMATS):
+ """
+ Check whether an input file has the valid file format and exists.
+ If an input file is a fofn, check whether all files names in the
+ fofn exist.
+ Return a list of absolute paths of all input files.
+ """
+ filename = real_ppath(filename)
+ if not getFileFormat(filename) in validFormats:
+ errMsg = "The input file format can only be {fm}.".format(
+ fm=",".join(validFormats))
+ logging.error(errMsg)
+ raise IOError(errMsg)
+
+ if not isExist(filename):
+ errMsg = "Input file {fn} does not exist.".format(fn=filename)
+ logging.error(errMsg)
+ raise IOError(errMsg)
+
+ if getFileFormat(filename) == FILE_FORMATS.FOFN:
+ fileList = getFilesFromFOFN(filename)
+ if len(fileList) == 0:
+ errMsg = "FOFN file {fn} is empty.".format(fn=filename)
+ logging.error(errMsg)
+ raise ValueError(errMsg)
+ fileListRet = []
+ for f in fileList:
+ if not isExist(f):
+ errMsg = "A file in the fofn {fn} does not exist.".format(fn=f)
+ logging.error(errMsg)
+ raise IOError(errMsg)
+ else:
+ fileListRet.append(f)
+ return real_upath(filename)
+
+
+def getRealFileFormat(filename):
+ """Return file format if filename is not a FOFN, otherwise return format
+ of the first file within FOFN."""
+ if getFileFormat(filename) == FILE_FORMATS.FOFN:
+ fileList = getFilesFromFOFN(filename)
+ assert len(fileList) != 0
+ return getFileFormat(fileList[0])
+ else:
+ return getFileFormat(filename)
+
+
+def checkRegionTableFile(filename):
+ """
+ Check whether the specified region table has the right format and exists.
+ Return absolute path of the region table file.
+ """
+ if filename is None:
+ return None
+ return checkInputFile(filename, validFormats=VALID_REGIONTABLE_FORMATS)
+
+
+def checkOutputFile(filename):
+ """
+ Check whether an output file is writable or not.
+ Return absolute path of the output file.
+ """
+ filename = real_ppath(filename)
+ if not isValidOutputFormat(getFileFormat(filename)):
+ errMsg = "The output file format can only be SAM or CMP.H5."
+ logging.error(errMsg)
+ raise ValueError(errMsg)
+ try:
+ with open(filename, "a"):
+ pass
+ except IOError as e:
+ errMsg = "Could not access output file {fn}.".format(fn=filename)
+ logging.error(errMsg)
+ raise IOError(errMsg + str(e))
+ return real_upath(filename)
+
+
+class ReferenceInfo:
+ """Parse reference.info.xml in reference path."""
+ def __init__(self, fileName):
+ fileName = real_ppath(fileName)
+ if getFileFormat(fileName) != FILE_FORMATS.XML:
+ errMsg = "The reference info file is not in XML format."
+ raise ValueError(errMsg)
+ self.dirname = op.dirname(fileName)
+ self.refFastaFile = None
+ self.refSawriterFile = None
+ self.desc = None
+ self.adapterGffFile = None
+ self.fileName = real_upath(fileName)
+ self._parse()
+
+ def __repr__(self):
+ """ Represent a reference info object."""
+ desc = "Reference Info Object:"
+ desc += "File Name: {f}".format(f=self.fileName)
+ desc += "Reference FASTA File: {f}".format(f=self.refFastaFile)
+ desc += "Reference Suffix Array File: {f}".format(
+ f=self.refSawriterFile)
+ desc += "Description: {d}".format(d=self.desc)
+ if self.adapterGffFile is not None:
+ desc += "Adapter GFF file: {f}".format(f=self.adapterGffFile)
+ return desc
+
+ def _parse(self):
+ """Parse reference.info.xml in reference folder."""
+ fileName = real_ppath(self.fileName)
+ if isExist(fileName):
+ try:
+ tree = ET.parse(fileName)
+ root = tree.getroot()
+ ref = root.find("reference")
+ refFile = ref.find("file")
+ refFormat = refFile.get("format")
+ if refFormat.lower().find("text/fasta") != -1:
+ self.refFastaFile = real_upath(op.join(
+ self.dirname, op.relpath(refFile.text)))
+ else:
+ errMsg = "Could not find the reference fasta " + \
+ "file in reference.info.xml."
+ raise IOError(errMsg)
+
+ for node in ref.getchildren():
+ if node.tag == "description":
+ self.desc = node.text
+ if node.tag == "index_file" and \
+ node.get("type").lower() == "sawriter":
+ self.refSawriterFile = real_upath(op.join(
+ self.dirname, op.relpath(node.text)))
+
+ # Get the adapter annotation GFF file
+ annotations = root.findall("annotations/annotation")
+ for annotation in annotations:
+ if annotation.get("type") == "adapter":
+ self.adapterGffFile = real_upath(op.join(
+ self.dirname, annotation.find("file").text))
+ break
+ except IOError as e:
+ raise IOError(str(e))
+ except ET.ParseError as e:
+ errMsg = "Failed to parse {f}".format(f=fileName)
+ raise ET.ParseError(errMsg)
+ else:
+ errMsg = "{fn} is not a valid reference info file."\
+ .format(fn=fileName)
+ raise IOError(errMsg)
+
+
+def checkReferencePath(inRefpath):
+ """Validate input reference path.
+ Check whether the input reference path exists or not.
+ Input : can be a FASTA file or a reference repository.
+ Output: [refpath, FASTA_file, None, False, gff], if input is a FASTA file,
+ and it is not located within a reference repository.
+ [refpath, FASTA_file, SA_file, True, gff], if input is a FASTA
+ file, and it is located within a reference repository.
+ [refpath, FASTA_file, SA_file, True, gff], if input is a reference
+ repository produced by PacBio referenceUploader.
+ """
+ fastaFile, sawriterFile, refinfoxml = None, None, None
+ isWithinRepository, adapterGffFile = None, None
+ refpath = real_ppath(inRefpath)
+ if not isExist(refpath): # The inRefpath does not exist.
+ errMsg = "The input path {refpath} does not exist.".format(
+ refpath=refpath)
+ logging.error(errMsg)
+ raise IOError(errMsg)
+
+ if getFileFormat(refpath) == FILE_FORMATS.FASTA:
+ fastaFile = refpath
+ # Assume the input FASTA file is also located within a
+ # reference repository
+ refinfoxml = op.join(op.split(op.dirname(refpath))[0],
+ "reference.info.xml")
+ else:
+ refinfoxml = op.join(refpath, "reference.info.xml")
+
+ # Check if refpath is a reference repository produced by
+ # referenceUploader or is a FASTA file located within a reference
+ # repository.
+ try:
+ refinfoobj = ReferenceInfo(refinfoxml)
+ isWithinRepository = True
+ fastaFile = refinfoobj.refFastaFile
+ sawriterFile = refinfoobj.refSawriterFile
+ adapterGffFile = refinfoobj.adapterGffFile
+ except Exception as e:
+ isWithinRepository = False
+ if fastaFile is None:
+ errMsg = "Could not find reference fasta file, please " + \
+ "check %s.\n" % refpath + str(e)
+ logging.error(errMsg)
+ raise IOError(errMsg)
+
+ if getFileFormat(fastaFile) != FILE_FORMATS.FASTA:
+ errMsg = "The reference file specified is not in FASTA format. " + \
+ "Please check %s." % refpath
+ logging.error(errMsg)
+ raise IOError(errMsg)
+
+ if (sawriterFile is not None) and \
+ ((getFileFormat(sawriterFile) != FILE_FORMATS.SA) or
+ (not isExist(sawriterFile))):
+ errMsg = "Could not found the sawriter file {f}".format(f=sawriterFile)
+ logging.warn(errMsg)
+ sawriterFile = None
+
+ if (sawriterFile is not None):
+ sawriterFile = real_upath(sawriterFile)
+
+ return real_upath(refpath), real_upath(fastaFile), sawriterFile, \
+ isWithinRepository, adapterGffFile
+
+#if __name__ == "__main__":
+# refPath = "/opt/smrtanalysis" + \
+# "/common/references/lambda/"
+# refpath, faFile, saFile, isWithinRepository = checkReferencePath(refPath)
+# assert(faFile == refPath + "sequence/" + "lambda.fasta")
+# assert(saFile == refPath + "sequence/" + "lambda.fasta.sa")
+# assert(checkInputFile(faFile) == faFile)
+# assert(checkOutputFile("abc.sam") != "")
diff --git a/pbalign/utils/progutil.py b/pbalign/utils/progutil.py
new file mode 100755
index 0000000..3e6f0f7
--- /dev/null
+++ b/pbalign/utils/progutil.py
@@ -0,0 +1,69 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+"""This script defines faciliating functions for calling programs."""
+
+# Author: Yuan Li
+
+from __future__ import absolute_import
+from pbcore.util.Process import backticks
+import logging
+
+
+def Availability(progName):
+ """Return True if a program is available, otherwise false."""
+ return (backticks("which {0}".format(progName))[1] == 0)
+
+
+def CheckAvailability(progName):
+ """Raise a runtime error if a program is not available."""
+ if not Availability(progName):
+ raise RuntimeError("{0} is not available.".format(progName))
+
+
+def Execute(name, cmd):
+ """Execute the sepcified command in bash.
+ Raise a RuntimeError if execution of cmd fail.
+
+ Input:
+ cmd: a command-line string to execute in bash
+ Output:
+ output : the cmd output
+ errCode: the error code (zero means normal exit)
+ errMsg : the error message
+ """
+ logging.debug(name + ": Call \"{0}\"".format(cmd))
+ output, errCode, errMsg = backticks(cmd)
+ if errCode != 0:
+ errMsg = name + " returned a non-zero exit status. " + errMsg
+ logging.error(errMsg)
+ raise RuntimeError(errMsg)
+ return output, errCode, errMsg
diff --git a/pbalign/utils/tempfileutil.py b/pbalign/utils/tempfileutil.py
new file mode 100755
index 0000000..3b4911f
--- /dev/null
+++ b/pbalign/utils/tempfileutil.py
@@ -0,0 +1,236 @@
+#!/usr/bin/env python
+###############################################################################
+# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+# * Neither the name of Pacific Biosciences nor the names of its
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
+# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
+# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
+# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
+# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+###############################################################################
+
+# Author: Yuan Li
+
+"""This scripts defines class TempFile and class TempFileManager for managing
+temporary files and directories."""
+from os import path, makedirs, remove, fdopen
+import shutil
+import logging
+import tempfile
+import time
+from pbalign.utils.fileutil import isExist
+
+
+class TempFile():
+ """Class of temporary files and directories."""
+ def __init__(self, name, own=False, isDir=False):
+ """ Initialize a TempFile object.
+
+ Set file name, indicate whether we own it or not.
+
+ """
+ self.name = name
+ self.own = own
+ self.isDir = isDir
+
+ def __repr__(self):
+ fileOrDir = "directory" if self.isDir else "file"
+ return "TempFile({name}, {type}, own = {own})"\
+ .format(name=self.name, type=fileOrDir,
+ own=('True' if self.own else 'False'))
+
+
+class TempFileManager():
+ """ Manage all temporary files and directories. """
+ def __init__(self, rootDir=""):
+ self.defaultRootDir = rootDir
+ if (self.defaultRootDir != ""):
+ self.defaultRootDir = path.abspath(path.expanduser(rootDir))
+ self.fileDB = []
+ self.dirDB = []
+ self.SetRootDir(self.defaultRootDir)
+
+ def __repr__(self):
+ return "TempFileManager:\n" + \
+ " the default root dir is: {0}\n".\
+ format(self.defaultRootDir) + \
+ " registered files are : {0}\n".\
+ format(",".join([obj.__repr__() for obj in self.fileDB])) + \
+ " registered folders are : {0}\n".\
+ format(",".join([obj.__repr__() for obj in self.dirDB]))
+
+ def SetRootDir(self, rootDir):
+ """ Set default root directory for temporary files. """
+ changeRootDir = True
+ if (rootDir != ""):
+ rootDir = path.abspath(path.expanduser(rootDir))
+ if path.isdir(rootDir):
+ # self.dirDB.append(TempFile(rootDir, own=False, isDir=True))
+ # In case a dir (such as /scratch) is specified, create
+ # another layer of sub-dir, and use it as the real rootDir.
+ rootDir = tempfile.mkdtemp(dir=rootDir)
+ self.dirDB.append(TempFile(rootDir, own=True, isDir=True))
+ changeRootDir = False
+ elif not isExist(rootDir):
+ # Make the user-specified temporary directory.
+ try:
+ makedirs(rootDir)
+ self.dirDB.append(TempFile(rootDir, own=True, isDir=True))
+ changeRootDir = False
+ except (IOError, OSError):
+ # If fail to make the user-specified temp dir,
+ # create a new temp dir using tempfile.mkdtemp
+ changeRootDir = True
+
+ if changeRootDir:
+ try:
+ rootDir = tempfile.mkdtemp()
+ self.dirDB.append(TempFile(rootDir, own=True, isDir=True))
+ except (IOError, OSError):
+ # If fail to make temp dir
+ rootDir = ""
+
+ self.defaultRootDir = rootDir
+
+ def _isRegistered(self, tempFileName):
+ """ Is this a registered file or directory? """
+ tempFileName = path.abspath(path.expanduser(tempFileName))
+ if tempFileName in [obj.name for obj in self.fileDB] or \
+ tempFileName in [obj.name for obj in self.dirDB]:
+ return True
+ else:
+ return False
+
+ def _RegisterTmpFile(self, tmpFile):
+ """ Register a TmpFile obj. """
+ if tmpFile.isDir:
+ self.dirDB.append(tmpFile)
+ else:
+ self.fileDB.append(tmpFile)
+ return tmpFile.name
+
+ def RegisterNewTmpFile(self, isDir=False, rootDir="",
+ suffix="", prefix=""):
+ """Create a new temporary file/directory under rootDir and
+ register it in self.fileDB/self.dirDB. """
+ if rootDir == "":
+ if self.defaultRootDir == "":
+ raise IOError("TempManager default root dir not set.")
+ rootDir = self.defaultRootDir
+
+ fileOrDir = "directory" if isDir else "file"
+ thisPath = ""
+ if isDir:
+ thisPath = tempfile.mkdtemp(dir=rootDir,
+ suffix=suffix,
+ prefix=prefix)
+ else:
+ fHandler, thisPath = tempfile.mkstemp(dir=rootDir,
+ suffix=suffix,
+ prefix=prefix)
+ f = fdopen(fHandler)
+ f.close()
+
+ thisPath = path.abspath(path.expanduser(thisPath))
+ if self._isRegistered(thisPath):
+ errMsg = "Failed to register a temporary {0} {1} twice.".\
+ format(fileOrDir, thisPath)
+ logging.error(errMsg)
+ raise IOError(errMsg)
+
+ return self._RegisterTmpFile(TempFile(thisPath, own=True, isDir=isDir))
+
+ def RegisterExistingTmpFile(self, thisPath, own=False, isDir=False):
+ """Register an existing temporary file/directory if it exists.
+ Input:
+ thisPath: path of the temporary file/directory to register.
+ own : Whether this object owns this file.
+ isDir : True = directory, False = file.
+ Output:
+ the abosolute expanded path of the input
+ """
+ errMsg = ""
+ thisPath = path.abspath(path.expanduser(thisPath))
+ fileOrDir = "directory" if isDir else "file"
+
+ if not isDir and not isExist(thisPath):
+ errMsg = "Failed to register a directory as a file."
+
+ if isDir and not path.isdir(thisPath):
+ errMsg = "Failied to register a file as a directory."
+
+ if self._isRegistered(thisPath):
+ errMsg = "Failed to register {0} {1} as it has been registered.".\
+ format(fileOrDir, thisPath)
+
+ if not isExist(thisPath):
+ errMsg = "Failed to register {0} {1} as it does not exist.".\
+ format(fileOrDir, thisPath)
+
+ if errMsg != "":
+ logging.error(errMsg)
+ raise IOError(errMsg)
+
+ return self._RegisterTmpFile(TempFile(thisPath,
+ own=own, isDir=isDir))
+
+ def CleanUp(self, realDelete=True):
+ """Deregister all temporary files and directories, and delete them from
+ the file system if realDelete is True.
+ """
+ # Always clean up temp files first.
+ while len(self.fileDB) > 0:
+ obj = self.fileDB.pop()
+ if realDelete and obj.own and isExist(obj.name):
+ logging.debug("Remove a temporary file {0}".format(obj.name))
+ remove(obj.name)
+
+ # Then clean up temp dirs
+ while len(self.dirDB) > 0:
+ obj = self.dirDB.pop()
+ if realDelete and obj.own and isExist(obj.name):
+ logging.debug("Remove a temporary dir {0}".format(obj.name))
+ # bug 25074, in some systems occationally there might be a NFS
+ # lock error: "Device or resource busy, unable to delete
+ # .nfsxxxxxx".
+ # This is because although all temp files have been deleted,
+ # nfs still takes a while to send back an ack for the rpc call.
+ # In that case, wait a few seconds before deleting the temp
+ # directory, and try this several times.
+ # If the temporary dir could not be deleted anyway, print a
+ # warning instead of exiting with an error.
+ times = 0
+ maxTry = 5
+ while times < maxTry:
+ try:
+ shutil.rmtree(obj.name)
+ break
+ except (IOError, OSError):
+ times += 1
+ # wait 3 seconds
+ time.sleep(3)
+ if times >= maxTry:
+ logging.warn("Unable to remove a temporary dir {0}".
+ format(obj.name))
+
+ self.defaultRootDir = ""
diff --git a/setup.py b/setup.py
new file mode 100755
index 0000000..340abed
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,26 @@
+from setuptools import setup, Extension, find_packages
+
+import os
+import sys
+
+setup(
+ name = 'pbalign',
+ version='0.2.0',
+ author='Pacific Biosciences',
+ author_email='devnet at pacificbiosciences.com',
+ license='LICENSE.txt',
+ package_dir={'pbalign':'pbalign'},
+ packages = find_packages(),
+ zip_safe = False,
+ install_requires=[
+ 'pbcore >= 0.8.5',
+ 'pysam'
+ ],
+ entry_points={'console_scripts': [
+ 'pbalign=pbalign.pbalignrunner:main',
+ 'maskAlignedReads.py = pbalign.tools.mask_aligned_reads:main',
+ 'loadChemistry.py = pbalign.tools.loadChemistry:main',
+ 'extractUnmappedSubreads.py = pbalign.tools.extractUnmappedSubreads:main',
+ 'createChemistryHeader.py = pbalign.tools.createChemistryHeader:main'
+ ]}
+ )
diff --git a/tests/cram/test_mask_aligned_reads.t b/tests/cram/test_mask_aligned_reads.t
new file mode 100644
index 0000000..552a7bc
--- /dev/null
+++ b/tests/cram/test_mask_aligned_reads.t
@@ -0,0 +1,42 @@
+Test mask_aligned_reads.py
+ $ CURDIR=$TESTDIR
+ $ DATDIR=/mnt/secondary-siv/testdata/BlasrTestData/pbalign/data/test_mask_aligned_reads
+ $ OUTDIR=$CURDIR/../out
+ $ STDDIR=$DATDIR/../../stdout
+
+#Test mask_aligned_reads.py with movie.rgn.h5
+
+ $ CMPFILE=$DATDIR/in.cmp.h5
+ $ INRGNFOFN=$DATDIR/in_rgn.fofn
+ $ OUTRGNFOFN=$OUTDIR/out_rgn.fofn
+ $ TMP1=$OUTDIR/test_mask_aligned_reads.tmp1
+ $ TMP2=$OUTDIR/test_mask_aligned_reads.tmp2
+
+ $ rm -rf $OUTDIR/out_rgn
+ $ maskAlignedReads.py $CMPFILE $INRGNFOFN $OUTRGNFOFN
+ $ echo $?
+ 0
+ $ cat $OUTRGNFOFN | xargs ls -1
+ */out_rgn/m121215_065521_richard_c100425710150000001823055001121371_s1_p0.rgn.h5 (glob)
+ */m121215_065521_richard_c100425710150000001823055001121371_s2_p0.rgn.h5 (glob)
+ $ h5dump -d /PulseData/Regions $OUTDIR/out_rgn/m121215_065521_richard_c100425710150000001823055001121371_s1_p0.rgn.h5 | sed '1d' > $TMP1
+ $ h5dump -d /PulseData/Regions $STDDIR/out_rgn/m121215_065521_richard_c100425710150000001823055001121371_s1_p0.rgn.h5 | sed '1d' > $TMP2
+ $ diff $TMP1 $TMP2
+
+ $ h5dump -d /PulseData/Regions $OUTDIR/out_rgn/m121215_065521_richard_c100425710150000001823055001121371_s2_p0.rgn.h5 | sed '1d' > $TMP1
+ $ h5dump -d /PulseData/Regions $STDDIR/out_rgn/m121215_065521_richard_c100425710150000001823055001121371_s2_p0.rgn.h5 | sed '1d' > $TMP2
+ $ diff $TMP1 $TMP2
+
+#Test while cmp.h5 alignments are generated from multiple movie.bax.h5
+ $ CMPFILE=$DATDIR/in_2.cmp.h5
+ $ INRGNFOFN=$DATDIR/in_rgn_2.fofn
+ $ OUTRGNFOFN=$OUTDIR/out_rgn_2.fofn
+
+ $ maskAlignedReads.py $CMPFILE $INRGNFOFN $OUTRGNFOFN
+ $ echo $?
+ 0
+ $ cat $OUTRGNFOFN | xargs ls -1
+ */out_rgn_2/m130322_020628_ethan_c100499142550000001823070408081367_s1_p0.1.rgn.h5 (glob)
+ */m130322_020628_ethan_c100499142550000001823070408081367_s1_p0.2.rgn.h5 (glob)
+
+
diff --git a/tests/cram/test_pbalign.t b/tests/cram/test_pbalign.t
new file mode 100644
index 0000000..9e3b91c
--- /dev/null
+++ b/tests/cram/test_pbalign.t
@@ -0,0 +1,276 @@
+Note:
+Program name has been changed from `pbalign.py` in version 0.1.0
+to `pbalign` in 0.2.0, pseudo namespace pbtools has been removed also.
+
+Test pbalign
+ $ CURDIR=$TESTDIR
+ $ DATDIR=$CURDIR/../data
+ $ OUTDIR=$CURDIR/../out
+ $ STDDIR=$CURDIR/../stdout
+
+#Test pbalign with all combinations of input & output formats
+#input, reference and output formats are: fasta, fasta, and sam/cmp.h5
+ $ READFILE=$DATDIR/lambda_query.fasta
+ $ REFFILE="/mnt/secondary-siv/references/lambda/sequence/lambda.fasta"
+
+ $ SAMOUT=$OUTDIR/lambda.sam
+ $ CMPOUT=$OUTDIR/lambda.cmp.h5
+
+ $ rm -f $SAMOUT $CMPOUT
+ $ pbalign $READFILE $REFFILE $SAMOUT
+ $ tail -n+6 $SAMOUT | cut -f 1-11 | sort | md5sum
+ ea31763bc847a6c75d3ddb5fb6036489 -
+
+ $ pbalign $READFILE $REFFILE $CMPOUT
+ $ h5dump -g /ref000001 $CMPOUT > tmpfile
+ $ sed -n '2,11p' tmpfile
+ GROUP "/ref000001" {
+ GROUP "m120619_015854_42161_c100392070070000001523040811021231_s1_p0" {
+ DATASET "AlnArray" {
+ DATATYPE H5T_STD_U8LE
+ DATASPACE SIMPLE { ( 48428 ) / ( H5S_UNLIMITED ) }
+ DATA {
+ (0): 34, 136, 17, 17, 34, 17, 136, 136, 136, 17, 136, 34, 136, 68,
+ (14): 128, 34, 17, 136, 34, 17, 136, 17, 2, 34, 136, 136, 34, 34,
+ (28): 68, 17, 68, 34, 17, 136, 136, 136, 17, 136, 136, 1, 17, 68,
+ (42): 34, 17, 136, 136, 136, 34, 68, 34, 136, 17, 136, 17, 17, 68,
+ $ rm tmpfile
+
+
+
+#input, reference and output formats are: fasta, folder and sam/cmp.h5
+ $ READFILE=$DATDIR/lambda_query.fasta
+ $ REFFILE=/mnt/secondary-siv/references/lambda/
+
+ $ SAMOUT=$OUTDIR/lambda2.sam
+ $ CMPOUT=$OUTDIR/lambda2.cmp.h5
+
+ $ rm -f $SAMOUT $CMPOUT
+ $ pbalign $READFILE $REFFILE $SAMOUT
+ $ tail -n+6 $SAMOUT | cut -f 1-11 | sort | md5sum
+ ea31763bc847a6c75d3ddb5fb6036489 -
+
+ $ pbalign $READFILE $REFFILE $CMPOUT
+ $ h5dump -g /ref000001 $CMPOUT > tmpfile
+ $ sed -n '2,11p' tmpfile
+ GROUP "/ref000001" {
+ GROUP "m120619_015854_42161_c100392070070000001523040811021231_s1_p0" {
+ DATASET "AlnArray" {
+ DATATYPE H5T_STD_U8LE
+ DATASPACE SIMPLE { ( 48428 ) / ( H5S_UNLIMITED ) }
+ DATA {
+ (0): 34, 136, 17, 17, 34, 17, 136, 136, 136, 17, 136, 34, 136, 68,
+ (14): 128, 34, 17, 136, 34, 17, 136, 17, 2, 34, 136, 136, 34, 34,
+ (28): 68, 17, 68, 34, 17, 136, 136, 136, 17, 136, 136, 1, 17, 68,
+ (42): 34, 17, 136, 136, 136, 34, 68, 34, 136, 17, 136, 17, 17, 68,
+ $ rm -f tmpfile
+
+
+#input, reference and output formats are: fofn, fasta and sam/cmp.h5
+ $ READFILE=$DATDIR/lambda_bax.fofn
+ $ REFFILE="/mnt/secondary-siv/references/lambda/sequence/lambda.fasta"
+
+ $ SAMOUT=$OUTDIR/lambda3.sam
+ $ CMPOUT=$OUTDIR/lambda3.cmp.h5
+
+ $ rm -f $SAMOUT $CMPOUT
+ $ pbalign $READFILE $REFFILE $SAMOUT
+ $ tail -n+6 $SAMOUT | cut -f 1-11 | sort | md5sum
+ e5c29fba1efbbfbe164fa2797408dbf6 -
+
+ $ pbalign $READFILE $REFFILE $CMPOUT
+ $ h5dump -g /ref000001 $CMPOUT > tmpfile
+ $ sed -n '2,11p' tmpfile
+ GROUP "/ref000001" {
+ GROUP "m130220_114643_42129_c100471902550000001823071906131347_s1_p0" {
+ DATASET "AlnArray" {
+ DATATYPE H5T_STD_U8LE
+ DATASPACE SIMPLE { ( 79904 ) / ( H5S_UNLIMITED ) }
+ DATA {
+ (0): 136, 34, 136, 34, 136, 68, 34, 68, 68, 68, 17, 68, 136, 68,
+ (14): 136, 2, 34, 68, 68, 68, 17, 17, 136, 17, 17, 136, 136, 1, 17,
+ (29): 17, 17, 34, 68, 17, 136, 68, 2, 17, 34, 17, 34, 17, 68, 68,
+ (44): 68, 8, 136, 136, 17, 68, 34, 68, 34, 68, 136, 17, 2, 17, 130,
+ $ rm -f tmpfile
+
+
+#input, reference and output formats are: fofn, folder and sam/cmp.h5
+ $ READFILE=$DATDIR/lambda_bax.fofn
+ $ REFFILE=/mnt/secondary-siv/references/lambda/
+
+ $ SAMOUT=$OUTDIR/lambda4.sam
+ $ CMPOUT=$OUTDIR/lambda4.cmp.h5
+
+ $ rm -f $SAMOUT $CMPOUT
+ $ pbalign $READFILE $REFFILE $SAMOUT
+ $ tail -n+6 $SAMOUT | cut -f 1-11 | sort | md5sum
+ e5c29fba1efbbfbe164fa2797408dbf6 -
+
+ $ pbalign $READFILE $REFFILE $CMPOUT
+ $ h5dump -g /ref000001 $CMPOUT > tmpfile
+ $ sed -n '2,11p' tmpfile
+ GROUP "/ref000001" {
+ GROUP "m130220_114643_42129_c100471902550000001823071906131347_s1_p0" {
+ DATASET "AlnArray" {
+ DATATYPE H5T_STD_U8LE
+ DATASPACE SIMPLE { ( 79904 ) / ( H5S_UNLIMITED ) }
+ DATA {
+ (0): 136, 34, 136, 34, 136, 68, 34, 68, 68, 68, 17, 68, 136, 68,
+ (14): 136, 2, 34, 68, 68, 68, 17, 17, 136, 17, 17, 136, 136, 1, 17,
+ (29): 17, 17, 34, 68, 17, 136, 68, 2, 17, 34, 17, 34, 17, 68, 68,
+ (44): 68, 8, 136, 136, 17, 68, 34, 68, 34, 68, 136, 17, 2, 17, 130,
+ $ rm tmpfile
+
+
+#Test --maxDivergence --minAnchorSize --minAccuracy
+ $ READFILE=$DATDIR/lambda_query.fasta
+ $ REFFILE="/mnt/secondary-siv/references/lambda/sequence/lambda.fasta"
+
+ $ SAMOUT=$OUTDIR/lambda5.sam
+
+ $ rm -f $SAMOUT
+ $ pbalign --maxDivergence 40 --minAnchorSize 20 --minAccuracy 80 $READFILE $REFFILE $SAMOUT
+ $ tail -n+6 $SAMOUT | cut -f 1-11 | sort | md5sum
+ 29f8897b8ee6d4b7fff126d374edb306 -
+
+#Test whether pbalign interprets minAccuracy and maxDivergence correclty.
+ $ rm -f $SAMOUT
+ $ pbalign --maxDivergence 0.4 --minAnchorSize 20 --minAccuracy 0.8 $READFILE $REFFILE $SAMOUT
+ $ tail -n+6 $SAMOUT | cut -f 1-11 | sort | md5sum
+ 29f8897b8ee6d4b7fff126d374edb306 -
+
+#Test --hitPolicy random
+ $ SAMOUT=$OUTDIR/lambda_hitPolicy_random.sam
+
+ $ rm -f $SAMOUT
+ $ pbalign --hitPolicy random --seed 1 $READFILE $REFFILE $SAMOUT
+ $ tail -n+6 $SAMOUT | cut -f 1-11 | sort | md5sum
+ ea31763bc847a6c75d3ddb5fb6036489 -
+
+#Test --hitPolicy all
+ $ SAMOUT=$OUTDIR/lambda_hitPolicy_all.sam
+
+ $ rm -f $SAMOUT
+ $ pbalign --hitPolicy all $READFILE $REFFILE $SAMOUT
+ $ tail -n+6 $SAMOUT | cut -f 1-11 | sort | md5sum
+ 2022614eb99fe3288c332aadcfefe739 -
+
+
+#Test --hitPolicy randombest
+ $ SAMOUT=$OUTDIR/lambda_hitPolicy_randombest.sam
+
+ $ rm -f $SAMOUT
+ $ pbalign --hitPolicy randombest --seed 1 $READFILE $REFFILE $SAMOUT
+ $ tail -n+6 $SAMOUT | cut -f 1-11 | sort | md5sum
+ ea31763bc847a6c75d3ddb5fb6036489 -
+
+#Test --scoreFunction
+ $ SAMOUT=$OUTDIR/lambda_scoreFunction_editdist.sam
+
+ $ rm -f $SAMOUT
+ $ pbalign $READFILE $REFFILE $SAMOUT --scoreFunction editdist
+ $ tail -n+6 $SAMOUT | cut -f 1-11 | sort | md5sum
+ ea31763bc847a6c75d3ddb5fb6036489 -
+
+
+#Test --hitPolicy allbest
+ $ READFILE=$DATDIR/example_read.fasta
+ $ REFFILE=$DATDIR/example_ref.fasta
+ $ SAMOUT=$OUTDIR/hitPolicy_allbest.sam
+
+ $ rm -f $SAMOUT
+ $ pbalign --hitPolicy allbest $READFILE $REFFILE $SAMOUT
+ $ tail -n+8 $SAMOUT | cut -f 1-11 | sort | md5sum
+ 6e68a0902f282c25526e14e5516e663b -
+
+#Test --useccs=useccsdenovo, whether attribute /ReadType is 'CCS'
+ $ READFILE=$DATDIR/lambda_bax.fofn
+ $ REFFILE="/mnt/secondary-siv/references/lambda/sequence/lambda.fasta"
+ $ CMPOUT=$OUTDIR/lambda_denovo.cmp.h5
+
+ $ rm -f $CMPOUT
+ $ pbalign $READFILE $REFFILE $CMPOUT --useccs=useccsdenovo --algorithmOptions=" -holeNumbers 0-100"
+ $ h5dump -a /ReadType $CMPOUT | grep "CCS"
+ (0): "CCS"
+
+#Test --forQuiver can not be used together with --useccs
+ $ pbalign $READFILE $REFFILE $CMPOUT --useccs=useccsdenovo --algorithmOptions=" -holeNumbers 0-100" --forQuiver 1>/dev/null 2>/dev/null || echo 'fail as expected'
+ fail as expected
+
+
+#Test whether pbalign can produce sam output for non-PacBio reads
+# $ READFILE=$DATDIR/notSMRT.fasta
+# $ REFFILE="/mnt/secondary-siv/references/lambda/sequence/lambda.fasta"
+# $ SAMOUT=$OUTDIR/notSMRT.sam
+#
+# $ rm -f $SAMOUT $CMPOUT
+# $ pbalign $READFILE $REFFILE $SAMOUT
+
+
+# Test whether (ccs.h5) produces
+# identical results as (bas.h5 and --useccs=useccsdenovo).
+ $ READFILE=$DATDIR/test_ccs.fofn
+ $ REFFILE=/mnt/secondary-siv/references/ecoli_k12_MG1655/sequence/ecoli_k12_MG1655.fasta
+ $ CCS_CMPOUT=$OUTDIR/test_ccs.cmp.h5
+
+ $ rm -f $CCS_CMPOUT
+ $ pbalign $READFILE $REFFILE $CCS_CMPOUT
+
+ $ READFILE=$DATDIR/test_bas.fofn
+ $ BAS_CMPOUT=$OUTDIR/test_bas.cmp.h5
+
+ $ rm -f $BAS_CMPOUT
+ $ pbalign $READFILE $REFFILE $BAS_CMPOUT --useccs=useccsdenovo
+
+ $ h5diff $CCS_CMPOUT $BAS_CMPOUT /AlnGroup /AlnGroup
+ $ h5diff $CCS_CMPOUT $BAS_CMPOUT /AlnInfo /AlnInfo
+ $ h5diff $CCS_CMPOUT $BAS_CMPOUT /MovieInfo /MovieInfo
+ $ h5diff $CCS_CMPOUT $BAS_CMPOUT /RefInfo /RefInfo
+ $ h5diff $CCS_CMPOUT $BAS_CMPOUT /ref000001 /ref000001
+
+
+#Test pbalign with -filterAdapterOnly
+ $ READFILE=$DATDIR/test_filterAdapterOnly.fofn
+ $ REFDIR=/mnt/secondary-siv/testdata/BlasrTestData/pbalign/data/references/H1_6_Scal_6x/
+ $ OUTPUT=$OUTDIR/test_filterAdapterOnly.sam
+ $ rm -f $OUTPUT
+ $ pbalign $READFILE $REFDIR $OUTPUT --filterAdapterOnly --algorithmOptions=" -holeNumbers 10817,14760" --seed=1
+ $ tail -n+6 $OUTPUT | cut -f 1-4
+
+# Test pbalign with --pulseFile
+# This is an experimental option which goes only with gmap,
+# it enables users to bypass the pls2fasta step and use their own fasta
+# file instead, while keep the ability of generating cmp.h5 files with pulses
+# (i.e., --forQuiver). Eventually, we need to support --algorithm=blasr.
+ $ OUTFILE=$OUTDIR/test_pulseFile.cmp.h5
+ $ REFPATH=/mnt/secondary-siv/references/Ecoli_K12_DH10B/
+ $ REFFILE=/mnt/secondary-siv/references/Ecoli_K12_DH10B/sequence/Ecoli_K12_DH10B.fasta
+ $ pbalign $DATDIR/test_pulseFile.fasta $REFPATH $OUTFILE --pulseFile $DATDIR/test_pulseFile.fofn --forQuiver --algorithm gmap --byread
+ $ echo $?
+ 0
+
+ $ OUTFILE=$OUTDIR/test_pulseFile.cmp.h5
+ $ REFPATH=/mnt/secondary-siv/references/Ecoli_K12_DH10B/
+ $ REFFILE=/mnt/secondary-siv/references/Ecoli_K12_DH10B/sequence/Ecoli_K12_DH10B.fasta
+ $ rm -f $OUTFILE
+ $ pbalign $DATDIR/test_pulseFile.fasta $REFPATH $OUTFILE --pulseFile $DATDIR/test_pulseFile.fofn --forQuiver --algorithm blasr --byread
+ $ echo $?
+ 0
+
+#Test pbalign with space in file names.
+ $ FA=$DATDIR/dir\ with\ spaces/reads.fasta
+ $ pbalign "$FA" "$FA" $OUTDIR/with_space.sam
+ $ echo $?
+ 0
+
+#Test pbalign with -hitPolicy leftmost
+ $ Q=$DATDIR/test_leftmost_query.fasta
+ $ T=$DATDIR/test_leftmost_target.fasta
+ $ O=$OUTDIR/test_leftmost_out.sam
+ $ pbalign $Q $T $O --hitPolicy leftmost
+ $ echo $?
+ 0
+ $ tail -n+6 $O | cut -f 4
+ 1
+
+
diff --git a/tests/data/1.config b/tests/data/1.config
new file mode 100644
index 0000000..8d43a60
--- /dev/null
+++ b/tests/data/1.config
@@ -0,0 +1,25 @@
+# This is a config file for pbalign where users can specify
+# values for an arbitary subset of optional arguments for pbalign.
+# Lines which start with '#' are comments. Otherwise each line
+# should specify the value for exactly one optinal argument.
+# Note that:
+# [1] Positional arguments, including inputFileName, outputFileName,
+# and referencePath, can not be specified in a config file.
+# [2] Sepcial arguments, including --verbose, --version (-v..),
+# --debug and --profile, in a config file will be ignored.
+# [3] Arguments specified in a config file will be overwritten
+# by arguments on command-line.
+
+# Aligner's options.
+--maxHits = 20
+--minAnchorSize = 1
+--minLength = 100
+--algorithmOptions = "-noSplitSubreads -maxMatch 30 -nCandidates 30"
+
+# SamFilter's filtering criteria and hit policy.
+--scoreFunction = blasr
+--hitPolicy = randombest
+--maxDivergence = 40
+
+# Miscallaneous
+--seed = 10
diff --git a/tests/data/dir with spaces/reads.fasta b/tests/data/dir with spaces/reads.fasta
new file mode 100644
index 0000000..a523c90
--- /dev/null
+++ b/tests/data/dir with spaces/reads.fasta
@@ -0,0 +1,5 @@
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/13
+GCTGTTTTCTCCAGCGCAGCACCGTAAATTACTGCTGAGCCATCATGACG
+CCGATGGAGCCTGTCCGGGCGGTCCCTGGCGTGACCAGACGCCGGAGGCG
+GCACTGGCAAGCAACTACCTGCACTGCAGTTCATGTGTTGGCAACCGCCC
+ATACCGGTTTATGTCCACGCACACGGGCGATAGTCAGCGCCGTCCAAATG
diff --git a/tests/data/ecoli.fasta b/tests/data/ecoli.fasta
new file mode 100644
index 0000000..729dcfc
--- /dev/null
+++ b/tests/data/ecoli.fasta
@@ -0,0 +1,997 @@
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/7/0_1165
+GAATCGTCGTCAAATACTCGCCATGTACCCTCTTCTTCCCATCCCGCTCA
+AATCCGACATCAATGCAGGCCTTCATCGCTTCTACGCGGGTCCATAGTTG
+GCAAGTACCACGCATTTTGTTCGCGCGTCACCCACGGACTGCCTAGTTAC
+TGCTACCCGGCCATCGAAGGCTGACTTTATGGCCTCCGAAACCACCCGCA
+GCCGCCCGGCAACTTCCATGAAATCCCGGAGGCTAAACGGCATTTCAGTT
+TCAAGGACTCGTTGCCACGTCACTGCAATAAACCATCGGAGACAGCAGGC
+GGGTACACGCATACTTTCGTCGCGATAGATGATCGGGGATTCGTAACAGT
+TCACACCGAGCCCGCGAGATATGAATTCAAACAACGGGTTCCTGACGTCG
+CTCTCACGCTTACTCGTTTTCCCCAGGCCAGTGGCTTTAGCGTACCTCCG
+GGACCACACCGGTGCAAACCTCAGCAAGGCAGGGTGTGGAAGTAGGAACT
+TTCATGTCAGTCCACTTCTCCTTCTCGCCGCGAGCGGGTTTTGCTCATCC
+CGTTGTGACCTCTGAAGCGGTGATTGACGGCGAGCCAAGTACCGATTTTG
+CCACGCATCATGCCCTGTTCGACCAGCTCTCCATCGATCCCGGTACCGCG
+GCCCTGGCAGGATATCGCTCCGGTCGTCACTGCCTGCCACCTTCTGCTCT
+GCGGCTTTCTGTTTTCAGGACTCCAAGAGCTTTTACTGCTCGCCTGTGTC
+CAGCCTTCTCGCGACGATGCACGAATGTCCCGCGGCCGAAATATCTGGCG
+ACCAGAGGCGGCAATAAGTCGCGTCATCCATGTTTGTTATCCAGGGCCGA
+TCAGCAGAGTGTTAATCTCCTGCATGGTTTCATCGTTACCCGGACGGATG
+TCGCGTTCCGGCGGACGGTTCTGCCAGTGTATTGCAGTATTTTCGTACAA
+TCGCTCGGCTTCATCCTTGTCATGCAGATAGCCCAGCAATCCGAAGGCCA
+GACGGGCCACACTGAATCAATGGCTTTATCCGTCAACACTGTTCTGGGCT
+GCTGACTGACACGGCCCCGTGATTCCTCTCTGCTCTTTCGCGAGCGTTTT
+GAATGGTTCTCGCGGCGGCATTCATTCCATCCATTCGGGTAACTCGCGAT
+CGATGATTTACGGTC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/8/2069_2682
+CGGTGTATCAGGCAAGGCCACTCATATCAGGTGCAGCTTGACTGTCATCA
+ACACGGCCTTTCAGCAACACCCGATACTTCTTCCAGGGCCTTCCAGCAAC
+GAGGTGTGCCTTCCTTCGTTGCAGTTTCCAGATCTCAGCATCCTGAAGCG
+GCCGCGATATGCTCACTGGGCTACCTTGCATCAGGCCTTTTTTTTGCTTT
+TCTTCAAAAAAAAGAAAATGATGTTGCCATCGTAGAGAACATGCTGCTAA
+CGTGAGAGAAGAAGAGATTGAATCTCAGAGAGAGAGACAGAGCGGTCATA
+CAGCAGCTTAACAGTGCGGGACCAGGTGGGTTAGAGAGAGGTTCTGGATT
+AGCATCGAGAGAGAAGCGCGATATGCTGCGCTGCTGGCATCCTTGAATAA
+GAGAGACTACGCACGCTTTCTCGCAACTCTCCCCACAGCTTCTGTTTTGG
+GCAATATCAACCGCCGCTAGTACCATGGCAATCTCTGCTCTTGCCCCCGG
+CGTCGCGGCACTCGGCATATCCGCATAAGCGAATGTTGCGAGCATTGCGT
+ACCGTTTGCCTTAGTATTTCCTTAAGCTTTGGGCCACACCACGGTATTTC
+CGATACCTGTGTG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/8/2724_3021
+CACAAGGTATCGGGGAAATCACCGATGGTGTGGCAAAGCTTGAAGGAATA
+CTAGGCAAAGGTACTGGCAAGTGGCTCGCGACATTCGCTTATGCGGATTA
+TTGCCGTAGTGCCGCGCGCCGGGGGCAAGATGCAGAGATGCATGGCTAAA
+GGCGTGCGGTTGAGATTGCGAAAAAAGCTGTGGGGTAAGTTGTCGAGAAG
+AGTGCGGAGATGCAAGGCAGTCGGCTAATTCAAGGATGCAGCAAGCGCAG
+GGAATATCGCGCTGTGACGATGCTAATACCAAACCTTACCAACCACT
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/13/0_278
+GTATAGAAATGGATCCACTCGTTATTCTTCGGGACGAGGTGTTCAGTTGA
+CCTCTGGAGAGAACCATGTATCATGAATCGTTATCTGGGTTGGACTTCTG
+CTTTTAGCCAGAATACATGGCCTGATATGTTACATGAGAGAATGGTATTC
+CTCATGTGAGTGGCTGTCTTTCGTCTTTCTCTTTGCATTTTCGCTAGCAA
+CTTATGTGCATCGATTATCAAGCTATTGCCGCGGCCAGATAGTAAGCGAT
+TTCAAGCTAAGAAACACCGACCATTAGC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/13/327_954
+CTTAAGCGATTTATCTTCAAGAATTAATACAGCTATAATCTGGCGCTAGG
+ACATAAGCTAAATAAATCCGATGCACATTATATGATACGCGAAAATGCAA
+GAGCAAGCAGAAAACATAAGCCACACATGAAGAGAATAACAGATTCTCTC
+CATTAACATATTCAGGCCAGTTAAAAAACAATCATGAGAGCTTAAAAGAC
+AGAAGTCCAACCCAAGATAACGAAATAATATACACTGGTTCTCTCCAGAG
+GGTTTCATTACTGAACACTCTCCGAGAATAACGAGGGATTCCATTTCTAT
+ACTACATCAACTGTAGGGGTTGTAATAGTTTATCCGATTTCTATCGCTGT
+AGGGGACACGAGAACCACCCGAGCCTGATGTGGTTAAAAGACAGGAACAA
+TCTTTACTACAGCAATACACTATTTAAGGTGATATATGGAAAAGAATTTT
+GAAAGAGTTCGAAGAAGCATACCTCAAGGATGTGATGGAACAATACCAGA
+GACTATCCGTATGACTAAACGACTATTGATAAAAATCAATGGTGTGGACA
+ATTCAAGCGATGCAATGGAGCAACGCTGCCCATCGGAATGCATGGTTAAG
+CTGAACGAAATGTCTTCCTTGTACATC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/13/1004_1580
+TACGGAAACATTTCTTTCAAGGCTTAACCATGCATTCCCGATTGCAGCTT
+GCATCCATTGCCATCGCTTGAATTGTCCACACCATTGATTCGTTTATCAA
+TAGTCGATAGTCTACGATACGGTCTGGTATCTGTTCCATCACATCCTGAG
+AGATGCTCTTCGAACTATCTTCAATTCATTCCTTCCATATATCACCTTAA
+TAGTGGATTGCGGTAGTAAAGATTGTGCCTGTCTTTTAACCACATCAGGC
+TCTGTTCCTCGTGTACCCCTACAGCGAGAAATCGGATAAACTATTTACAC
+CTACAGTTTGATGAGTATAGAAATGGATCACTCGTTTATTTCGGACGAGT
+GTTCAGTAATGAACCTCTGGAGAGAACATGTATATGGTTATCTGGGTTGG
+ACTTCTTGCTTTTGCCAGATAACTGGCCTGATATGTTAATGAGAGATCGT
+AATTCCCTCATGTGTGGATGTTTTTCGTCTTGCTCTTGCATTTTCGCTAG
+CCAATTAATGTGCCTCGATTATCAGCTATTGCCAGCGCCAGATATAAGCG
+ATTTAAGCTAAGAAAACGCATTAAGA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/13/1625_2202
+CTTAATGCGTTTTCTTAGCTTAAATCGCTTATATCTGGCGCTGGCATAGC
+TGATAATCGATGCACATTATTCTAGCGAAAATGCAAGAGAAAAGACGAAA
+CCATGCCCACATGAGGAATACGATTCTCTCATTAACATATTCAGGCCCAG
+TTTATCTGGCTTAAAAGCAGAAGTCGCAACCCAGATACGATCATATACAT
+GGTTCTCTCCAGAGGTTCATTACTGAACACTCGTCGAGATAAGCGAGTGG
+ATCCATTTCTATACTCTCAAACATGTAGGGGTGTAATAGTTTATCCGATT
+TCCTCGCCTGTAGGGTACACGAGAACACTCGAGCCTGATGTGGTTAAAAG
+ACAGGCACCATTTTACTACACGCAATCATATTTTAAGGTGATTAATGGAA
+GAAGAATTTGAAGAGTTCGAAGAGCATCCTCAGGATGTGATGGAACCAAT
+ACCAGGCACTCATCCGTATGCACTACGACTATTGATAAAAATCAATGGTG
+TGGACAATTCCAGGATGCAATGATGCAAGCCATGCAATCGGAATGCATGG
+TTAAACTGAAGAAATGTTTCCTGTAAT
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/13/2251_2836
+ATTACAGGAAACATTTCTTCAGGCCTTACCATGCATTCCGTTGCAGCTTG
+CATCCTTGCATCGCTTGAATGTCCCACATATGATTTTTAATCAATAGTCC
+GTAGTCATAGGATAAGTCCTGGTATTGGTCTCATCACATCCTGAGGATGC
+CTCTTACGAACTCTTCATTCTTCTTCCATATATCACCATTTAAATAGTGG
+ATTGCGTAGTAAGATTGTGCCTGTTCTTTAACCACATCAGGCTCGGTGGT
+TCTCGTGTACCCCCTACAGCGAGAACTCGGATAAACTAGTTACAACCCCT
+ACAGTTTGATGAGTATACGAAATGGATCCACTCGTTATTCTTCAGGACGA
+GTGTTTCAGATAATGACCTCTGGAGAGAACCATGTAATTGATCGTTATCT
+GGGTTGGACTTCTGCTTTTAAGCCCAGGATAACTGGCTGATATGTTATGA
+GAGAATCGGTAATTCCTCATGGTGGCCATGTTTCGTCTTTGCCCTTGCAT
+TTCGGCTAGCATTAAATGTGCATCGATTAATAGACTATTGCGCAGCCAGA
+TATAAGCGATTTAAGCTAAGAAAACGCATAATAAG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/13/2879_3129
+CTTTAAATGCGTTTTTCTTGCTTAAATCGCTTATATCTGGCGCTGGCCAT
+AGCTGATAATCATGCACATTAATTGCTAGCGAAAATGCCAAGAGCAAAGA
+CGAAAACAAATGCCCACATGAGGATACCGATTCTCTCATTACATATTAGG
+CAGTTATCGGGCCTTAAAGCAAGAAGTCCAACCAAATAACGATCCAATAT
+ACAATGGTTTCCTCGTCCAGAGGTTACATTACGAACCTCCGCCGAGAATA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/14/2522_3325
+CGTTGTCTTGTATACGGGGAAGTTCCTGGCTTTCGGGTGGCGAGCATCTG
+CGCCACACCACCGAGCCATACTGGCACCGAGAGAAAAAGGATGCCGGTCA
+TAACACCGGCCCAATGGCTGGCCCCCATGCTGCAGGGTGGCTCCGGGTAA
+AGAATGATCCGGCATGGCGGGCAGCCCCCAAGGACAATCTGGAATACGCC
+ACCTGACTTGGCCCCGGCGAACTCTGGGAAACAATATGAATTACAGCGCC
+CATCAAGGCAGAGTCTCATTGTAACTGCGCCGTTAACCCGGACGTGGCTG
+ACGTCCCGCCCGGCAATCGCGTACCTGATACCAGCCGTCGCTCAGTTTCT
+GACGAAACGCCGGGAGCTGTGGTGGCCAGTGCCCGGATGGCCTTCAGCCC
+CCGTTTTTCCACCGAAGGTGATGCGTCGACAAATCGTTGGTAAATCCCCG
+TAAAAGCAGATGCGATGCCCGGTTGACGCCAGAGGGAGTGTTGTGTCGTC
+GCCTGCCATTTGTCGGTGTACCTCTCCGTTTGCTCAGTTGTTCAGGAATA
+TGTGCAGCACTCGCCGTCGCGCAGTAATGCGGCGTGATTCGCACTGATGA
+ACCAAAACAGCAACAGCAGCACATCGCCCGGCTGTGCCGCTGACAACGGC
+AGCCTGATACAGCCCCGTCGCCTCCAGATAATCCAGATAGAGATTCTGGC
+CGTTCTACGCCACCAGTCATCCTCACGATGAAAGTCCGGCATCTTCATCC
+CCGCCAGATGATAAGCATCCGGAACAAGTGTGTAACAGTCGTCACACGTG
+CTC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/14/3370_4191
+GAAGCACGGTGTGACGGACGTTACACACGTTCGGGATTGCTTATCATCTG
+GCGGGGATTGAATGCCGGACTTTCATCGTGAGGGATGAACTGAACGGCAG
+AATCTCCTATCTGGATAATCTTGGAGGCGATCGGGGCTGTAGATCAGTGC
+GTTTGTCAAGCGGCACAGCCGGGCGATGTGCTGCTGTGCTGTTTTGGTTC
+ATCAGTGCCGAAACGCGCAATTTATATTGCGGCGAGGCGAGCTGCTGCAC
+CATATTCCTGAACAACTGGAGGCAAACGCAGAGAGGTACAACCGACACAG
+GCAGCGACGCACACACTCCCTCTGGCGTCACCCCGGGGCATGGCCGCGCA
+TCTGCCTTTACGGGATTTTCAAAGATTTGGTTCGCCGCATCGACTTCGTG
+TGAAAACGGGGGGGGCTGAAGCCATCCCGGCACTGGCCACACAGCTCCGG
+CGTTTCGTCAGAAACTGAGGCGCGGCTTGGTATCAGGTTTTACGGATTGC
+CGGGCGGGACGTCAGCACGTCCGGTTTAAGGCGCAGATTACAGAGACTTG
+CCTGATGGCGGCTGTAATTCATATTGTTCCCAGAGTCGCCGGGCGCAAGT
+CAGGTGGCGCCGTATTCCAGATTGTCCTGGGGGCTGCCGCCATTGCCGGA
+TCATTCCTTTACCCGGCGCGGGCCACCCTTGCAGCATGGGGGGCAGTCCT
+TGGGGGCCGGTGGATGACCGGCATCCTGTTTTCTGCTCTCGGTGGCGCAG
+TATGGTGCTCGGTGGTGTGGCGCAGATGCTGGCACCGAAAGCCAGAACTC
+CCGCGTATACACGACAACGGA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/14/4238_4294
+TCCGTTGTCTGTATACGGGGAGTTCTGGCTTTCGGTGCGCAGCATCTGCG
+CCACAC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/15/6210_6438
+TCCCCCCCGGGGGGGGGGCGGAGTCTTTTGGGGCCCCCCCCGGGGGGTTT
+GGACAAACCCAGGAAAAACCCCGCGGGGAGAGAAAAGGGCCACGGCCCCA
+AACCCTTTTGGGCCCCAAAAAGCAAAAACCTTTTGACCCCACCCCCCCCC
+TTTTTTTTTGCCACCTGCAAAAAGTTTTCAAATGTCCGTTTTTTTGGCAG
+CCCGCCCCATAACCGGTTTTTTTTTTTA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/15/6494_7499
+TTTAAAAAACCGGTAAAATGAGGGCCCGGCTTTTTGCCCCAAAACGAAAC
+ATTGAACTGGCAAAGTTTGCAAAGGTCCACCCCAAGTTTTTTTTATTTGT
+GCTTTTTGCCAAGTGGGGCCGGCCTCGCGGCGGGGGTCCTGGTCCACGCC
+AAGGAAACCCGCCCGGAAAACAGGCTTTTCCCATCCCGGCCGGTCCCCAA
+ATGGGAATGGCCTCAACAGAATTTTAACGGTTTTGCTGCGCTTGGGAGAA
+AACAAAGGGGTTTGTTGGAAAAATTTCACGCTTGAATTTTTTTTTTTACA
+AGCGGCCCAGCCAATAAAGGTGGAGAGATGGCACCCCTACAGCCCATTCC
+TTTTTCCGGATGAACGTCCGCGGGGAGACCACTTGCCAGTCCCGGAATGG
+GAACGCCAACCCCGCCCAGATTGTTTTTTTTTGCGCAGAAGAGGGGGTGT
+CCCCGGCCAAAATAAAATACCCGGCCTGTCCCGTGCAGGTTATTTGTGCT
+TGGAATACCGAGGGCCCTTTTGCAAAAAAAAGTGTAACAGCGGGTTTCCA
+GGAAGGCCAATTGAAAAATGCCGGGACTTGGCCTTTGAATTTGAACGTTT
+GTTAACAGCAAAAGCCGGATGGCCGATCAACCGTCCAAAAATGCGTGATG
+CAACCTTGATTGCACCGTAAAATTCCCGTCTCCTCAGGAGGGCGAAAAAA
+TGAAAACAACCAAAGAGACCTTCAAATCAACAAAAACTTTTGTTTTTCAG
+CCCACTGCTTTTTTTTTTCGCAGGCCTGACCGTTTCTTGACGTGGTTGCC
+CCAAGCGGACGAGGCGGAGAACGGCCAAAGCGCGGCGCAGCCGGAAACCG
+TTGAAAACGAGAAAAAAGATCCACGCAGCGGTTTTTGCGGCAAGAAAAAA
+GACAGCCCGCCCAATTTATTGGGGATCCTCAACTGGTTGAGGACAAGGCT
+TCCCAAGCGGAACAGCGAAAGAACAGGCAAAACGCGTGCCTTGGCAAAGA
+AAACA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/15/7563_8532
+TTTGTTTTTGCTGCCAGCAAAAAACGCGGTGGGATTTGTTTCTTTTTTCG
+CGTCCGTGAGCCCTTTTCCCCCCCTCACAGTTTTGAGGAATTCCCAATAT
+GCGGCTTGTTTTTTCCCTATGCCGCAACCGCTTGCCCGGTTTGATTTCTT
+ATTTGTGCGCCGTTTTGTTTTCAACCGTCCGCTTTGCCGCCGCGCTGGGC
+GTTTTTTTTTTTTTCCTCCCCGCCCTTCCCGTCGCTTGCAAAAAAACCCG
+TCAAAGTAAAACGTCCCAAAAAAGCCTGCGAAGCCAGTTGGCCTTTTTGG
+AAACAGTTTTTTTTTTTTGGTTTTGGGAATTGAAAAGTCCTCTTTGGTCC
+ATTATCGCCCCCTCCCTGAAGAGACGGGAAAAATTTTTACGTTTGCATCC
+CAGTGCATCAAAAAACAGCAATGACCGGTGATTTCGCAATCGGTTTGGCT
+GTTAAAAACAAAGTTCATCAGCCCAGTTTCCCGGCAAAATTCAAAAAATG
+GCCCCCTTCCTGACCGCCTTGTTTAAACACTGCAAGGCCCCTCGGGGTTT
+ATCCAAAAGCCCCAAAAAACAACCTGCACGGAAAAAACAAAGGCCGGTAA
+AAAAAATATGCGAACAAACCTTCTTGCGCAAAACATTCTTGGGGGATTTT
+TTTTTTTTTTGCGGTCCCCATCCGAGGACTGGCAAGTGGTCTTCCCCGGG
+AACGTCAATCCGGAAAAGATTGGCTGGGTAGGGGGGTTTTTTTTTTTGTT
+TTTTTTTTTTTTTTTGGCCCAAAATCCCAACCTAAATTGGCTTGTCCCGC
+TGTAAATCAGCCGTTGGATTTATCCAACCAAACCCTGTTTTCTCCAGCGA
+CAAAAAAAGCAAAACCGTAAAAATTTTTACTGTTGAAGCCAATCGGAATT
+TGAAAACGCCGATGGAGCCTGTATCCCGGGCCGGTCCCCCTGCGTTGGAC
+CCAGAAATACGCCGGGAGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/16/0_404
+TGCACGAGGCAGCGGCAAGTTTCTCTCTGTTCGCGTCATTTCAATCCTTC
+CGGATATAGCGCACGTGGCGTTAATCGTGCCATGTTTTCTGTTGGTTGTC
+CTGCACCATCCTCTCCTGCAGCCTCGCCAGCAGCGCACTGAGATTCTTCA
+GCTGCAGCGGGAAATACTGATGCGCAGTCGCCGCCAGCGCATAAATCCGA
+AGCAAGTCGTGTGCCTCATTGCGTCGCTTTTTGCTGTCCCTTACATTGTA
+TTTTTTTCCTGCTCATCCACCATTTTTCGACGCTCTTCAGCAGTCAGTCC
+TGCTTGCTGCTTCGTTCAATCAAAAATATCTCTGGTTATTTTCGGGAAGT
+GAACCGGCACCGGGAGCAGGTTCATCCTCCTTCCGGCGTCAGTGTGAATT
+GCGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/16/447_1003
+GCCGCTTCACACTGAAGCCGGAAGGGGATGAACCGCTCCGGTGCTTGTTC
+AGCTCCGAAAAATTGCCGGATATTTTTTGATCTGACCGAATGCGCAGCAG
+CTGACTGCTGAATGAGCAGGTCGAAAAATGGGTTGATGGCAGGAAAAATA
+TACTGTGGGACAGCAAAAAGCGACGCAATGAGGCACTCGGACTGCTTCGT
+TTATTCGCTGGCTGCGCTGCGCATCAGTATTTCCTCGCTGGCAGCTGGAT
+CTCCAGTGCGCTGCTGGCTGAGCCGTGCAGAGAAGGTAGTGATGGTTGCA
+GTCAACCAATCAAGAAAACACTGGCAGAATTTACACCGTGTGCCTTATCC
+GGAGAGGATGATGACGCGACAGGTATAGAATTGCGCTTGTCCCGTGCGGC
+ACTGCATGACCTGATGACAGGTAATTACGGGTGGCAACAGTACTAGAAGA
+CGTGACGAAGTGGTGGAGTTTACGGCCACTTCCGTGTCTACTGAAAAATA
+ATATTTGCTAGATTGCTGGAAGTGCAGACCGGCATGAACACAGGGCAGGA
+CTGCAG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/16/1051_1636
+CTGCAGGTTCTCTGCGTCGCTGTGTCATGCCGGATCTGCTATCTTCCAGC
+TCTGCAATGATTATTTTTTCAGGTCAGACACGAAGTGTGCCGTAATACTC
+CAACCTTCCGTCTACCACGTTCGTTTCTGTATGTTGCCACCCGTTACCTC
+TGATCATTCAGGTCCATGCAGTGCCGCAGGGTGGGGTGGGTTGGGGCGGG
+CAGCGGCAAGTTCTTCCTGTCGCGTCATTCATCCTCTCCGGATAAGGCAC
+GGGCGTAATCTGCCAGTGTTTTCTTGTTGGTTGCTGCACCAACCTCCCTT
+CCTGCAGTCCGCTCGCCCAGCAGCGCACTGAGAATCCAGCTCCAGCCGGG
+AAATACTGATGCGCAGCGCCCCAGCGCATAAACGAAGCAGTCGAGTGCCT
+CATTGCGTCGCTTTTTGCTGTCCCACAGTATTTTTTTCCTGCCCATCCAC
+CCATTTTTTTCGACCTGCTCTTCCAGCAGTCAGCTGCTGCGCTTCGGTCC
+AAGATCAAAAAATATCCGGGTTAGTTCGGGAAGTGAACGGCACCGGGAAG
+CGGTTCATCCCCTTCCGGCCGTCAGTGTGAAGCGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/16/1680_2264
+CCGCTTCCATGACGCCCGGAAGGGGATGAACCGCTTCCCCGGTGCCGTTC
+ACTTCCCGAAATAACCCGGATATTTTTGATCTGACCGAAGCGCAGCAGCT
+GACTTGCTGAAGAGCAGGTCGAAAAATGGGTGGATGGCAAGGAAAAAATA
+CTGTGGGACAGCAAAAGCGACCGCAATGAGGCACTCCGACTGCTTCGTTT
+AATGGCCCGCTGGGCGGGCGCTGCCGCATCAGTTATTTCCCGCTGGCAGC
+TGGATCTCAAGTGGCGCTGCGGCCTGAGGCCTGCAAAGGAAGAGGATGGT
+TGCCAGCAACCCACAGAAAACACTGGCAGATTACCGCCCGTGCCCTTACC
+GGAGAGGATGAAATGACGCGACAAAGGAAGAACTTGCCCGCTGCCCGTGC
+GGGCAACTGCATGACCTGGATGGACAGGTAAACGGGTGGCATCAGTAACA
+GAAAGACGGACGAAGGGGGTGGGAGTTTACGGCCCACTTCCGTGTCTGAC
+CTGAAAAAATATATTGCAGAGCTTGGAAGTGCAGACCCGGCCATGGACAA
+CCAGCGGGGAACTGCAGGGGGGGGGACCTGCAAG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/16/2310_2884
+TGCGAGGTCCCTGGCGTCGCTGTGTCATGCCGGTCTGCCACTTCCAGCTC
+TGCAATAATATTTTTTCAGGTCGACACGAAGTGGCCCGTAAACTCTTCGC
+CGTCTTTCGTACTTGTTGCTACCCGTTTACCTGTCATCCAGGTCCATGCC
+AGTGCCCGCAGGGCAGCGGGCAAAGGTTCTTCCTGTCCGCGTCCCCATTC
+ATCCTCTCGGGATAAGGCACGGGGGTAATCCTGCCAGTGGTTTTCTTTGT
+TGGTTGCTGCACCATCCTCTTCCCTTGCAGGCCGGCCAGCAGCGCACCCC
+TGAAGATCCAGCCTGCCAGCCCGGGAAATACTTGGATGCGCAGCGCCGGC
+CAGCGCATAAACCGAAGCAGTCGGAGTGCCCATTGCCGTCGCTTTTTTTT
+GCTGTCCCACAGTATTTTTTTTCCTGCCCATCCCACCCATTTTTCGACCT
+GCCCTCTTCAGCAGTCAGCTGCTGCGCTTCGGTTTCAGATTCAAAAATAT
+CCGGTTATTCGGGAAGTGGAACGGCACCCGGGAAGCGGTTCATCCCCTTC
+CGGCGGTCCAGTGGTGGAAGCGGA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/16/2931_3514
+CCGCTTTCACACTGACGCGGAAGGGGATGAACCCGCCTTCCCGGTGGCCG
+TTTCACTTCCCGAATAACCCGGATATTTTTGATCTGACCGAAGCGCCAGC
+CAGCTGAAATGCCTGAAGAGCAGGTGAAAAAATGGGTGGATGCAGTGAAA
+AAAATACTGTGGGACAGGCAAAAAGCCCGACGCAATGAGGCAACTCGACT
+GCCTTCGTTTATGCTGCTGGCGGCGCTGCGCATCAGTAGTTTCCCCGCTG
+GGGCAAGCCCTGGATTCTCAGTGGCGCTGGCTGGCCCGAGCCCCTGCAGG
+AAGAGGATGGTGGGCAAGCAAACCACAAGTAAAACACTGGCAGATTACCC
+CCGGTGCCCTTATCCGGAGAGGATAATTGACGGCGACAGGAAGGAACTTG
+CCGCTGCCCGTGCGGCACTGCATGACCTGATGACAAGGTAAACGGGTGGC
+AACAAGTACAGAAAGAACGGACGAAGGGTGGAGTTTACGCCACTCTCCGT
+GTCCTGACCTGAAAAAAAATATATGCAGAGTCTTGGAAGGTGCCAGACCG
+GCATGACACAAGCGACGCAGGGGGACCTGACAG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/16/3564_4141
+CTGCAGGTCCCCTGCCGTCCGCTGTGTCATGCCTGTCTGCACTTCCAGCT
+CTGCAATATTATTTTTTCAGGTCAGGAACCACGGAAGGTGGCCGTAACTT
+CCCACCCTTCCGTCCGTCTTTCTGTACTGGTTGCCCGTTTACTGTCATCA
+GGTCATGCAGTGCCCAAGGGCACGGCAAGTTCTTCCCTGTCGGCGTCATT
+CATCCTCTTCCGGAAAGGCACGGGGCCGTTATCTGCAAGTGTTTTTCTTG
+TTTGGTTGCCTGCACCATCCTTTTTCCTGCAAGGCTCGCCAGCAGCGCAC
+TGAGATCCAGCTTGCCCAGCGGGAAATACTGATTGCGGCCAGCGCCCGCC
+CCAGCCGCATAAACGGCAAGCCAGTCGAAGGTGCCTAATTGGCGTCCGCT
+TTTTTGCTGTCCCACAGTATTTTTTTCCTGCCATCCACCCATTTTTTCGA
+CCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCCGGTTCCAGATCAAAAATA
+TCCGGGTTATTCGGGAAGTGAACGGCAACCGGGAAGCGGGGTTCATCCCC
+TTCCGGCGTCAAAAGTGGGTGAAGCGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/16/4191_4774
+TCGCGCCTTCCACACTGGACCGCCGGGAAGGGGATGAACCGCTTTCCCGG
+TGCCGTTTCACTTCCCGAAATAACCCGGATATTTTTGATCTGACCGAAGG
+CGCAGCCAAGCCTGACTGCTGAAAGAGCAGGGTGAAAAATGGGTGGATGG
+CAGGAAAAAAATACTTGTGGGAACAGGCCAAAAAGCGGACGCAATGAGGC
+CACTCGACTGCTTCGTTTATGCGCTGGCGGCGCTGCCGCATCAGTATTTC
+CCGCTGGCAGCTGGATATCAGTTGCGCTGCCTGGTCGAGCCTGGCAGGAA
+GAGGAGGTGCCCAGCCAACCAACCAAGGAAAACAACGGCCAGATTACGCC
+CGTGGCCTTATCCGGAGAGGGATGAATTGACGCGCAGGAAGAACTTGCCC
+GGCTGCCCCGGGCGGCACTGCATGACCTGATGACAAGGTAAAGGGTGGCA
+ACAGTACAGGAAAGACGGACGAAGGGGTGGGAGTTTTTTACGGCCACTTC
+CGTGTCCTGACCCTGAAAAATATATTGCAGAAGCTGGAGTTGCAGACCGG
+CATGACACAAGCGGGACGCAGGGGACCTTGCAG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/16/4818_5217
+CTGCAGGTTCGTCGCTGTGTCATGCCGGTCGCACTTCCAGCTCTGGCAAT
+ATATTTTTTCAGGTCAGACCACGGAAGTGCCCGTAAACTCCCAACCCTTC
+GTCCGTCTTTCTGTACTGTTGGCACCCGTTTACCTGTCCATCAGGTCATG
+CAGTGCGCACGCAGCGGCAAGTTCTTCCCTGTCCGCGTCATTCATCCTCT
+CCCGGGATAAAGGCACGGGGTTAAATCTGCCCCCAGTGGTTTTCTTGTTG
+GTTGCCTGCACATCGCCTCTTTCTGCAGGCCGCCGCCCCAGCGCACTGAG
+GATCCAGCTGCCAGCGGGGGAATACTGATGCGCCAGCGCGCCAGCCGCAT
+AAACGAAGCAAGTCGAGTGCCTCCATTGAGGTCGCTTTTTGCCTGTCCC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/17/0_336
+GATGAAGGGTAAAGTTAAACGATGCTGATTGCCGTTCCGGCAAACGCGGT
+CCGTTTTTTCGTCCTCGTCGCTGGCAGCCTCCGGCCAGAGCACATCCTCA
+TAACGGAACGTGCCGGACTTGTAGAACGTCAGCGTGGTGCTGGTCCTGGT
+CCAGCAGCACCCGCAAGAATGCCAAGGCAGCACCGTCGGTGGTGCCATGC
+CCACGCAACCAGCTTAACGGGCTGGAGGTGTCCAGCATCAGCGGGGTCAT
+TGCAGGCGCTTTCGCCCTCAATCCGCGCGGGGCGCGGTGCGGTATGACCG
+GGTCATGTTGCCCTGCGGCTGGTAATGGGTAAAGGT
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/17/380_1046
+ATCCTTTACCCATTCCAGCCGCAGGGCAAACAGTGAAACCCGGCTCATGA
+CCGCAACCGCGCCCGGCTGGATTGAGTGCGGAAAGCGCCTGCAATGACCC
+CGCTGATGCTGGACCACCTCCAGCCGTAAAGCTGGTTGCGTGGATGGCAC
+CACCGACGGTGCTGCCGTTGGCATTCTTGCGGTTGCCTGCTGACCAGACC
+AGCACCACGTCTGGACGTTCACAAGTCCGGCACGTTCCGTATGAGGATGT
+GCCTCTGGCCGGAGCTGCCAGCGACGAGACGAAAAAAAACGGACCGCGTT
+TGCCGGAACGGCAATCAGCATCGTTTAACTTTACCCTTCATCACTAAAGG
+CCGCCTGTGCGGCTTTTTTTACGGGATTTTTTTATGTCGATGTACACAAC
+CGCCCCAACTGCTGGCGGCAAATGAGCAGAAATTTAAGTTGATCCGCTGT
+TTCTGCGTCTCTTTTTCGTGAGAGCTATCCCTTCCACCACGGAGAAAGTC
+TATCTCTCCACAAATTCCGGGACTGGTAAACATGGCGCTGTACGTTCCGC
+GAATTGGTTTCCGGTGAGGTTATTCCGTTCCCCGTGGCGGCTCCACCTCT
+GAATTTACGCCGGGATAATGTCAAGCCGAAAGCATGAAGTGAATCCGCAA
+TCTCTCTCAACAACAA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/18/0_398
+CCTCTCCCCCACCCCCCCCCCCCCGACTCCCCCCACCACCCCCCCCCCCA
+ACCGATGGTTTGAGTACGGTCATCATGCTGACACTAAGACTCTGGCATCG
+CTGTGAAGACGACGCGAAATTCAGCATTATATCACAGCGTTTCTTTTACA
+AACCGTTGTCTCCCTCTGCCTTTGATGGCGAATGCCGAGCGATCAGACAC
+TCATAATGCGAGATACTCACGTGCATCCTGAACCCATTGACCATCCACCC
+GTAATAGCGATGCGTAATGATGTCGATAGTTACTAACGGGTCTTGTTCGA
+TTAACTGCGCAGAAACTCTTTCCAGGTGACCAGTGCAGTGCTTGATAAAG
+GAGTCTTCCCAGGATGGCGAACAACAAGAAACGGTTTCCTCTTCCGTC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/18/447_1210
+GACGAGACGAACGCAGTTCTTTGTTGTGTCGCCATCCTGAGGAAGACTCC
+CTGTTTATCAAGCGGACACGGTTGCACTTCTGATACGGGACGCTGGATAG
+GAAGTTGTCTGCGGCAGTTAATCGAACAAGACGCCCGTACGTGGCTTTGT
+TTATCCGCAGACGTAACCCTGATCGACAGACGAAAGCTCTTTGAGTTACG
+CCATCGGCTGGAAGGTATTACGCATCGCTATACGCGGGTTGAAGTCCAAT
+GGGGTTTTGCCGAGTTGCATCAAAAAAAAAAAAACACATAACAAACAAAA
+CAGAGATGGAAAACAGCCAAGTGAACGTAGGAGCAGTGACGGGAGGGGAG
+CAGACACGCGACTGGGCTATGCACGATGTCTGACGGCCGGAAGCTGGCGC
+GTACGACGAAGATGTGCGTGCGGTGCTTGCGGGAATAAAACAAAAGCCCC
+GTTGTCGGTGCAGTGGTATGATCACGACGGCGTTTGCTGGCGGCAAGGTT
+CACATCGTGTATCGGTAGGGTATTGGGCGGTGCAGAATTACGCAGGCAGT
+TGCGAGAGTGCGAATTTCGGAGAATCATTGGACAGAAACGGTGTGGGCCG
+CTGTCTGGAACTTGTCAGTCGCCGCGGGATCCACGCGCCTGATGAAACGG
+AGGAGAACAGGACCGGAGTGCGCCGAAACTGGCGTAATACGTGAAGACGC
+CAAGCCGAACCGGCGCGTTTAGCGGTTGGCGATGTCTGTGCTCCACCGCA
+GAAGACGCAGAGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/18/1246_2761
+TCTGTCTTTCTGGAGGGTAGGCAAGGGAAATTCGTCACAAGAACGGCCGG
+GCGGATTGGCGTCTTCCACGAAGGAACGTGAGAGTGGGTGTCTCTTACGG
+CCTTGAGAGAGAAGAGATGAGCAGGGAGTAGCGATGCTTGGTCGAAATGT
+TGCTGAATTCTTCGCGTCGTCTTCACAGCGATGCAGAGTCTGTAGTGTCC
+CAGATGATGACCGTACTCAACATCGGGTTGATGTATTATCTTACTGTGTT
+CCTTTACGATAAACATTGCTGCATAGTGCTGAAGCTTCGACAGATAGGTA
+TGCAAGAGATATATCAGTGAGCTGACGCTGAGTTTCGCAATGAGTTTTAC
+GAGTCTGGAGCAAGAGATTGACATTGCGCGCGTTAGTTGCAATGTCTGGA
+TTTGCAGCTCCGTGTCTGTGTCTGGCAGAGCAGTGCACGAACGGTGTGTG
+TAGTAGCTAGATAAGGGTCTAAACTAGCAAGTAAGAACTAGCTCGAGCTA
+TTACCCAAGATATTACGGATGGATGACAGTTTTAAGTCTGAATGAAGACA
+AGATCCCCATTTCTGCAATGTGCGAGAATGACTGATACGTGCAAATTATT
+ATCACGGACGTACGTGGAAACGATACATTGCCTCTCTGGTAGCAAAACAT
+ATAGATGATTTAAACCAATATTACATAACAATCCTCGCACTCGCGGAATT
+TATTTATCTGAACACTCGCTACGGCGGTTTTGTTTTATGGAGATGATAAA
+TGCACTTCCGAGTCCACAGGAGAATGGAATGGAGAGCCCATTCAACAGAG
+TTATCGAAGCGGAGAAACATCAACGACTGCTACGACACTGATGATATGGG
+CGCAGATAGCACATGCAGACGTAACCAATATTCGATTGAAGAACTGAAAG
+AACACGCAAGCCGCTGATGGCGTTTCTTCTGCGTGTAATTTGCGGAGACT
+TTTGCGATGTCTTTGACACTTCAGGAGTGGAACGCACGCCAGCGACGTCC
+AAGAAGCCTTGAAAGCAGTTCGTCGATGGGCTTCGGGAATGCAGGATATT
+CCCACCTGCCGGTTAAGGATGGAAGAGAGTATCTGTTACGAATCAGCGTA
+AAGTTTGACTTAAATCGACCAGTAACAGGTGGCCTTTTGAAGAGGATAAG
+AAATGGAAGAAGGCGAAGTCATGAGGTCGCCGGATTTTACCCGCCTACAA
+CCTTTATATAAGAAACAATGGATAATTACTGCTACAGGGACCCAAGGACG
+GTAAAGAGTTTGGATTAGGCAGAGACAGGCGAATCGCATCACTGAAGCTA
+GTGACGGACGCAAGATCTGATGATCAGTGGGTATTCAGGGCATCGACAAA
+CTTAGCAAGCACTACGGCGTTGGGGGGGGAAGCGGAACTCCCGACAGCTG
+ACTCAGATATCGTGTTCCTCGTAGTGTTTCTGGGCTTGATCGTCATACGC
+CTGCTCCTGCGGCCCTAGGGAAGGCACGTCAGAGCGAGAGTGCAGCTAGC
+AGCTCATAACTACAA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/18/2809_4330
+GTTTGGCCTACAGCTGACCTGTATTGGGCAGAGTCGGCGAGTCTGTCTTA
+GAATTCTCTGCGGGTCGCAGCGTGCGAGTTGGTTTCGTGAGGCGATCAAG
+CGCTAGCCGTGTGACAGCGTAAGCGAGAGATTATGGTCTGACGCGATTGG
+ATTCTCAACGACTGTCGCCGGCTTGTGTGTGTGTCTGAAAACTAGCTGTG
+ATGGCTTGGCCTGATAGTAACTTTGCTTCAGGTGAGTTGCGATTCGCCCT
+GGTTCATATCTTGCTATGATTCTATATTATTCCTGGCGTTGTAGCCAGCC
+GCTCCGTTTGGGTCGCCTGTGGGCCGCGCCAGTATATCCATTGTTTCTTA
+TATAGCCGTGTATCCTTGGAAGGGGTAAATCCCGGGAGTGCGCGCTGATG
+TTCGACTGACCGTGCAGAGCTATCTAATCATGGTTTCTTGGCACTCTGCT
+GTCAAGAAGGCACTGCTGTATGTATGTCGAGTCCGATCTTTATGTCAGAG
+CCAGTTGTATCCGCGTCGATTCGGTAGAACAGATACTCGGTCGTATCCAG
+TGCCTTGAGGCGGAGATGCTCAGATGCCGTGCAATATGTCACTGAATCCA
+TCGACGAGTGGGATATTCGAAGCTTCTTCGCCGAGACGAATCGCCGTGGC
+GTGCTCGCTATCGTGCTCGTGAACGGTTGCTTTCAAGTGACGCATATCGC
+AAGTCTCGCCGCATGATACACGCATGAAAAACGCTCGCAGCTCAAGGCCG
+GGGGAGGAGGTGTATCGTTATCAGTATACGATAGACATTTCGAGTGTTTT
+GGCGTGAGAGTCTTTGGCATTGTGCTATCTGCGCCATACCATCATGCCAC
+TCCAGTGCGCTCGCTAAGCCAGCGCGTGCGGTTGGATGTGCTTGGTCCGG
+GTCTTCGATTCAATCTACGGTGAACTCCTGGTCTTCAGTTTGCACTTCTT
+TCCGCTGTCTCTGTGACTGCGAGAGAGGTGGCATGTTATGCAGTACTCCA
+TAGAAACGCACAACCTGCCGTAGGCGCGAGCTATCCAGGGATAACAAATG
+AAATCGCCGCAAAAGGATGTGGAGATGTGGTTATTAGTATATTCGGTTTA
+ATACATTCTATAGATGTCTATTTGTACAGGAGAGGTGCAAGTATCAGCGG
+CTATCTTATCCACGCGTAGCTACTCGGGTGATATATAAACTTTTTGGCGG
+CACTGGTATGAGGGAGGTTTTCATCTGTCATCGCAGGCACTTTCGACAGA
+ATAGGGATTTTGTTACTTCATGATAGACTGCTACTGAGAAAGGCCATATG
+CATTGAGACTGTAGTGTTGATGGCCCGCCTGTTCAGGCTGAATATTCTGA
+GTATTACACACTGTGCAGTCTACATACAAGCGAGGTGGCGCTGTTATTCG
+ATGATGTACTGCATCGCGCAGACGAGGACACCAGGAGAGTCTGCAACAAT
+CGATTGGATGGTACGCGCCCAATCCTTGTGTGCTAAGCGCAGACTCTACC
+GGATCAGTTGATGAGTCAGTT
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/18/4375_4894
+ACGCTGCGTTGGGCCTTTGCAAACTGTGGTATGCGTAAGTCCCGTATCAA
+TCGAGCCTGTAACGGTATCAGTCGTGAGTTGATTGCGGAATAAACAGTAA
+AGCATAAGACCTCAACCCCGGTTCGGATCAGATGTTGTGAGTATCGAAGT
+CTCATCTGACACTACAGACGTGACGCGCTGGCAGAGGTCGCTGTGGAGCA
+CGCGCAGACGGAGGATTCTGTCTTCTTCCAGCAGAGCGTTATCTCTGTGT
+TATTAACGAACCGATCTGCACTCTGGTCCTTGTGTTGAATGGCGTGGCCG
+GCCGGTCAGAAACGATCAACTCGCAGATACTCACCTGCATCCTGAACCAT
+TGAACCTCCAACCCCGTAATAGCGGATGCGTAATGAATGTCGGATAGTTA
+CTAACGGTCTTGTTCGATTAACGGCGCCAGACACTCTCCGGTCACCAGTG
+CGTGCTTGGATAACGGAGTCTTCCCAGGATGGCGAGACACACAATTGAGA
+GACGATGATGTTCCGCTGC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/18/4953_5418
+GCGGACAAACAGTTATCTTGTGTGTTGTGTCCATGCCTGGGAGTGCTGCT
+ACTATCATGCACTGCGACTGGCTGTACCCTTGGAACAGAGTTTCCTCGCG
+TGCCAGTTAATCGAACCCAGGCTCTAGGTTTATATACTAGCGACCTTATC
+ATTCTGCCGCTCAGTGCGCTATTAACGGGGGATATGGGAGGCTGCGAATC
+GAGGTATCAGAGAGTCGACAGGCTCGGGGTATAAGCTGCATTACTTGAGT
+GGGATGTAGACGCTGGGCATTCGCATGCCGGAAGAGCTGAGGTCGCGGGT
+TTTTGTAAACATAGTGTAGACGCTTAGTGAAACGATTGCTGAGATTTTCG
+CCGCGATACAGTCTTCAACTTCGCGATCGCCAGAGATGTAGTGAGTGCTC
+GAGTATGATTGACTCTGATACTACAAACGTGGAGGTGAGAGGTAAATAGC
+GAGTTAGTTATATCT
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/21/0_506
+TACTGCCCTGCGTCGCCTGCCGGTATGAAGATCCGCGAATCTGGCGGACG
+GCTTACCAGCCGCCGTCGCATCACAATGCAGCGAACTATGCGTGACGAAG
+AGCTGGCCATTGCCTCAGGTCCGAAGAGATGCAGGCAAAGTTCTGGCCGT
+GCTTAAGGGCAAATACACCCATGACCGGTGGAAGCCTTCATCGTGAGGGG
+ATATGGCCGCAGTGAGGAGAATAACATCACGCAGTCCGGCGCACGGAGTG
+GAGCAAGCGTGACAAGTCCACGTATGTACCCACCGACGAATCCGAAGCCT
+ACGGCGCTGAACGCCAGCGGTGTGGTGAATATCATCGTGTTCGATCCGAA
+AGGCCTGGGCGCTGTTCCGGTTCCTTCAAAGCCGTCAAGGAGAAGCTGGA
+TACCGTCGGGCTCTAATTCCGAGCTGGAGACAGCGGTGAAAGACCTGGGC
+AAAGCGGTGTCCTATAAAAGGGGATGTATGGCCGATGTGGCCATCGTCCG
+TGTATT
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/21/553_2265
+TAATACACGACGATGGGCCACATCGCCATAACATCCCTTATAGGACAGCC
+GCTTTGCCCAGGTCTTTCACCGCTGTCCCAGCTCGAATTAGAGCCACGAC
+GGGTATCCGCTCCCTTGACGGCTTTGGAAAGGAACGACAGCGCCCAGCCT
+TTCGGAATTCGGAACACGATGATGATTTCACTCACACCGCTGGCGTTCCA
+AGCGCGTAGGCTTCGATATCGGCGTCGGGTCAACGTGGACTTGTCACGTT
+TGCTCCACTCCGTGCCGGCCGGACCCTGCGGTGATGTTATCTCCTCACTG
+CGGCCCATATCCACCTCAACCGGATCGAGGCTTCACCGGTCATGGTGTAT
+TTGCCCTTAAGCACGGCAAGGAAACTGCCCTGCATCTCTTCGACCTGAGC
+AAATGGCCAGCTCTTCGTCACGCAATGTTTGCATGAAGATTGCGACGGCG
+GCGTAAGCCGGTCCGCCAGATCTGCGGATCTCATCCGCAGGCGACGCAGG
+TCATCTGCGGATTCACTTCATGCTTTCGGCTGACATATCCCGGCGGTAAA
+ATTTCAGAGTGGAGCCCGCACGGGAACGGATAACCTCACCGGAAAACAAT
+CGGCGAAACGTACAGCGCCATGTTTACCCAGTCCGCGAATTTGTGAGAGA
+ATAGACTCTTCTCCCCGTGGTGAAGGGATAGGCTCTCACGGAAAAAGCAG
+ACGCAGGAAACAGCGGATCAAACTTAAATTCTGCTCATTGTTGCCGCAAG
+CAGTTGGGCGGTTGTGTACATCGACATAAAAAAAATCCCGCTAAAAAAAG
+CCGCACAGGCGCCTTTAGTGATGAAGGGGTAAAGTTAAACGATGCTGATT
+GCCGTTCCGGCAAACGCGGTCCGTTTTTTTCGTCTCGTCGCTGGCAGCCC
+TCCGGCCAGAGCACAATCCTCATAACGGACGTGCCGGACTTGTAGAACGT
+CAGCGTGTGCTGGTCTGGTCAGCAGCAACCGCAAAGAATGCCAACGGCAG
+CACCGTCGGTGGCCCATCCCACGCAACCAGCCTACAGGCTGGAGGTGTCC
+AGCAATCAGCGGGGTCATTGCAGGCGCTTTCGCCACTCAATCCGCCGGGC
+GCGGTTGCGGTATGGAGCCGGGTTCACTGTTGCCCTGCGGCTGGTAATGG
+GTAAATGGTTTCTTGCTCGTCATAAACACTCTTACACTGGTGTTCCAGCA
+AATCGTTAACGCATCAGAATGCCGGGTTACCTGCAGCCAGCGGTGCCGGT
+GCCCCTGCATCAGACCGATCCAGCGCAGTGTCACTGCGCGCCTGTGCACT
+CGTTGGTGCTGCGGCCAGATGGCGGCGGGCCGTTTTCACGTCATACCGGG
+GGTTCTGCCAGCAGGCGTGCCTGTTCTTCGCGTCCGTGAGCCTCTCACAG
+TTGAGGATCCCCATAAGCGGCTGTTTTCTGCGCAACCGCTGCGGGATCTG
+CGCGTTCACGTCCGGCTGCGCCCGCGCTGGCGTTCTCGCCCTCCGTCGCT
+GGCACCACGTCAGAACGTCAGCCTGCCGAAGCAGTGGGCTGAAACATTGT
+GATTGAAGTCCCTTGGGTCATTCCGCCCTCCTGAGAGACGGGATTTAACG
+TGCATCCAGTGCATCACGCATGACGGTGATCGCCATCGGTGCTGTTAACA
+AGTTCATCAGCCAGTCCGGCATCAATGGCCCTCCTGACCGCTGTACCACC
+TGCAGCCCGGTA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/21/2313_4029
+ACCCGAGGCCTGCCCAGTGTACACGCGGTCAGGAGGCCATTGATGCCGGA
+CTGGCTGATGAACCTTGTTAACAGCACCGATCGCGATCACCGTCATGGCG
+TGATGCACTGGATGCACGTAAATCCGTCTCGTCAGGAGGGCGAATGACCA
+AAGAGACTCAATCAACAACGTTCAGCCACTGCTTCGCGCAGCTACCGTTA
+CGACGTGGGCCAGCGACGAGGGCGAGAACGCCAGCGCGCGCAGCCGGACG
+TGAACAGGCGCAGATCACCGCAGCGGTTGCCGGCAGAAACAGCCGCCTTA
+TGGGGATCTCAACTGTGAGGAGGCTCCGGACGCGAAGAACAGGCCACGCG
+TGCTGGCAGAAACCCCCGTGTATGACCGTGAAAAACGGTCCCGCGCATTC
+TGGCCCCGCAGCACCACAGAGTGCACAGGCGCGCAGTGACACTGCGCTGG
+ATCGCTGATGGCAGTGGGGCACCGGCACGCTGGCGCAGGTAACCCGGCAT
+CCTGATGCCGTTAACGATTTGCTGAACACAACCAAGTGTGTAAGGGATGG
+TTATGACGGCAAGAAACCTTTAGACCCATTACCAGTCCGCAGGGCAACAG
+TGGACCCGGCTCATACGCCAACCGCGCCCAGGCGGATTGAGTGCGAAAGC
+GCCTGGCAATGACCCCGCTGATGCTGACACCTCCAGCCGTAACTGGTGCC
+GTGGGAGGCACCACACCGACGGTGCTGCCGTTGCATTCTTGCGGTTGCTG
+GCTGACCAGACCAGCCCACGCTGACGTTCTACAAGTCCGGCACGTTCCGT
+TATGAGGATTGTGCTCTGGCCGGAGGCTGCCAGCACGAGACCGAAAAACG
+GACCGCGTTGCCGGAACGGCAGATCAGCATCGTTAACTTTAACCCTTCAT
+CACTGAAAAGGCCGCCTGTGCGGGGCTTTTTTACGGATTTTTTTATGTCC
+GATGTACACCAACCGCCCAACTGCTGGCGGCAAATGAGGCAAGAAATTTA
+AGTTTGAATCCGCTGTTTCTGCGTCTCTTTTTCCGTGAGGCTATCCCTTG
+CACCACGGAGAAAGTCCTATCTCTCACAAATTCCGGGACTGGTAAACATG
+GCGCTGTACGTTTCCGGCCGATTGTTCCGGTGAGGTTATCCTTCCCGTGG
+CGGCTCACCTCTGAATTACGCGGATATGTCCAAGCCGAAGCATAAGTGAA
+TCCGCCAGATGACCCTGGCGCGCCTCCGGATGAAGACCGCAGGAATCTGG
+CGGACGCCGGCTTACCTGCCGCCGTCGCATCATCATCGCAGACATTGCGT
+GACGAAGAGCTGGCCATATGCTCAGGTCCAAGAGATGCATGGCAGTTTCT
+GCCCGTGCTTAAGGGCAAATACACCAATGACCGGTGAAGCCTTCGATCCG
+GTTGAAGGTGAGATGGCCGCAGTGAGGAGAATAACATCACGGCAGTCCGG
+CGGCACGGGAGTTGGAGCAAGCGTGACAAGTCACGTATGGACCCGACGAC
+GGATATCGAAGCTTACGCGCTGAACGCAGCGGTGTGGGTGAATACATCGT
+GTTCGATCCGAAGGCTGGGCGCTTGTTCCGTTCCTTCAAAGCCGTCAAGG
+AGAAGCTGGATTACCCGTGTGGCTCAATTCCGCAGCTGGAGACAGCGGTG
+AAAGACCTGGGCAAAGCGGTGTCCTATAAGGGGAGTGTATGGCGATGTGG
+CCCATCGTCGTGTATT
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/21/4078_5075
+TAATACACGACGATGGCCACATCGCCATACATCCCCTTATAGGACACCGC
+TTTGCCCAGGTCTTTCACCGCCTGTCTCCAGCTCCGATTAGAGCCACGAC
+GGGTATCCAGCTCTTCCTGACGGCTTTGAAGGGAAGGAACAGCGCCCAGC
+CTTCCCCCTCGGATCGAACACGATGATATTTCACCACACCCGCTGGCGTT
+CAGCGCGTAGGCTTCGATATCGTCGGTCGGGTCATACGTGGACTGTCAAC
+GCTGCTCCACCCGTCCGCCGATGCCGTGATGTTATTCTCGCTCACTGCGG
+CCATATCCACCTTCAACCGGATCGAAGGCTTCACCGGTCATGGGTGGAAT
+TTGCCTTAAGCAGCGGCCAGAAACTGCCTGCATCTCTTCGACCTGAGCAA
+TGGCCAGCTCTTACGTCACGCATGTTCTGCATGATGATGCGACGGCGGCG
+GTAAGCCGGGTCCCGCCAGAGTTCTGCGGATGCTCATCCTGGCAGGCGTA
+CGCAGGGTCATCTGCGGATTCACTTCATGCTTCGGCTTGACATATCCAGG
+CGTAATTCAGGAGGTGGAGCCGCCACGGGAACGGATAACCTCACCGGAAA
+CAATCGGCGAAACGGTACAGCGGCCATGTTACCAGTCCCGGAATTTGTGA
+GAGATAGACTTTCTCCGTGGTGAAGGGATAGCGTCTCACGGAAAAAAGAG
+ACGCAGAAACAGCGGATCAAACAGTTAATTTTCTGCTCATTGGCCGCCAG
+CAGTTGCGGTTGGTACATCGACATAAAAAAATCCCGTAAAAAAAGCCGCA
+CGGCGGCCCTTTAAGTGGATCAAGGGTAATAGTTAGACGATGCTGAATGC
+CGTTCCGGCAAACGCGGCACCGTTTTTTTCGTCTCGTCGCTGGCAGCCTC
+CCGGCCAGAGCACATCCTCATAACGGAAACCGTGCGGACTTGTAGAACGT
+CACGTGGTGCTGTCGGCAACAGCACCGCATAGAATGCCAACGGCTAG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/22/0_346
+TTGGAAAGCCAGTTGATCATCAGCGCAGGTTAATCTGGAACCGCGAACGA
+ATCACGCACTCACAAAACGGGATCGTGAAAGAAATCAAAGCGCCGGACAC
+GTTCAATCTTTGGTCCTGACGCCAGCAGTGAAACCACTCAAGTTTGCCAA
+CCAAATGTATATCGATACCGGCGCAGTGTTCGGGAAACCTAACATTGATT
+CAGTACAGGGGGAGAAGGCGCATGAGACTCGAAAGCGGTACGCTAAATTT
+CATTCGCCCAAAAAAGCCCCGAATGATGAGCGACTCACCACGGCCCACGG
+CTTCTGACTCTCTTTCCGGTTACTGGATGTGATGGCTTGCTATGGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/22/390_999
+CCCCCATAGCAGGCATCACATAGTAACCGGAAGAGCAGTCCAGAAGCCGT
+GGCCCGTGGTGAGTCGCTCATCATCGGGCTTTTTGGCGAATGAAATTTAG
+ACTACGCATTTCCGAGTCTCATTGCGGCCTTCTCCCTGTACCTGAACTCA
+ATGTTAGGTTTCCGCAGACACTGGCGCCGGTATTCGATGATACATTTGGT
+TGGCAAACTTGAAGTGGATTTCACGTGCTGGCGTATGACAAAGATGAACG
+TGTCGCCGGCCTTTGAATTTCTTTCACGATCCGTTTTGTGAGTTGCTGAT
+TCGTTCGCGGTTGCCAGATTACCTGCTGATGATCAGACTGAGCTTTCCAA
+ACTCGTATTCGTCAAAGGGATAATCGCGGTGGCAGAGAGAGAGTATTTTT
+TATTTTGCCTCACCAGGTTTCGGATGATGTAACGGAAGTTCATCCTGCTT
+TAATGGGCAAGAGCTTTAGCCAGAATTTCTTTGTCGTAATCCGAGATAAA
+GAACAGCCACCGCCATTAAGCAGCCAGTGAATTAACGTTTCCACGCTCCT
+TGATAAGCCATCAATCATCCATTTGCCTCATGGTTTCACGTGACAGCTCT
+GAACCAGGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/22/1051_1684
+CAGCCCTGGGTTCAGAGCTGTACGTGGGGAAACCATGAGCAAATGATGAT
+TGATGGCTTTATCAGAGCGTGGAAACGTTCAATCCTGGGCTGCTTAATGC
+GGTGGCTGGTTCTTTAATCTGCGATTACGACAAAGAAATTCATGGCCTAA
+AGGCCTTGCCCATAAAGCCAGATGAACTTCCGTTAATCATCGAACTGGTG
+AGGCGAAAGATAACAAAATATGTAGTCTGCCACGGCCGATTATCCTTTGA
+CGAATAGCGGTTGGAAAGCCAGTTGATCATGCAGAAGGTAATCGGAACCC
+GGGCGAAGCGAATCAGCAACGTCACAAAACGGGATCGTGAAAGAAAGTCA
+AAGGCGCGCGGACACGTTCATCTTTGGTCATACGCCAGCAGTGAAACCAC
+TCAAGTGTTGCCAACCCAAAATGTATATCGATACCGGCGCAGTGTTCTGC
+GGAAACCTAACATTATTCAGGTACAGGGAGAAGGCGCCATGACGACTCGA
+AACGTCAGCTAAATTTCATTCGCCAAAAAGCCCGATGATGAGCGACTCAC
+CACGGGCGCACGGCTTCGACTCTCTTCTAGCACCGCGACGCACACGCGAG
+CGGGGTACTGAGATGTGATGGCTGCTATGCGGA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/22/1732_2248
+CCCAAAAGCCAGCCTCACATCAGTACCGGAAGAGAGTAGAAGCCGTGGCC
+CGTGGCTGAGTCGCTCATCATCGGGCGTTTTTTGGCGAATGAAATTGTAG
+CGTACGCTTTCGAGTCTCATGCGCCTTCTCCTGTACTGATCAATGTTAGG
+TTTCCGCAGAACACTGCGCGGTATCGATATACAATTTGGTTGCAAACTTG
+AGTGGTTTCACTGCTGGCGTATGGACCAACCAGATGAACGTGTCCCGCGG
+CCTTTGATTTCTTTCACCGATCCCGGTTTTGTGAGGTTGCTGATTCGTTC
+GCCGGTTCCAGATTACCTGCTGATGATCAACTGGCTTTCCAAATCGTATT
+CCGATCAAAGGGATTAATCGGCGTGGCAGGATAACATATGTTTTTATCTT
+TGCTCACCATTCGATGATTACGTGAAGTTCATCTGCTTTATGGGCCAAGA
+GCTTTAGCCAGAAGTTCTTTGGTCGTATCGAGGATAAAGAACCAGCCACG
+CCATGGCCGTGATTAA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/24/0_354
+ATCACGAATAGTCGGCTCCAACGTGGGTTTTCATAAAGTCTCGGCATCAC
+CATCCGTCGGCAAACCAGATAAGGGTGTTGCGCTGCTTATGCTCTATAAA
+GTAGGCATAAACACCCAGGCAGCATTTTGGAATAGACCGACACGGGCAGA
+CTTAACCAACATTCACCTCCACGGATGTAGTCGCTGCCATCGCATTCATG
+ATGGCCCGCTGAAAGGGCAGTGTTTCCCCAGCGCCCTTTCCCTGGTATGC
+GGATTCTTTCCGGGAGGATAGTAATTAGCATCCGCCCATTCAACGGCGGT
+CTGTTGGCTCCGGCCTGAACAGTTGAAGCGAAGCCCGGCGCGGACAAAAT
+GCCG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/24/401_1026
+CGGCATTTGTCCCGCGCCGGCTTCGCTCACTGTTCAGGCCGGAGCCACAG
+ACCGCCGTTGAATGGGCCGGATGCTAATACTATCTCCCGAAAGAATCCGC
+ATACAGGATAGGGCGCTGGGAAACACTGCCTTTCAGCGGCCATCAGAATG
+CGATGGGAGGACTACATCCGTGAGGTGAATGTGGTGAAGTCTGCCTGTCC
+GGTTATTCCAAAATGCTGCTGGGTGTTTATGCTACCTTTATAGAGCATAA
+GCAGCGCAACACCCTTACTGGTTGCCCCGACGGATGGTGATGCCGAGAAC
+TTTATTGAAAACCCACGTTGAGCCGACTATTCGTGATATTCCGCGCTGCT
+GGCGCTGGCCCCGTGGTATTGGCAAAAAGCACCCGGGATAACACGCGTCA
+CCATGAAGCGTTTCAACTAATGGGCGTGGACTTCTGGTGACTGGGCGGTA
+AAGCGGCCAAAAAACTACCGTGAAAAGTCCGGTGGATGTGGCCGGGTTAT
+GATGAACTTGCTGCTTTGATGATATATTGAACAGGAAAGACGCTTCCGAC
+GTTCCTGGGTGACAGCGTATTGAAGGCTCGGTCTGGCCAAAGTCCATGCC
+GTGGCTCCACGCCAAAAGTGAGAGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/24/1074_1708
+CCTCTCACTTTTGGCGTGGGAGCCACGGATGGACTTTGGCCCAGACCCGA
+GCCCTTCAATACGCATGTCACCCAGGAACGTCGGAGAGCCTTCCTGTTCA
+AATATCACATCAAAAGCAGCAAGTTCATCATAACCCGCACAATCCACCGA
+CTTTTCACGGTAGTTTTTTTGCCGCTTTAGCCGCCCAGGCCCAACAGAAG
+CCACGCCCATTAGTGAAACGCTTCATGGTGAGCGTGTTTATCCCGTCTTT
+GCCATACCACGGGGCCAGCGCCAGCAGCGACGGGAATATCACGAATAGTC
+GGCTCAACGTGGGTTTTCATAAAGTTCTCGGCATCACATCCGTCGGCAAC
+CAGATAAGGGTGTTGCGCTGCTTATGCTCTATAAAGTAGGCATAAACACC
+CAGCAGCCATTTTGGAATAACCGACCACGGCAGACTTCAACCACATTCAC
+CTCACGGATGTAGTCGCTGCCCATCGCATTCCATGATGGCCGCTGAAAGG
+GCAGTGTTTCCGCACGCCCCTTCATGGTATGGCGGATTCTTTCGGGAGAT
+AGTAAATTAGCATCCGCCCATTCAAAGGCGGTCTGGTGGCTCCGGCCTGA
+ACAGTGAGCGAAGCCCGGGCGGACCAAAATGCCG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/24/1752_2380
+CGGCATTTTGTCCGCGCGGGCTTCGCTCACTGTTCAGGCCCGGAGCCACA
+GACCGCCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGATCCC
+ATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGGCCATCATG
+AATGCGATGGGCAGCGACTACCATCCGTGAGGTGAATGTGGTGAAGTCTG
+CCCGTGTCGGTTATTCCAAAATGCTGCTGGGTGTTTTATGCCTACTTATA
+GAGCATAAGCAGCCCGCAACACCCTTATCTGGGTTGCCGACGGATGGTGG
+ATGCCGAGAACTTTATGAAAACCCACGTTGAGCCGACTATTCGTGGATAT
+CCGTCGTGCTGCGCTGGCCGTGGTATGGCAAAAAGCAACCGGGAATAACA
+CGCCTCACCATGAAGCGTTTCACTAATGGCGTGGCTTCTGGTGCCTGGGC
+GGTAAAGCGGCAAAAAACTACCGTGAAAAGTCGGTGGATGTGGCGGGTAT
+GATGAACTTTGCCTGCTTTTGATGATGATATTGAACAGGAAGGCTCCCGA
+CGTTTCCTGGGTGACAAGCGTATTGAAGGGCTCGGTCTGGCCAAAGTCCA
+TCCGTGGCTCCACGCCAAAAGTGAGAGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/24/2426_3071
+CCTCTCACTTTTGGCGTGGAGCCACGGAAATGGACTTTGTGCCAGACCCG
+AGCCTTTCAATACGGCTTGGTCACCCACGGAACGTCGAGAGCCTTCCTGT
+TCAATATCATCATCCAAAAGCAGCAAGTTCATCATAACCCGCCCCCACAT
+CCACCGACTTTTCAACGGATAGTTTTTGCCGCTTTACCGCCCAGGCACCA
+GAAGCCACGCCATTAGTGAAACGCAATCTCATGGTGAGCTGTGTTATCCC
+GGTGCTTTTGCCATACCACGGGCCCAGCGCCAGCAGCGACGGAATATCAC
+GAATAGTCGGCTTCAACGTGGGGTTTTCAATAAAGTTCTCGGCATCACCA
+TCCGTCGGACACCAGATAAGGGTGGTTGCGCTGCTTATGCTCTATAAAGT
+AGGCCTAAACACTCCCAACAGCATTGTGGAATAACCGACACGGGCAGACT
+TCACTCACATTCACCTCACGGATGTAGTCGCTGCCCATCGCATTCATGAT
+GCCCCTGGAAAGGGCAGTTGTTTCCCAGCGCCTTCTGGTATCGGATTCTT
+TCGGGAGATAGTAAATTAGCACCGCCCATTCAACGGCGGTCTGTGGCTCC
+GGCCTGAAACAGTGAAGCGAAGCCCAGGCGCGGGACAAAATGCCG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/24/3116_3741
+CGGCATTTTGTCCGCGCCGGCTTCGCTCAACTGTTCAGCCGGAGCCACAC
+GCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGAAATCCGCTA
+CCAGGAAGGGCGCTGGAAAAACTGCCCTTTCAGGGGCCATCTGAATGCGA
+TGGGCAGCGACTAACATCCGTGAGGTGAATGTGGTGAAGTGCTGCCCCCG
+TGTCGGTTATTCCAAAATGCTGCTGGGTGTTTATGCCTACTTTATAGAGC
+ATAAGCAGCGCAACACCCTTTATCTGGTTGCCGACGGATGGTGATCCGAG
+AACTTTATGAAAACGCAACGTTGAGCCGACTAATGTCGTGATTTCCGTCG
+CTGCTGGCGCTGGCCCCGTGGTATGGCAAAAAGCACCGGGATAACCACGC
+TCACCCATTGAAGCGTTTCACTATGGCGTGGCTTCTGGTGCCTGGGCGGT
+AAAGCGGCAAAAAAACTACCGTGAAAGTCGGTGGATGGTGCGGGTTATGA
+TGAACTTGCTGATTTTGATGATGATATTTGAACAGGAAGGCTCTCCGAAC
+GTTCCTGGGTGACAAGCGTATTGAAGGCTCGGTCTGGCCAAAGTCCATCC
+GTGCTCCACGTCCAAAAGTGAGAGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/24/3790_4270
+CCTCTCACTTTGGCGTGGAGCCACCGGAATGGATTTGGCCAGACCGAGCC
+TTCAATACGCTTGTCCAACCCAGGAACGTCGGAAGCCTTCCTGTTTCAAT
+ATCATCATCAAAAGCAGCAAGTTCATCATAACCCGCCACATGCCACGCGA
+CTTTTCCAGCGGTAGTTTTTTGCGCTTTACCGCCCAGGCACCAGAAGCCA
+CCGCCCATTAGTGAAACGGCTTCATGGGTGAGCGTGTTATCGCGGTGCTT
+TTTGCCATACCCCACGGGGCCAGGCGGCCAGCAGCGACGGAATATTCACG
+AAATAGTCGGCTCAACGTGGGGTTTTCATAAAGTTCTCGGCATCATCCAT
+ACGTCGGCAAACCAGATAAGGGTGTTTGCCGCTGCTTATGCTCTATAAAG
+TAGGCATAAACACCCAGCAGCATTTTTGGAATAACCGACACGGGCAGACT
+TCACCACATTCACCTCCACGGATGTAGTCG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/25/138_620
+ACATCCGGTTGCCCAGGGCAATAGTTCTGCGTTCTGTACGGGGGGAAATG
+CGCTGTGGGGTCACGCGTTGGTGTTCTCAGGAGATCAGCACGGCAGACGA
+GGGGACTGTGTCAGGATTCGTGGTATTGGTCCGCTGATGCAAAATGTATT
+ATGTGAAACGCCTGCCGGCGTTTTTGTCATTATGGAGCGTCGAGGAATGG
+GTAAAGGAGAGCAGCTAAGGGCATACCCCGGCGCCGAAGCGAAGGAGCAA
+CCTGAAGTCCACGCAGTTGCTGAGTGTGATCGATCGCCATCAGCGAAGGG
+CCCCCCGCCGCCCGCTACACATGCGTGCTGCTGAACCAGTACGACCGGTG
+CTGGGACATGCAGGGGAATACCAACATATCCCGGTGTCACGGCTGGTGCT
+CCGGCTGGTGAGCAGCTGAGCAGACTCCGCCGGAGGCGGATTTGCGAATC
+CTCCGGCTCCAGCACGACGCGTGGCTGGGTAC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/25/675_3031
+GTACCCAGCACCGGTCTCGGAGCACGGAGGATTCAAATCCCTCGGCGGAG
+TTCTGCTCCCTGCTCACCAGCCCCGGAACACCACCGTCGCACACGCGATA
+TGTTGGCTATCCCTCAGTTCCAGCACGGCGTACTGTTCAGCCAGCGCGCA
+CGCTTTTTAAGCCGTCCACCGGACCTTCAATCGGCCCTGTGACGCTGATG
+AAAACTACAACGAGCATACACATCTCACGCAATCTGAGCAGTGTGTTCTC
+CAGCTGCAGGTGTGCTTCCCTTCTCGCTCATCGCGCCGCCGCGTTTCACA
+CTCAGAGTCGCGAGGTTCCTCTGCTCTACCTCTATCCGTCCACGCCGCGA
+GCATCCCCAACAACATAGCGCTCCCAAAAACCTGGCCCGAGGGCGTTCAC
+ACTAAGGAACCTGAATGCCTGTTATATGCACGATCAGTCCTGACATAGCT
+CCGACCCAATCGACAACGCGACCACCCGGTCCGTTCAGTCCTTGCGCCCT
+GTGGCCGTCATCTGCACTGCGTAAAGGCCCCCTATCCGTACCGTGACCCC
+CACGAGACGAGAGACGAGCATCCTCCCGTACGCAACCAGGCAAGAAACAT
+GGGCGCGCGTGGGCGAGGCCAATGTGGTTAAGGTAAACCAACCCGCAGTG
+CGCCTGCTGAGAATGTGACGGGGGGCATTCTGTCTATACCCGATATTGCT
+CGCGTTGCGTGTCGCTAGAATACACGACACCGGTGGATGCCACAGTCCTG
+GTCTTTCCCGGGTGCAACCCATGTCTGCGGCCATCACTCCAGACACCGAC
+GGGCACCAATCTCTCTCGAGCCAGCGAACCCAATCAGAGCCATGTCGAAA
+GAGCCGGACGGAGGAGAACAGATGCAGACCGAAACAAGGCCGCCCTCGGT
+GAGTGTATGCGTGACGTCGATCCTGTTCTTGGGGCCTTCCCGAACGCCAG
+AGTATACGACAACCGGATACAGCGCGGGTAAGCAGAACACTATCTCCTCA
+CCTGGATAACATGGCTTGCCCAGGCAATGGTCTGCCTGGTTCTGTAACGG
+AGGGGAGTGCGCGTGCCGCGGCTCGCGTGGTTTCTCAGGAGATCAGCGCA
+CGGCAGACGGCGGGGACGGGGTCAGGTTGTGGTGCATGGCTCGGCTGATG
+CCCAAAAATGTTTTTATGTGAACCGCCTGCGGGCGGTTTTTGTCGATTTA
+TGGGACGCGTGAGGACATGGGAAAGAAGCAGCGTTGAAGGGCCATACACC
+GCCGAAGCGAAAGGACAACCTGAAGCCACGCAAAGTTGCGAGTGTGAATC
+GGAGCCACCAGCGAAGGGCCGATTGGAAGGTCCGGTTGATGCCGCCTTAC
+AAAACGGCGCGCGGCTGCTGAACAGCGTCACCGCGGTGCATGGACCACTG
+AGGGGACGATACCAACATATCCGGGGCACGGTGTTCCCGGGCTGGTGGAG
+CAGGAGCAGACTTCCGCCGGAGCGGATTTGAATCCTCCGGTCCGAGACGG
+GTGCTGGGTAGGTCTCTGTGTTTTTTCAATTTTCATATCATTAAATCTAA
+TTTGCAGATATTTAAATTTTAAGCACCGAGAGGAGGACAGAGAAAGAGAG
+AGTATATATCGTATATATTCCTTCTCTTTCTCTGTTTCGTGATACATTAT
+AGGATTTTACTAGGTTTTGTATCTATTTTTCTCTCTTGTGTTATTATAAA
+GAAGATATATCTTCTTAGTTGTTGTTATGTTCGTTGCTTCTGTGTATGTT
+GTTTCTAGTTGTGCTTAGCGTTGCTTGCTTTTTTTTTTTTTTTTTTTTAT
+AGTTTTTTAGTCTTCGTGATTTTTCTTAATTATCTGGTCTTTTGTTCTTT
+GTATATGTTTGTTCTTATTTTTTTCGATCCACTCAGCAAACCTGTTTGTT
+CTTTGGTTTTTGTGGTACTTTCTTTTTTTTGTTTTTTTTTATTGTTGTTG
+TTTGCGCTTCGTCGCTTTCGTCTTGGCTTGGTGGTTTATGTCTTCTTTCT
+TCTTATTTCTTTTTGTCTTCTCTTTACCCATCCTCCCCGGCTCCCATAAA
+ATGGCAAAACCGCCGCAAGGGCGCGTTTCACATAAAACATTTTTGCATCA
+GCGACCCAATCCACCACAACCTGACCACCGTCCCCCTTGCGGTCTGCCGT
+GCCTGAGTCCCTGGCAGAAACCCGGACGCGTGACCCACGCGCAAGTTTCA
+CACGTAACAGATACCAGGCCAGGAACATTGCCTGGGCCATACCATGTTAT
+CCCAGTTGAGGGAGAAAAAGTGTTCTGGCTTACCGTCATCGTTGTCTTAT
+ACGGGAGTTCTGGCTTTCGGTGCCCCAGCATCCTTGGCCCACACCACCCG
+AGGCAC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/25/3077_3717
+GTGCTCGGTGGTGTGGGCGGCAGACTGGCTGGCACCGAAACCAGAAACTC
+CCGTATACATACAGACAACCGGATAACGGGTAAGCAGACACACCGTATTT
+CGTCCTCTGGAAACAAGGTTTGCCCCAGGGCCAAATGTTCTGCCCTGTTT
+GTACGGGGGGGAAATCCGCGTGGGGTCAACGCGTGGTTTCCCCCTCCCAG
+GAGATCAAGCACGGCAGAAGCCGAAGGGGACCCGGTGGGTCAGGTGTGGG
+GATTGGCGCTGATGCAAAATGCTTTATGGTGAAGACCGCCCTGCCCCGGC
+TGGTTTGTCATTTTATGGAGCGTCGGAGGAAGTGGGTAAAGGGAAGCCAG
+GTAAAGGCATACCCCGCGCGAAGCGAAGGGACAACCCTGTGAAGTCCCAC
+GATTGCTGAGTGTGGGATCGAATGCCAATCCGCGAGGCGCCGATGAAGGT
+CCGGTGGGATGGCTTTGTTTAAAAAGCGTGCTGGCTGAACAGTACGCCCC
+GGGTGTGGACACCTGAGGGGAATACCCAACCATATCCGGTGGTCCACGTG
+GTGGTGTTTCCCGGGCCCTGGTGAGCAGGACAGACCTCCGCCGGAGGGAT
+TTGAATCCTCCCGGCTCCCCGAGACGGGGTGGCCGGGTAC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/25/3771_4379
+GGGTACCAGGCAACCCGTCTCGGAGCCCGGAAGGATTCAAATCCCTCCGG
+CCGGATGTCTGCTCTGCTCACCAAGCTCCGGGAACACCACCCGTGGACAC
+CGAATATGGTATCCCTCAGTGTCAGCAACCGGCGTACTGTGTTCAGCAGC
+ACGCTTTTTTTAAGCCATCCACGGACCTCAATCGGCCCCTTCGGCTGACT
+GCATCCCGATCACACTCAGCAAGCTGCGTGGACTGTCAGGGTTGTCCCTT
+CGCTTGCCGCGCGCGGGTAGCCTTGACTGCTTCTTTACCCACTTCTCACG
+CTCCCAATAAATGACAAAAACCGCCGCCCGCAGGCCGGTTTGCACATAAA
+GACATTTTGCCATCGCGACCCAATCACCACAACTGACCACCGTCCCCCTT
+CGCTCTGCCGTGGGGCCTGATCTCCTGGAGAAAACCGACGGCCGTGACCA
+CGCGCATTTCCCCGTACAGGAACCAGGCAGAACATGCCCTGGCAACCATG
+AGTATCCGTGGAGGAAATAGGTGTTCTGCTTACCGTATCCGTTTGTCCCT
+GTCATACGGGAGTCCGGCTTTCGGTGCCAGCATCTTGCGCCACACCCACC
+GAGCCACA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/25/4430_5057
+GTGGCTCGGTGGGTGCTGGCGCAAAGCATTGGGCACCGAAAGCCCAGAAC
+GTCCCCGTATACAGGACAACCGGAAATAACGGTAAGCAGAAACCACCCCT
+ATGTTCTCTCCTGGATACAATGGTTGCCCAGGGCAATGTTCTGCCCTGTT
+CTGTAGGGGGAAAAATGCGCGGGGTGGTGGCGTCCCCACCGCGGTGGTTT
+CCAGGAGAGCAGCGACGGGCAGGACGAAGGGGACGGTGGTCCCAGGTTTG
+GGTGATTGTGGCCGCTGATGCCAAAGTTTATGTGGAACCGTGCGGGCCGG
+TTTTTGTCATTGATTGGAGCGGTGGAGAACCGGGTAAAGGAACAGATAAA
+GGGGCATACGCGCGAAAGCCCCGAAGGAACAACCTGAGCCCACGCAGTTG
+CTGAGTGTGATCCGATGCCCCATCCAGCCGAGGGCCCGATTGAAGGTCCC
+GGTGGGATGGCTTTAAAAATGCCCGTGCCTGCTGAAACAGTACGCCCGGG
+CCTGGGACACTGAGCGGGAAGTACCAACCATATCCGTGGTCACGGGTGGG
+TGTCCGGGCCTGGGTGAGCAGGAGCAGCTCCGCCGGAAGGGATTGGAATC
+CCCGGTCCGAGACGGTGGCTTGGCGTA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/25/5106_5726
+GTTACCCAGCACGTCGGTCGGAGCCGGAGAGGCGAGAGAGCCTCCGGCGG
+ACGCTGCTCCTGCTCCCACGCAGCCAAGGAACACCACCGTGACACCGGAT
+ATGGGTATTTCCCCTCAGTGTCCCAACGCACCGGCCGTAGCTGTTCAAGC
+CAGCACGCTTTTTAAGCCCCATCCCACCCGGACCTTCAGTCGAGCGCCTT
+CGCTGATGGCAATCGGATCACACTCAGCAACTGCGTGGACTTCAGGTGTC
+CCCTTCGCTTCGCGCGGGGGTATGCCCCTTACTGCTTCCTTACCCATTCC
+TCACGCCCCAAAATGACAACAACCGCCGCAGGGCGGTTCACATAAAACAT
+TTTGCTGCATCAGCCGACCAATCACCACAACCTGACCACCGGTCCCCCTT
+CGTCTGCCGTGATGATCCTCTGAGAACCCACGCGGGACGCCCACGCGCAT
+TTCCCGTACAGAAAACAGCCCAGAACATGCTGCCCTGGGCCAAACCATGT
+TAATCCAGTGAGGAGAAAAATAGGTGTTCCGGCTTACCGTTATCTCCGTG
+GTCGTATACACGGGAGTCTGGCTGTTCGGTGCCAGCCCATCTGGGCGCGG
+GCGCCCACACACGAGGCCAC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/25/5774_5927
+GTGCTCGGTGTGGTCGGGCGCCAGATGCTGGCACCCCGAAAGCCAGAAAC
+TCCGTTATACAGACAAGGGATTAAGGGTAAGCAGAAACCCTATTTTCCCT
+CACTGGATAACATTGGTTGCCAGGGCAAACTGTTCTGCTGCCCTGTTTCT
+GTA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/26/0_67
+TCGACATTTCCTCGCACACATTCCGGCCCGCACTGGCCGGGGAAAACAGT
+ACGAGAACGACGCCAGA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/26/109_954
+TCTGGCGTTCGTTCTCCGTACTTGCTTTACCACCAGGCCAGTGTTAGCGT
+TAAACTTCCGGAGGGCCACACCGGTGCAAACTCAGGTCAAGCAGGGTGGT
+GGAAGTAGGAATTTTCATGTCAGCCACTTCTTTCGGAGCGGGGTTTTTGC
+TATCACGTTGTGAACTTCTGAAGCGGTGATGACGGGAGCCGTAATTTTGT
+GACGATTCATCCCACCTGTTCGACAGCTCTCACATCGATCCCGGTACGCT
+GCAGGATAATGATCCGGTGTCATGCTGCACGGACACCTTGTCTGCTCTGC
+GGCTTGCCCTTGCTTTTCAAGGAATCCAAGAGCTTTTACTGTTCGGCCCT
+GTGTCAGTTCTGACGATGCACAGAATGCGCGCGGAAATATCGGGAACAGA
+GCCAATAAGTCTCATCCCATGTTTTATCCAGGGCGATCCAGCAAGGTTAA
+TTCCTGCTGGTTTCATCGTTAACGCCGGAGTGATGTCTGCGTTCGGCTGA
+CCGTTCTGGCAGTGTACTGCAGTATGTTTTCGACAATGCGCTCGGCTTCA
+TCCTTGTCATAGATAACCCCAGCAAATCCGAAGGCCAAGACGGGCACACT
+AATCATGGCTTTATGACGTAAATCCGTTTGGGTGCGACTCGCCACGGCCC
+CGTGATTTCCTGCCTCGCGAGTTTTTGAATGGTTCGCGGCGGCATTCATC
+CATCCATTCGGTAACGCCAGATCGGATGAATTACGGTAAACTTGCGGTAA
+AATCCGCGCATGTACAGGATCATTGTCCTGCCCTCAAAGCCATGCCATCG
+GCAACTGCTGGTTTTCATTGATGTGCGGGACCAAGCCATCCAACT
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/27/195_501
+TGATGAGCGTTCGTTTCTGGATGATTTTGCTGCCTCTTTTGAGGCCACCG
+CATCTCGTGTGAAGTGGCGCGCCTCATGGAGCCTTCGTGGCGCGGTGGAG
+GCGACGTGCGGGCTGATTGTTGTGACGCTGCGCATTCGTTTCTGACGTTT
+TCGCCCGCACCGGCACTGGTGGCCGGCCGCGTTTTGCGAGGATTCTGCGG
+CTGCGGCACTTTTTCCGCTTCATGGCCTTTGCTGATGCGCTTCCTGCGCC
+CGGAGGACGCTTTCCTGAGGCTTGACGATGCAGCCTGTCCGGCGGACGTG
+CGGCGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/42/2357_2612
+CCGCGCCCGAACGTCGCGCAGAGCAAACAGTGCCTCAATGGAAAGCAGCA
+AATCCCCTGTTGGTTTGGGGTAAGCGCAAAACCAGTTAACCGCCTATTCT
+CTTAGCTGAATCTTCAAACCCGAAATCACGAGTAGATAAGCGCACTAAAT
+CCGATAGACCGTTTACAGTGCTGGCTGAATACCACAAAAAACCCCCCCAA
+AAGAAAGTTTGAAAGCAACCTGCAACGTATTGAGGCGCAAGAATCAGCGC
+ACATG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/42/2655_3333
+CATGTGCCTGATTCTTGCGCTCAATACGTTGCAGGTTGCTTTCATCTGTT
+TGTGTATTCAGCCAGCACTGTAAGGTCTATCGGATTTAGTGCGCTTTCCC
+TACTCGTGAATTTCGGTTGCGATTCAGCGAAGAGAATAGGGCGGGTTAAC
+TGGTTTTTGCCGCTTACCCCACCAACAGGGGATTTGCTGCTGTTCCATTG
+AGCCTGTTTTCTCTGCGCGACGTTCGCGGCGGCGTGTTTGTGTGCATCCA
+TCTGGTATTCTCCTGTCAGTTAGCTTTGGTGGTGTGTTGGCAGTTTGTAG
+TCCTGAACGAAACCCCCGCGATTGGCCACATTGGGCAGCTAACCGGAATC
+GCACTTACGGCCAATGCTTCGTTTCGTATCACACCACCAAAGCCTTCTGC
+TTTGAATGCTGCCCTTGTCTTCAGGGCTTAATTTTTAAGAGCGTCACCTT
+CACTGGTGGTCAGTGCCGTCTGCCTGATGTGCTCAGTATCACCGCCAGTG
+GTATTTATGTCAAACACCGCCAGAGATAATTTTATCACCGCAGATGGTTT
+CTGTATGTTTTTTATATGTGAATTTTATTTTTTTGGCAGGGGGGCATTGT
+TGGTAGGTTGGAGAGATCTGAATTGCTATGTTTAAGTGAGTTGTATCTAT
+TTATTTAGTTCAATAAATACCAATTGGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/42/3378_4072
+CCCAATGTATTATTGAAAAATAAATAGATACAACTCACTAAAACCATAGC
+AATTCCAGATCTCTCACCTACCAAACATGCCCCCCTGCAAAGAATAAATT
+CATAAAAAAAACATACAGATTGAACCATCTGCGGTGATAAGATTATCTAT
+GGCGGTGTTGACAAAAAAAAAAAAATAAATACCACTGGCGGTGAATACTG
+AGCACATCAGCAGGACGCACTGACCACCAAATGAAGGTGACCGCTCTTAA
+AAAATTAAGCCCTGGAAGAGGGCAGCATTCAAAGCAGAAAAGGCTTTTGG
+GTGTGTGGTGATACGAAACGAAGCATTGCCGTAAAGTGCGATTCCGGATT
+ATGGCTTGCCAATGTGCCAATCGCCGGGGGGTTTTCGTTCAGGACTACAA
+CTGCCACACACCACCAAAGCTAACTGTACAGGAGAATCCAGATGGATTGC
+ACAAACACGCCGCCGCGAACGTCGCGCAGAGAAACAGGCTCAATGGAAAG
+CAGCAAATCCCCCTGTTGGTTGGGGTAAGCGCAAAAACCAGTTAACCGCC
+CTATTCTTCGCTGAATCGCAAACCGAAATCACGAGGTAGAAAGCCGCACT
+AAATCCGATAGACCGTTACAGTGCTGGCTGAAATACCACAAACAGATTGA
+AGCAACCTGCAACGTATTGAGGCCGGCAAGAACAGGCGCACATG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/42/4118_4795
+CATGTGCCGCTGATTCTTGCGCTCATACGTTGCCAGGTTTGCTTCAATCT
+GTTTGTGGTATTCAGCCAGCATCTGTAAGGTCTATCGGATTTAGTGCGCT
+TCTACTCGTGATTTTCCGGTTTGCGATTCAGCGAGAGAATAGGGCGGTTA
+ACTGGTTTTGCGCTTACCCCAACCAACAGGGGATTTGCTGCTTTTCCCCA
+TTGGAGCCTGTTTCTCTGCGCGACGTTCGCGGCGGCGTGTTTGTGCATCC
+ATCTGGATTCTCCTGTCAGTTAGCTTTGGTGGTGTGTGGCAGTTGTAGTC
+CTGAACGAAAACCCCCCGCGATTGGCACATTGGCGCAGCTAATCCGGAAT
+CCGCACTTACGCCAAATGCTTCGTTGTTTCCGTTCACACAACCCCAAAGC
+CTCCTGCTTTGAATGCTGCCCTTCTTCAGGGCTTTAATTTTTAAGAGCGG
+TCACCTCATGGTGGTCAGTGCGTCCCTGCTGATGTGCTCAGTATCACCGC
+CAGTGGGTATTTATGTCAACACCGCCCAGGAGATAATTTATCACCGCAGA
+ATTGGGTTATCTGTATGTTTTTTATATGCATTTAATTTTTTGGCAGGGGG
+CATTGTTGGTAGGTGAGAGATCTGAATTGCTATGTTTAGTGAGTTGTATC
+TATTTATTTTTCAATAAATACAATTGG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/42/4841_5464
+CCAAATTTCAATGGTAAGTAATTATTGAAAAAATAAATAGATACAACTCC
+TAAACATAGCAATTCAGATTCTCCTACAAACAATGCCCCCCTGCAAAAAA
+TAAATAATATAAAAAACACTAGCAGATAACCGATCTGCGGTGATAAATTA
+TCTCTGGCCGGTGTTGACATAAATACCACGTGGTGCGTGATACTGCGAGC
+ACATCAGCAGGACGCACTGACCACCATGAAGGTGACGCTCTTTAAAAATT
+AAGCCCTGAAGAAGGCAGCATTCAAAGCAGAAGGCTTTTGGGCTGGTCGT
+GATACGAAACGAAGCCATTGAGCCGTAATGCGGATTCCGGCATTCAGCTG
+CCAATGTGCCCAATCGTGGGGGGTTTCGCGTTTCAGCGACTCTGCCCGCC
+CACACCGACCCAAAGCTAACTGAGCGAGGGAGCTCAGACATGATGCACAA
+ACACGCGGCTGACACGGCCGCCGCGAACGTCGCGCAAGAGAAACAGGCGT
+CTAATGGAAAGCAGCAAATCCCCTGTTGGTTGGGGTAAGCGCAAAACAGT
+TAACATCGCCCTATTCTCTCGCTGAATCGCAAACCGAAATCACGAGTAGA
+TAAGCGCACTAAATCCGATAGAC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/44/507_877
+CTGAGAGTTAATTTCGCTCACTTCGAAAACCTCTCTGTTTACTGATAAAG
+CTTCCAGATCCTCCTGGCAACTTGCACAAGTGACAACCCTGAACGACCAG
+GCGGTCTCCGTTCATCCTATCGGATCGCCACACTCACCAACAATGAGTGC
+CAGATATAGCCTGGTGGTTCAGGCGGCGCATTTTTATTGCTGTGTTGCGT
+GTAATTCTTCTATTTCTGATGCTGAATCAAGATGCGTCTGCCATCTTTCA
+TTAATCCCCTGAACTGCTTGGTTAATACGGCTTGAGGGTGGGGGAAAATG
+CGGAATAATAAAAAAGGAGCCTGTAGCTCCGCTGATCGATTTTGCTTTTC
+ATGTTCATCGTTCCTTAAAG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/44/923_2037
+CTTTAAGGAACCGAGTGAAAACAGGAAAAAGCAAAATCATCAGGGAGCTA
+CAGGCTCCTTTTTTATTAATTCGCATCACCCTCAAGCGTATTAACCAACA
+GTTCAGGGATTAATGAAAAGATGGCAGACATCATTGAATTCAGCATCAGA
+AATAAGAAGAATTACAGCGAAACACAGCAAATAAAAATGGCCGCCGCCTG
+AACCACCGGCTATATCCTGCTGCCAACTCATTGTTGTGAGTTGTGGCGAT
+CCGATAGATGAAACGAAGACGCCTGGTCGTTCAGGGTTGTCGGACTGTGT
+GCAAGTTGCCAGGAGGATCTGGAACTTATCGTAAACCAGAGAGGTTGAAG
+TGAGGCAAATTAACTCTCCAGGCACTGCCGTGAAGCGGCAGGAGCAGGCA
+ATGCATGACCGACTGGGGATTGTGACGCAGACCTTTTCCATGAATTGGTA
+ACACCATCGATTGTGCTGGAACTGCCTGGATGAACCGGGAAAGAAACCAG
+CAAATACATCAAACGCCGCCGACCAGGAGAACGAGGATATTGCGCTAACA
+GTAGGGAAACTGCGTGTTGAGCCTTGAAACAGCAAAATCAAACACCAACG
+AGCAGCTGAGTATTACGAAGGTGTTATCTCGGATGGGGTAAGCGTATTGC
+TAAACTGGAAAGCAACGAAGTCCGGGGAAGACGAGAAACCAGTTCTTTGT
+TGTTCCGTCCAATCCTGGGAACGACTCCTGCGTTATCAAGCACCTGCAAC
+TGGTGACTGGAAGAGTTTCTGCGGCAGTTAATCGAACAAGACCCGTTAGT
+AACTATCGACATCATTACGCATCGCTATTACGGGGTTGGAGGTCAATGGG
+TTCAAGGATGCCAGGTGAGTATCCTGCATATGAATGTCTGACCGCTGGCA
+TTCGCATCCAAAGGAGAGTGAGATCGGTTTTAGTAAAAAGATAACGCTTG
+TGAAATGCTGAATTTCGCGTCGGTCTTCACAAGAGATGCCAGAGTCTGAG
+TGTCAGAATGATGACCGTACTCAAACATCGGGTTGAGTAATTATCTTACT
+GTTTCTTTACATAAACATTGCTGATACCGTTTTAGCCCTGAAACGACATA
+CATTGCAAGGAGTT
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/44/2083_3176
+AAACTCCTTGCAATGTAGTCGTTTCAGCTAAAACGGTATCAGCAAGCTTT
+ATGTACAAGAAAGCAGTAAGATAATAAGCTCAACCCGATGTTTGAGGTAC
+GGTCATCATCTGACACTAGCAGACTCTGGCTCGCTGTGAAGACGACGCGA
+AATTCAGCATTTTCACAAGCGTTACTCTTTTACAAACGCGATCTCACTCT
+CCTTTGATGCGATGCCAGCGTCAGACATCATATGCAGATACTCACCTGCA
+TCCTGAACCCATTACCTCCACCCCGTAATAGCGATGCCGTAATGATGTCG
+ATAGTTACTAACGGGTCTTGTTTCGATAACTGCCGCAGAAACTCTTCCAG
+GCACCAGTGCAAGTGCTTGAATAACAGGAGTCTTCCCCAGGATGGCGACA
+ACAAGAAACCTGGTTTCCCGTCTTCACGGACTTCGTTGCTTTCCAGTTCT
+AGCAATACGCTTATCCCATCCGAGAATACACCTTCGTAATACTCACGCTG
+CTCGTTGAGTTTTGATTTTGCTGTTTCAAGCTCACACGCAGTTTCCCTAC
+CTGTTAGCGCAATATCCCTCGTTCTCCTGGTCGCGGCGTTTGATGTATTT
+GCTGGTTTTTTTCCCGTTCATCCAGCATTCAGCACAATCGATGGTGTTAC
+CAATTCATGGAAAAGGTCTGCGTCAAAATCCCCAGTCGTCATGCATTGCC
+TGCTCTGCCGCTTAAACGCAGTGCCTGAGAGTTAATTTCGCTCACTTCGA
+ACCCTCTCCTTGTTTTACTGATAAGTTCCAATCCTCCTGGCAACTTGCAC
+AGTCCGACAACCCTGAACCGACCAGGCGTCTTCGTTCCATCATCGGATCC
+GCACACTCACAAACAAATGAGTGGCAGATATCAGCCTGGTGGTCAGGCGG
+CGCATTTTTTACTTGCTGTGTTGCGCTGTAATTCTTCTATTTCTGATGCT
+GAATCATGATGTCTCGCATCTTTTCATCTACATCCTGAACTGTTGGTTAA
+TACGCTTGAGGGTGGGAAATGCGAATAATAAAAAAGGAGCCCTGTAGCTT
+CCCTGATGATTTGTCTTTTCAGCTGTTCATCGTTCCTTAAAGA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/44/3224_4396
+CTTTAGGAACGACTGAACTGAAAAAAAGCAAAATCATCAGGAGCTACAGG
+CTCCCTTTTTATTATTCCGCAATTCCCCCTCAAGCGTATTACCAACCAGT
+TTTCAGGGATTAAATGGAAAGATGGCAGACCATCATTGATTCAGCCCATC
+AGAAATAGAAGAATTACAGCGCAACCAGCAAATAAAAATGCGGCCGCCTG
+ACCACCAGGCTATATCTGCCACCTCATGTGTGTGAAGTTGTGGCGTCCGA
+TAGATTTTGAACGAAGACGCCTGGTTCCGTTCAGGGTTTTTGTCCGCGAA
+CTTGTGCCAAGTTGCAGGAGCGATCCTTAGGAACTTATCAGTAACAGAGA
+GGGTTCGAAAGTGAGCCGAAATTAACTCTCAGGCACCTGCGGGAAAGCGG
+CAAGAGCAGGCAATGGCAATGCGACTGGGGATTTGACGCAGATTTTCCCC
+CCTGAAATTGGTAGACACCATCCGATTGTGCGGGAACTTGGCTGGACTGG
+AACGGGAAAAGAAACCAGGCATACATCCAAACGCGGCGACCAGGAGAACG
+AGGAATATTGCGCTAACAGTAGGGAACTGCGGTGTGAGCTTGAAAACAGG
+CAAAATCTCAAAACTCAACGAGCTGCGGTGAGGCTATTTACGAAGGGTGG
+TTATCTCGGATGGGAGTAAAAAGCCGTATTGCTAAACTGCGAAAGCAACT
+GAAGGGTCCGTGGAGACCGGAAAACAGTGTTCTTTGTTGTTCGCCATCCT
+GGGAGACTCCCTGTTATCAAGCACTGCACTGGGGACCTGAAGAGTTTCTG
+GCGGCAGTAATCGAACAAGACCCGTTAGTAACCTATCGAACATCATTACG
+CAATCGGCTATTACGCGGGTGGAGGTCACATGGGTTTCCAGGATGCCAGG
+GTGGGAGTAAATCTGCCCCATATGAATGTCTGACCGCTGGCCATTCGCAT
+CAAAGGGGAGAGTGAGGATCGGGTTTTTTAAAAGATTAACGTTCGTGAAA
+ATGCTGAATTTCGGCCGGTCCGTCCTTCACAGCGATGCCCCAGAGTCTGT
+AATGTCCGGATGAAATGCCCGTATCAACATCCGGGGTTGAGTATTATCTT
+ACTGTTTCCTTTTACATAAACCATTTGCTGATACCGTTTAGTTCTGAAAC
+GACATACCATTGCAAGGAGTTT
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/44/4449_4913
+AAACTCCTTGCCAATGTATGTCCCGTTTTCAGCTAAACCGTAATCACAAT
+GTTTTAAATGTAAAGAAACAGTAAGATAATACCTCCAACCCGATGTTTGA
+AGTAACGGTCATCATCTGGACAACTACAGACTCTGGCATCTGCTTGTGCA
+GAACCGACGCGAAAATTCAGCATTTCAGCAAGCGTTATTCCTTTTACAAA
+ACCGATCCTCAACTCTCCCTTTGATGCCGAATGCCAGCGGGTCCAGACAT
+CATCATTGCAGAATACTCACCTGCCCATCCTGAACCCATGACCTCCAACC
+CCGTAATAGCGATCGCGTAATGATGTCGATATACTAACGGGGTCCTTGTT
+CATTAACCTGCCGCAGAAACCTCTTCCAGGTCCCACCCAGTGCCAGTGGC
+TTTGCAACAACCAGGAGTCCCTTCCCAGATGGCGGAAACAAAAACAAAGA
+AACTTGGTTTCCCA
diff --git a/tests/data/ecoli_lp.fofn b/tests/data/ecoli_lp.fofn
new file mode 100644
index 0000000..06c29ac
--- /dev/null
+++ b/tests/data/ecoli_lp.fofn
@@ -0,0 +1,2 @@
+/home/UNIXHOME/yli/yliWorkspace/private/yli/data/testLoadPulses/m121215_065521_richard_c100425710150000001823055001121371_s1_p0.pls.h5
+/home/UNIXHOME/yli/yliWorkspace/private/yli/data/testLoadPulses/m121215_065521_richard_c100425710150000001823055001121371_s2_p0.pls.h5
diff --git a/tests/data/example_read.fasta b/tests/data/example_read.fasta
new file mode 100644
index 0000000..b3d19b3
--- /dev/null
+++ b/tests/data/example_read.fasta
@@ -0,0 +1,5 @@
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/13/0_3797
+GCTGTTTTCTCCAGCGCAGCACCGTAAATTACTGCTGAGCCATCATGACG
+CCGATGGAGCCTGTCCGGGCGGTCCCTGGCGTGACCAGACGCCGGAGGCG
+GCACTGGCAAGCAACTACCTGCACTGCAGTTCATGTGTTGGCAACCGCCC
+ATACCGGTTTATGTCCACGCACACGGGCGATAGTCAGCGCCGTCCAAATG
diff --git a/tests/data/example_ref.fasta b/tests/data/example_ref.fasta
new file mode 100644
index 0000000..8098cc0
--- /dev/null
+++ b/tests/data/example_ref.fasta
@@ -0,0 +1,62 @@
+>example_reference
+CCGCATATTGCCAGCATGGCCTTTAATGAGCCGCTGATGCTTGAACCCGCCTATGCGCGG
+GTTTTCTTTTGTGCGCTTGCAGGCCAGCTTGGGATCAGCAGCCTGACGGATGCGGTGTCC
+GGCGACAGCCTGACTGCCCAGGAGGCACTCGCGACGCTGGCATTATCCGGTGATGATGAC
+GGACCACGACAGGCCCGCAGTTATCAGGTCATGAACGGCATCGCCGTGCTGCCGGTGTCC
+GGCACGCTGGTCAGCCGGACGCGGGCGCTGCAGCCGTACTCGGGGATGACCGGTTACAAC
+GGCATTATCGCCCGTCTGCAACAGGCTGCCAGCGATCCGATGGTGGACGGCATTCTGCTC
+GATATGGACACGCCCGGCGGGATGGTGGCGGGGGCATTTGACTGCGCTGACATCATCGCC
+CGTGTGCGTGACATAAAACCGGTATGGGCGCTTGCCAACGACATGAACTGCAGTGCAGGT
+CAGTTGCTTGCCAGTGCCGCCTCCCGGCGTCTGGTCACGCAGACCGCCCGGACAGGCTCC
+ATCGGCGTCATGATGGCTCACAGTAATTACGGTGCTGCGCTGGAGAAACAGGGTGTGGAA
+ATCACGCTGATTTACAGCGGCAGCCATAAGGTGGATGGCAACCCCTACAGCCATCTTCCG
+GATGACGTCCGGGAGACACTGCAGTCCCGGATGGACGCAACCCGCCAGATGTTTGCGCAG
+AAGGTGTCGGCATATACCGGCCTGTCCGTGCAGGTTGTGCTGGATACCGAGGCTGCAGTG
+TACAGCGGTCAGGAGGCCATTGATGCCGGACTGGCTGATGAACTTGTTAACAGCACCGAT
+GCGATCACCGTCATGCGTGATGCACTGGATGCACGTAAATCCCGTCTCTCAGGAGGGCGA
+ATGACCAAAGAGACTCAATCAACAACTGTTTCAGCCACTGCTTCGCAGGCTGACGTTACT
+GACGTGGTGCCAGCGACGGAGGGCGAGAACGCCAGCGCGGCGCAGCCGGACGTGAACGCG
+CAGATCACCGCAGCGGTTGCGGCAGAAAACAGCCGCATTATGGGGATCCTCAACTGTGAG
+GAGGCTCACGGACGCGAAGAACAGGCACGCGTGCTGGCAGAAACCCCCGGTATGACCGTG
+AAAACGGCCCGCCGCATTCTGGCCGCAGCACCACAGAGTGCACAGGCGCGCAGTGACACT
+GCGCTGGATCGTCTGATGCAGGGGGCACCGGCACCGCTGGCTGCAGGTAACCCGGCATCT
+GATGCCGTTAACGATTTGCTGAACACACCAGTGTAAGGGATGTTTATGACGAGCAAAGAA
+ACCTTTACCCATTACCAGCCGCAGGGCAACAGTGACCCGGCTCATACCGCAACCGCGCCC
+GGCGGATTGAGTGCGAAAGCGCCTGCAATGACCCCGCTGATGCTGGACACCTCCAGCCGT
+AAGCTGGTTGCGTGGGATGGCACCACCGACGGTGCTGCCGTTGGCATTCTTGCGGTTGCT
+ATCGGCGTCATGATGGCTCACGGGAAATACGGTGCTGCGCTGGAGAAAAAGGGTGTGGAA
+ATCACGTTGATTTACAGCGGCAGCCATAAGGTGGATGGCAACCCCTACAGCCATCTTCCG
+GATGACGTCCGGGAGACACTGCAGTCCCGGATGGACGCAACCCGCCAGATGTTTGCGCAG
+>2
+CCGCATATTGCCAGCATGGCCTTTAATGAGCCGCTGATGCTTGAACCCGCCTATGCGCGG
+GTTTTCTTTTGTGCGCTTGCAGGCCAGCTTGGGATCAGCAGCCTGACGGATGCGGTGTCC
+GGCGACAGCCTGACTGCCCAGGAGGCACTCGCGACGCTGGCATTATCCGGTGATGATGAC
+GGACCACGACAGGCCCGCAGTTATCAGGTCATGAACGGCATCGCCGTGCTGCCGGTGTCC
+GGCACCCTAGTGAGCCGGACGCGGGCGCTGCAGCCGTACTCGGGGATGACCGGTTACAAC
+GGGATTATCGCCGGTCTGCAACAGGCTGCCAGCGATCCGATGGTGGACGGCATTCTGCTC
+GATATGGACACTCCCGGCGGGATGGTGGCGGGGGCATTTGACTGCGCTGACATCATCGCC
+CGTGTGCGTGACATAAAACCGGTATGGGCGCTTGCCAACGACATGAACTGCAGTGCAGGT
+CAGTTGCTTGCCAATAGAACCTCCCGGCGTCTGGTCACGCAGACCGCCCGGACAGGCTCC
+ATCGGCGTCATGATGGCTCACAAAGGTTACGGTGCTGCGCTGGAGAAACAGGGTGTGGAA
+ATCACGCTGATTTACAGCGGCAGCCAGGGGTGGATGGCAACCCCTACAGCCATCTTCCGA
+GATGACGTCCGGGAGACACTGATCTCCGGAATGGACGCAACCCGCCAGATGTTTGCGCAG
+AAGGTGTCGGCATATACCGGCCTGTCCGTGCAGGTTGTGCTGGATACCGAGGCTGCAGTG
+TACAGCGGTCAGGAGGCCATTGATGCCGGACTGGCTGATGAACTTGTTAACAGCACGAAT
+GCGATCACCGTCATGCGTGATGCACTGGATGCACGTAAATCCCGTCTCTCAGGAGGCAGA
+>3
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAA
+CCGCATATTGCCAGCATGGCCTTTAATGAGCCGCTGATGCTTGAACCCGCCTATGCGCGG
+GTTTTCTTTTGTGCGCTTGCAGGCCAGCTTGGGATCAGCAGCCTGACGGATGCGGTGTCC
+GGCGACAGCCTGACTGCCCAGGAGGCACTCGCGACGCTGGCATTATCCGGTGATGATGAC
+GGACCACGACAGGCCCGCAGTTATCAGGTCATGAACGGCATCGCCGTGCTGCCGGTGTCC
+GGCACCCTAGTGAGCCGGACGCGGGCGCTGCAGCCGTACTCGGGGATGACCGGTTACAAC
+GGGATTATCGCCGGTCTGCAACAGGCTGCCAGCGATCCGATGGTGGACGGCATTCTGCTC
+GATATGGACACTCCCGGCGGGATGGTGGCGGGGGCATTTGACTGCGCTGACATCATCGCC
+CGTGTGCGTGACATAAAACCGGTATGGGCGCTTGCCAACGACATGAACTGCAGTGCAGGT
+CAGTTGCTTGCCAATAGAACCTCCCGGCGTCTGGTCACGCAGACCGCCCGGACAGGCTCC
+ATCGGCGTCATGATGGCTCACAAAGGTTACGGTGCTGCGCTGGAGAAACAGGGTGTGGAA
+ATCACGCTGATTTACAGCGGCAGCCAGGGGTGGATGGCAACCCCTACAGCCATCTTCCGA
+GATGACGTCCGGGAGACACTGATCTCCGGAATGGACGCAACCCGCCAGATGTTTGCGCAG
+AAGGTGTCGGCATATACCGGCCTGTCCGTGCAGGTTGTGCTGGATACCGAGGCTGCAGTG
+TACAGCGGTCAGGAGGCCATTGATGCCGGACTGGCTGATGAACTTGTTAACAGCACGAAT
+GCGATCACCGTCATGCGTGATGCACTGGATGCACGTAAATCCCGTCTCTCAGGAGGCAGA
diff --git a/tests/data/lambda.rgn.h5 b/tests/data/lambda.rgn.h5
new file mode 100644
index 0000000..d5c6c62
--- /dev/null
+++ b/tests/data/lambda.rgn.h5
@@ -0,0 +1 @@
+# This is an aritifcial region table.
diff --git a/tests/data/lambda.sam b/tests/data/lambda.sam
new file mode 100644
index 0000000..8eb0acf
--- /dev/null
+++ b/tests/data/lambda.sam
@@ -0,0 +1,21 @@
+ at HD VN:1.3.1
+ at SQ SN:lambda_NEB3011 LN:48502 M5:a1319ff90e994c8190a4fe6569d0822a
+ at RG ID:f7d81fcc44 PU:/net/usmp-data3-10g/ifs/data/unixhome/yli/yliWorkspace/software/bioinformatics/tools/pbalign/tests/data/lambda.fasta SM:/net/usmp-data3-10g/ifs/data/unixhome/yli/yliWorkspace/software/bioinformatics/tools/pbalign/tests/data/lambda.fasta
+ at PG ID:BLASR VN:1.3.1.121192 CL:blasr /net/usmp-data3-10g/ifs/data/unixhome/yli/yliWorkspace/software/bioinformatics/tools/pbalign/tests/data/lambda.fasta /net/usmp-data3-10g/ifs/data/unixhome/yli/yliWorkspace/software/bioinformatics/tools/pbalign/tests/data/lambda_ref.fasta -sam -out /scratch/vUoNZr.sam -bestn 10 -nproc 15
+ at PG ID:SAMFILTER VN:v0.1.0 CL:samFilter /home/UNIXHOME/yli/yliWorkspace/software/assembly/cpp/pbihdfutils/bin/samFilter /scratch/vUoNZr.sam /net/usmp-data3-10g/ifs/data/unixhome/yli/yliWorkspace/software/bioinformatics/tools/pbalign/tests/data/lambda_ref.fasta /scratch/bP2PvR.sam -minPctSimilarity 70 -minAnchorSize 12 -minAccuracy 70 -minLength 50 -seed 1 -scoreSign -1 -hitPolicy randombest
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/105/0_2152/0_2152 0 lambda_NEB3011 25317 254 14M1I7M1D16M1D22M1I19M1I4M1I7M1I3M2I5M1I9M2I5M1I27M1I5M1D2M1I4M1I5M2I3M1I14M1D5M1I7M2I12M1D3M1I3M1D5M1I7M1D4M1I1M1I3M1D1M1D4M1I10M1D9M1I1M1I1M1I14M1I9M1D8M1I26M1I6M1I3M1I31M1I2M1I20M1D22M1D3M1D4M1I8M1I12M1D21M1I7M1I27M1I58M1I16M1I5M1I2M1I17M1I14M1I13M1I1M1D16M1D7M1I5M1I3M1I32M1I25M1D30M1I14M1I12M2I20M1I21M1I25M1D7M1I6M1I1M1I7M1I15M1I7M1I12M2I36M2I44M1I6M1I3M1I11M1I2M2I1M1I9M1D20M1D4 [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/115/1304_3321/0_2017 16 lambda_NEB3011 26981 254 58M1D9M1D5M2I25M1I7M1D12M1D20M1I29M1I13M1I30M1D57M1D13M1I5M1I17M1D8M1I14M1I3M1D6M1I1M2I6M1I10M2I32M1I32M1D2M1I14M1I17M1I8M1D1M1I27M1D8M1I4M1I3M1I30M1I10M1D10M1I6M1D5M1I28M1D8M1I6M1I1M1I7M1I1M1D19M1I5M1I25M1I29M1I6M1I17M1D10M1I16M3I2M1I22M1I4M1D8M1D8M1I7M1I21M1I2M1I2M2I11M1I43M1I40M3I22M1I41M1I13M1I7M1D7M1D23M1D4M1I14M1D3M1I5M1I5M1I3M1I7M1I6M1D29M1I14M1I19M2I10M1I3M1I3M1I14M1D13M [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/115/3365_7852/0_4487 0 lambda_NEB3011 26972 254 17M1I19M1D18M1I21M2I14M1I10M1D19M1D20M1D4M1I11M1I11M1I6M1I32M1D10M1D10M1I7M1I4M1I20M1I31M1D2M1D15M1D2M1I11M1I17M1I14M1D14M1D7M1I17M1D6M1I8M1D5M1D11M1I11M1I8M1I21M1I22M1I6M1I20M1I21M2I5M1I4M1I5M1I5M1D26M1D39M1D12M1I4M1D8M1D6M1I4M1D4M1I37M1D20M1I12M1I7M1D12M1I24M1D7M1I2M1I3M2I8M1I6M1I2M1I5M1D3M1D60M1I4M1I8M1D10M1I3M1I27M1I14M1I4M1I14M1I5M1I21M1I31M1I10M1I8M1I13M1D58M1I6M1I6M1I12M1I [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/115/7896_11181/0_3285 16 lambda_NEB3011 28177 254 14M1I7M1I32M1D6M1I5M1I22M1I34M1D15M1D6M1I13M1I4M1I4M1I7M1I1M1I1M1D21M1I3M1I6M1I5M1I20M1D3M1I4M1D24M1I5M1I7M1I6M2I4M1D6M1I7M1I7M1D5M1I3M2I23M1D12M1I6M1I2M1I4M1D35M1I1M1I2M1D17M1D4M1D5M1I12M1D4M1D12M1I10M1I1M1I15M1I2M1I34M1I4M1I5M1I12M1I17M1I5M1D3M1D12M1I4M1I3M1I9M1I2M1I4M1D4M1I4M1I8M1D11M1D19M1I6M1I17M1D29M1D14M1I20M1I4M1D6M1D17M1I25M1I29M1I1M1I5M1I2M1D2M1I4M1D9M1I23M1D4M2I4M1D6 [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/13/0_3797/0_3797 16 lambda_NEB3011 1302 254 5M1D24M1D20M1D6M1I6M1I18M1I4M1I14M3I37M1I12M1I23M1I1M1I2M1D39M1I26M1D9M1D8M1D23M1I5M1D4M1I1M1I4M1I4M1I8M1I11M1I1M1D11M1D4M1I3M1D22M1I8M1D1M1D12M1I5M1I10M1I8M1D2M1I19M1I8M2D31M1I10M2I14M1I1M1I16M1I1M1I12M1D1M1D29M1I4M1D10M1I20M1D4M1D28M1I15M1D5M2D5M1D6M1D20M1I1M1I12M1I1M1I8M1I4M1D3M1I3M1I3M1I27M1D8M1D21M1D7M1D4M1I7M1I11M1D11M1D6M1I19M1I5M1I2M1D7M1I2M1D8M1I7M1D2M2D12M1I3M1I13M1D5M1D45M [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/14/0_1593/0_1593 16 lambda_NEB3011 19821 254 15M1I3M1I29M1I6M1D12M1I4M1I14M1I1M1D9M1D8M1I1M1I35M1I16M1I1M1I13M2I19M1D7M1I13M1I20M1D2M1I3M1I9M1I3M1I2M1I10M1D4M1I19M1I2M1I20M1I1M1I5M1D6M2I11M1D10M1D36M1I6M1D5M1I41M1D3M1D2M1D5M1D19M1I17M1I14M1I5M1D14M1I4M1D6M2I10M1D10M1I5M1I1M1I7M1I3M4I16M1D25M1I1M1I2M2I3M2I37M1D6M1I2M2I2M1D12M1I2M1I1M1I1M1I13M1I3M1I44M1D1M1I15M1I2M1I30M1I15M1I10M1D4M1I30M1I5M1I8M1I20M2I36M1D31M1I20M1D8M1I6M1I8M1 [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/147/0_6711/0_6711 16 lambda_NEB3011 6727 254 9M1D2M1I4M1I6M1D14M1I26M2I9M1D2M1I17M2I12M1I20M1I17M1D15M1I25M1I4M1I3M1I9M1I37M1I8M1I28M1I4M3I5M1I7M1I17M1D5M1I6M1D10M1I4M1D11M1I2M1I3M1I21M1D1M1I10M1I26M1I24M1I17M1D9M1I1M1I7M1I3M1I1M1I35M1I5M1I6M1D5M1I3M3I3M1I20M1D5M1D3M1I3M1I10M1I3M1I18M1D10M1I5M2I6M1D10M1I34M1I8M1I16M1I18M1D4M1I34M1I3M1D29M1I21M1I2M1D31M1D9M1I27M1D53M1D7M1I9M2I1M1D19M1I12M1I59M1I8M1D5M1I39M1D1M1D14M1D5M1I10M1I13 [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/171/2019_3396/0_1377 0 lambda_NEB3011 38857 254 3M1D22M1D2M1I43M1D4M1I28M1I2M2I3M1I7M2I7M1D4M1I17M1I8M2I5M1I10M1D9M2I5M1I4M1I23M1I5M1D3M1D5M1I5M1I22M1I4M1D8M1D10M1D3M1D4M1D21M1I6M1D7M1D5M1I4M1I8M2I5M1I2M1D6M1D12M1I4M1I1M1I7M1D10M1D2M1D19M1I2M1I5M2I11M1I15M1D8M1I4M2I4M1I25M1I7M1I11M1D8M3I6M1I12M1I2M1I6M1I5M1I3M1I1M1D5M1I1M1D6M1I2M3I17M1D4M1I8M1I1M1I2M1D2M1D7M2I20M2I3M2I12M1I2M1I2M1I1M1I2M1D3M1D1M1D4M1I7M1D9M2I5M1D23M1D4M1D13M2D [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/180/0_2599/0_2599 0 lambda_NEB3011 40112 254 8M3I8M1I8M1I13M1I14M1I1M1I7M1I25M2I10M1D13M1D10M2I22M1D7M1I8M1I11M1D10M2I2M1I16M3I2M1I8M3I1M1I5M1I1M2I1M1I1M1I14M1I2M1I5M1I9M1D8M1I6M1D3M1D2M3I1M1I3M1I17M1I8M1I2M1I6M1I5M1I12M1D12M1I25M1I4M1D6M1D5M1I2M1I48M1I14M1D2M2I4M1D12M1I26M1I3M1D8M1I6M1D25M1D2M2I11M1I9M1D2M1I8M1I3M1I2M1I8M1I2M1I4M1I2M2I1M1I2M1I7M1I1M3I2M1I6M7I5M1I14M3I2M2I2M1I5M1I2M3I3M1I4M1I2M5I4M3I1M1I1M1I1M1I7M2I4M1I2M4I7M2 [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/180/2645_6512/0_1950 16 lambda_NEB3011 40647 254 29M2I5M1D20M1I7M1I10M1I4M1I1M1I25M1I18M1I18M1I2M1D3M1I25M2I2M2I23M1D2M1I2M1I15M2I6M1I4M1I5M1D17M1I51M1I8M1I17M1D4M1I6M1D3M1I8M1I9M1I1M1I2M1I3M1I28M1I5M1I2M1D15M1I10M1I2M1I5M1I13M1D8M1I11M1D3M1D8M1I12M1I22M1D24M1D11M1D1M1D14M1I19M1I17M1I58M1D18M1I6M1I7M2I5M1I9M1D11M1D15M1I3M1I34M1I15M1D23M1I9M1D10M1I33M1D9M1I12M1I2M1I17M1D10M1D7M1I4M1D10M1D12M1I7M1D1M1D14M1I6M1I38M1I5M1I7M1I21M1D [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/28/0_1464/0_1464 0 lambda_NEB3011 40287 254 10M1D11M1I1M1I29M1I23M1D2M1I6M1D3M1I11M1D5M1I13M1I2M1I3M1I13M1I12M1I18M1I25M1I40M1I7M1I20M1I13M1I7M1I28M1D9M1I5M1I21M1I7M1I3M1I8M2D36M1D9M1D2M1I16M1I31M1I30M2I25M2I11M1I15M1I42M1I34M1D16M1I33M1I1M1I7M1D3M1D15M1I12M1I5M1D13M1I31M2I6M1I5M1I7M1I12M1I1M1D11M1I16M2I14M1I30M1I12M1I9M1I19M1I5M1D11M1D14M1I35M1D16M1D21M1I6M1D9M1I19M1D24M1I70M1I2M1D17M1D11M1I1M1I20M1I28M1I4M1I4M1I9M1I27M1I3M1I [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/45/0_2526/0_2526 16 lambda_NEB3011 2041 254 8M1I6M1I2M1I6M1D12M1I29M1I23M1D5M1D16M1D12M1I9M1D23M1I5M1D15M2D10M1I26M1I4M1I10M1D4M1D3M1D6M1D5M1I2M1I4M1I5M1I21M1D4M1D3M1D14M1I2M1I1M1I4M1D1M1I8M1I9M1D17M1D2M1D21M1I1M1I9M1I14M1I17M1I5M1I7M1I5M3I4M1I25M1D14M1D11M1I1M1I30M1I12M1I7M1D27M1D1M1D8M1D10M1I9M1I39M1I5M1I10M1I10M1D15M2I3M2I1M1I12M1D11M1D2M2I2M1I3M1I2M1D8M1I50M1I13M1D10M1D8M1I3M1I7M1I3M1D8M2I7M2I16M1I5M1D7M2I15M1I6M1I5M1I2M1I [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/47/0_1953/0_1953 16 lambda_NEB3011 11636 254 9M1I2M1D13M1I1M3I5M3I28M1D6M1I28M1I18M1I1M1I8M1I4M1D9M1I5M1I2M1D4M1I53M1I3M1I11M1D3M1I8M1I14M1D37M1I35M1I14M1D32M1I2M1I6M1D12M1I2M1D37M1I2M1I13M1I1M1I46M1D8M1D10M1I38M1D2M1I28M1D15M1D3M1I5M1I18M1I2M1I4M1I1M1I23M1D4M1D5M1D1M1D3M1D4M1I6M1I30M1I16M1I4M1D26M1I5M1I7M1D4M1I13M1I16M1I3M1D48M1I7M1D11M1D1M1D19M1I28M1D6M1D16M2I10M1D2M1I6M1I11M1I10M2I6M1I10M1I5M1I1M1I19M1I5M1I12M1I16M1D1M1D7M1 [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/49/0_7870/0_7870 256 lambda_NEB3011 30502 254 26M1I7M1D14M1I28M1I24M1D3M1D3M1I4M1I25M1I13M1D4M1I77M1D15M2I23M1I23M1I12M1I8M1D5M1I7M1I16M1D16M1I31M1I9M1I7M1I9M1D1M1I4M1D9M1D2M1D2M1I8M1I35M1I5M1I18M1I2M1I9M1I2M1D4M1D17M1I8M1I24M1D3M1I30M1D2M1I16M2I18M1D20M1D3M1I6M1D11M1I8M1D21M1I2M1I2M1I25M1D4M1I7M1D11M1D26M1D3M1I18M1D3M1I7M2I10M1D7M2I36M1D5M1I27M1D13M1D5M1I2M1I13M1D8M1D18M1D17M1D8M1I28M1D9M1D10M1D2M1D4M1I2M1I8M1I9M1I16M1D8M1I11 [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/53/0_1306/0_1306 16 lambda_NEB3011 35500 254 11M1I1M1I1M1I8M1I4M1I4M1I22M1I2M1I4M1D2M1I24M1D39M2D5M1I10M1I5M1I15M1I13M1I18M1D16M1I3M1I14M1I1M1I4M1I4M1I19M1D7M1I7M1I2M1I46M1I7M1D14M1D3M1I1M1I18M1D8M2I40M1D17M1D13M1D10M1I4M1I20M1I26M1I10M1D13M2I5M1I10M1I4M1I2M1I8M1I26M2I9M1D25M1I26M1D22M1I2M1D2M1D3M1I14M1I2M1I21M1D8M1D21M1D4M1I11M2I25M1D8M1I8M1I15M1I13M1D9M1D6M2I5M1D1M1I3M1I5M1I21M1D21M2D30M1I8M1I25M1I15M1I36M1I12M1I1M1I16M1I7M1 [...]
+m120619_015854_42161_c100392070070000001523040811021231_s1_p0/70/0_3728/0_3728 0 lambda_NEB3011 31688 254 12M1I18M1I8M1D6M1D4M2I25M1I7M1I10M1D13M1D6M1I9M1I5M1I22M1I26M2I2M2I6M1I7M1I1M1D6M1I14M2I13M2I4M1I1M1I3M1I2M1I3M1D20M1I2M1D5M1I12M1I1M2I22M1I18M1I10M1I21M1I44M1I7M1D23M1D23M1D9M1I1M1D15M1D2M1I26M1I7M1D8M1I13M1I1M1D7M1I8M1D13M1I2M1I5M2I12M1I2M1D5M1D1M1D29M1D5M1I11M1D25M1D12M1I7M1I12M2D4M1I14M1I1M1D9M1I5M4I10M1D3M1D12M1D4M2I30M1D11M1I1M1I1M1D12M1I7M1D4M2I5M1D69M1I13M1D5M1D1M1D5M1I7M1I13 [...]
diff --git a/tests/data/lambda_bax.fofn b/tests/data/lambda_bax.fofn
new file mode 100644
index 0000000..80b3bd2
--- /dev/null
+++ b/tests/data/lambda_bax.fofn
@@ -0,0 +1 @@
+/home/UNIXHOME/yli/yliWorkspace/private/yli/data/testLoadPulses/m130302_011223_pd1_c000000092559900001500000112311511_s1_p0.2.bax.h5
diff --git a/tests/data/lambda_query.fasta b/tests/data/lambda_query.fasta
new file mode 100644
index 0000000..f305b10
--- /dev/null
+++ b/tests/data/lambda_query.fasta
@@ -0,0 +1,1000 @@
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/13/0_3797
+GCTGTTTTCTCCAGCGCAGCACCGTAAATTACTGCTGAGCCATCATGACG
+CCGATGGAGCCTGTCCGGGCGGTCCCTGGCGTGACCAGACGCCGGAGGCG
+GCACTGGCAAGCAACTACCTGCACTGCAGTTCATGTGTTGGCAACCGCCC
+ATACCGGTTTATGTCCACGCACACGGGCGATAGTCAGCGCCGTCCAAATG
+CCACCCGCCACCATCTCCGCCGCGTGTCCCATATCGAGCAGAATAGCCGT
+CCACACATCGATGCTGGCAGCCTGTTGCCAGAGGGCGATAATGCCGTGTA
+AACCGTCATCATCCCCGGAGTACGGCTGCAGCGCTCCGCGGTCCGCCTGA
+CAGCGTGCCGACACCGGCAGCACGGCGATGCCGTTCATGACGATAACTGC
+GGGCCTGTCAGAGTTGGTCCCTCATCATCACCGGATAAATGAGGCCAGCG
+TCGCGAGTGCCTCCTGGGCAGTCAGGCTGTAGCCGGACACCGCATCCGTC
+AGGCTGCGATCCAAGCGGCCTGCAAGCCGCCACAAAAGAAAACCCGCGCA
+TAGGCGGTTCAAGCATCAGCCGGCTCACTTAAAGCCATGCTGGTCAATAT
+GCGGGAGATTACGGCAGCTCTGCTGTCACTCTTCTCCTCCTCTGTTGATT
+GTCCGCAGCCCGGATTGATCAAATGCCGCGCCCGCCCAGTGCGGCCGGTT
+TAAGACCGGCTGCACGGCGTCTCCATCGTTTCACGGACCTGCCTGGCAAA
+AATTTCCTGATAGTCGTCCACCGCGTTTTTGCGCACCTTCTCGTGGTAAC
+TCAGCCGGCTTTCTATCACATCCACCGCTTCCCTGACTTTCTTCAGACCA
+TCCGATGCCATACGACGGGGGGGGGGGGCGGGGGGGAGCCTATCCAGTCG
+CAGTTCGCGCGCCAGCACTGCGGGCTTCTGAAAACGAAGCGCGCTTTGAA
+GGTAACGTCACACGCGCGACGATGGCCTCTTCCAGCCAGCACAGAAACAT
+CTGGCTCGCCTGACGGGATGCGAGCGAATTTTTCGCCTGTTGCCGCCCCA
+TAAAGTAACGTCCCAGCGACTGCGTTCGCACTGGCCCGTGCCCGTGGAGT
+AGCTCATCTGGGCGTAATCTCCGGGAAAAGCTCCTCATACAGACCCTCCA
+GCCGGCAAGCGATATACCCGCAGCAGTGACGCTCAAACACGGAGTAGCCC
+GTTATCCGTATCCTTGAGCCGTCTGCAGGTTCAGTGAGTCCACCCGGCAT
+CAGTGCAGTAGCTTTGCGCCTCCCAGCCGGACGGCGCTGCGGCTTAATAC
+GCGGCAATTCACCCATCCACCGCGGTCAGCCTTTCCCGCGCGCCTGATGT
+TCGCGCCAGAATACAAATACCATCGCTGACTGCTATCCAGCTCACCTCCA
+ATGGTGCGCGGGCATACAATCGCCTTTCCACAATGGCGCTCTGCAGCTGC
+GTTGTTCTTGCAGCGTGTCCCGAGCATCTTCATCTGCTCCATCACGCTGT
+AAAACACCATTTGCACCGGCGGAGTCTGCCCCGTCCTCCACGGAGTTCAA
+AAACGGAGAGAGCGCGCCGCCGTGTAATCACGGGTATTCCATGTCCCATT
+TCTGCGGCAATCAGCCAGGATAACCCGTCCTCGCTGACGTAATATCCCAG
+CCCCGGCACCGCTGTCATTAATCTGCACACCGGCCACAGGCGTTCCGGCT
+GTCCGCGTATTGTTCGGGTTGCTATGCCGCTTCCGGCTGACCATCCGAAC
+CTGTGTCCGGAAAAGCCGCGACGAATGTATCCCAGGTGGCCTGAACGAAA
+TTCACCCGTAAAGCAGTCTGCAACAACCTTCACGAACATCATGGTAAACG
+TGCAGTTTCCGCTCAACGTCAATGAAAGCAGCATCATCCTCGGCAAACTC
+TTTCATGCCTTCAACCTCCGCGGGGAAAAGCACGGCTCTTCCTCCCCGAT
+CCCCATATAGCGCCAGCTTGGGCGATGACTGAGCGCCGGAAAAAAGACCC
+GACGATATGATCTGATGCAGCGGATGGCGTTGCGGCATAGCCGTTATGCG
+TACCAGATCGTCTGACGCGGGCATTGCCACGGTAAAGTGGGTCACATGCT
+GCATCCACACTTTCCACTCGGTGGGTCCACAACCGCAACTGCCTCCAAAG
+TCGCATCGCCACCGCCGTGATAATCCGGCATATTCGCGAGCGATTGTCAT
+GCCGTCCGGCCCAGAAGGGTGGAATGGTCCTTCCCATAAAAAATGCCTGC
+AGTCCCCTGCTCGCTGTGTCATGCCGGTCTGCACTTCCAGCTCTGCAATA
+TAATTTTTTCAGGTCAGACACGGAAGGGCCGTAACTCCACCCTTCGTACT
+CTTTCTGTACTGTTGCCACCCGTTTACCTTCACAGGTCATGCAGTCGCAA
+CGGGGCAGCGCGCAATCTCTTCCCTGTCCCCGCGTCATTCATGCCCTCTC
+CGATAAGGCACGGGCGGTAATCTGCCAGTGTTTTGTCTTTAGTTGCGTGC
+TGCCCATCCTCCTTCCTGACAGGCCTCCAGCAGCCACTGCGACCAGCTGC
+CAGCGGGAATACCTGATGCGCAGCCCGCCGGACCAGCCGCATAAACGAAG
+CAGTCGAGTGCCTCATATTCGTCGCTTTTTGCTGTCCCAACAGTATTATT
+TTTCCTGCCATCCCACCCATTTTTCGACCTGCTCTTCAGCAGTCAGTCGC
+TGCGCTTCGGTCAGATCACAAATAATCCGGTTATTCGGAAGTGAACGGCA
+CCGGGAAGCGGTCCATACCCCTTCCCGCCGTCAGTGTGAAGCGGTTATAA
+TATCTGCCTCTTTTCGCGTATCCGTACCGATTTCGGTAAGGTAAACTCCG
+TTTTTGTTTCGCTACGTGCATGCTGGCCACACGGCCTTTCCGTAGACATC
+CCCTTTGAATGGGGACACCCCGGAAAGCCCCATGGTTTTTTCGAGCGTTC
+ATACCACAATGTCGGGTCAATCCGCCAGTATCGCCAGCAGAATACGGTTA
+TCACATTTCTGCACCATTCCGGCGGTATAGGTTTATTGATGGCCTCATCC
+ACACGCAGCCAGCCGTCCTGTCATACGTCGTGGCCGGGCCCATAATAATT
+CCTGCCGGTCAATCAGCCAGCTTCCTCCCCGGCCCATCCCATACGCGCAT
+TTCCGTAGCGGTCCAGCTGGGAGTCGATACCGCGGCAGGTAAGCCACAAG
+GTCAGCGAACGGGCGCGAATAAATGCTCTTTCCGCTCTGCCATCACTTCA
+CTCCGGCCGTTCGCCTCAATTTTCGCCTCCCACCGGTCTCACCGAGCGTC
+GGGTGTTTACGAAAGGTTTTACGTTTTCCCGTATCGCCTTTCGTTCATCC
+AGGTCTTTGACAATCTGCACCTCAGTGGTGAAGCGGGCTGTACATCTGTC
+CCAGATGTGAAAGCACACTGTCCAGGTGGCTCAATCTCTTCACCGATGGA
+CGAAACCAGAGAAGCCCATCACGGGTCCCAGATCCTCGGTCCTTTGTCCG
+CAATATATACGGGCATCAGTAAATTCCAGATCTGCTGGCGATGACGCAGC
+ATTATGCTCGCAGAGATAAAACACTGCTTGAGGGGTCATCCGGCGTCCAT
+TTGAGGCCCAACGGGTCCTTCTTTGTCGCCAAATTTAAGATACCTGCTCC
+TCCCCAGCAATGCGGGCAGGCAACATGAAAACGCATAAAATGCGGGGGGG
+ATTCACTTGCTTGCACCGCTCAATCTGACAGGTGACCTCTCAACTTTTGC
+GTGGAGCCACGGATGGACTTGGCCAGACCGAGCCTTCAATACCTTGT
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/14/0_1593
+ACCGACAGCAAGGTTTTGGGTAGGCTGATTTGTCAAAACGCCTGCCCCTG
+CATCAGACGTAGCCAGACGGAACGATATCTGATGGCCACGGGATCGGCGC
+AACCTGCCGGAAAGGGACGAATCTCACCTCGGCCCCAAGTAATTCAAGAA
+CATCTGCAACGGAATTTTTGCCAGAATATCCCTGCCAACCTGAGTTCAGT
+TCAAGTCAGGCTTGGCGGCATCATTTTCCGCAAATACGGTAATTTATTTT
+TCGCCGTGGAAAGCCCTGCCAGCGGCCGTCCAGTGTCGCATTCTTCGGTT
+GTTTACCCGCAAGCGCGTTAGTCAATGGTGGTTAGCCAAAATCTGGAATC
+ATTCCGAGCGCTGCGGCCAGTTCATTCAGCGTATCAGTGCCGTCCATGGG
+TGACAGCGTCGATAACATTCTGCAATCGCGGCCAGTACAAAAGCGGTGTT
+CGGCAATCTGGGTATTGTTTGTTCCCCTGAGCGCGGTTTTGGTCTGTTGG
+CGTTCCGGTCCAGTGCCGGACTGTCCAGTGGGCTTTTCTGTTCGTTCATC
+ATTAACAACCTTAAACCGCATTTTGGCGTGCAGCAAGCGTTTCAGACGAT
+GCTGTTGGTTGCACTGCTGAGCTGCACTATCCCTTTCTCGTTGTGTCCGC
+ATCATCAAGCGCGACAGTGCTGAAGCTATATCTTCTGCAACGTTTTGCCC
+GAATTTTTTTGCACGTATTGCCGCCGCTTCTGCCAGCACTTTGCTCTGCG
+GATGCTGATACCGCACCTTCCCGCAGCCTCTGTCGCCTTCGTGGATGGCA
+CGTTGACGCACTCCCGCCCGCCGCTGTTTTTGCGTCTGCCGCGGCAGAGG
+CGCTCCGTTCCGGCTGGCTGTTTCAGATGAAGCGCTGGGCATTCGTCTCG
+ACCCGTTTTTTGCGCCCTGGCAGAATTTTCTGCCGCCGTTGCCGAGGAAG
+GGCTGGGCAAGCGACCGGCACTTGATGATGCGTTCGTTCTGATGATTTTG
+CTGGGGGCCGTCTTTTGAAGGGCCAGCCGCATCTCGGCTGAAGTGGCCCG
+GACTTGACGGCTTTCGTGGCCGCGTGGAGGGCAGACGTGGCGGCCTGATT
+GTTGTGACGCTGGCAGCATTCTTTTCTGACGTTTCGCGACCGCACTGGTG
+GCCGCCGCGTTTTTTGAGGACTCTGCGGCTGCGGGCACTTTTTCGCGCTT
+CAGTGGACTTTGCTGATGCCGCTTCTGCGCCGAGGACGCTTCTGAGCTGA
+CGAAATGCAGCTGTCGCGGGCGGACGTGCTGGCGGCGCAGTGGCTGAGTC
+AGTTGCATCAGTTCACAGGGCCGCGACCCGTGAGGCAGCTGATGGCAGCT
+GCATCGCCGGCTGATTTCTTGCGCGTCTGCCGTAGCTCTGTGCACCACGG
+ACGCGTTACGCGGGCCACCTCTTCCACCGCATCAGTTCAAGACGAGCGCA
+GCACTTCCGGCCGGGCATCATCCTCCGTCATGGCGCACAGAGAAATCATT
+CGTCGTCCCCGGTTGTGAAATCTTTCATACACGGTATGGTCGCCGGCGTG
+CGATGGTGGAAAACCGTCAACGCTGACAGGATGACACTGTATT
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/28/0_1464
+GCAAAGAGGCATTATTCATTACCGCTGGGGACGCATAATAGCTTCTGTGC
+GCCGGGACGTTGCCGCGCTAACAGGCGAACCAGTAACAGCCATAAATCAG
+GCGCGGCCTAAACTGGCACGCGGCCCGCGTCTTCTGGTTATCCGAAGGTA
+AAGTCCTGGCGAACGGTGTATTACCCGGTTTGCTAACAGGGAAGAACGGC
+GAAGGAAAGATGAGCACGAACCTGGTTTTTAAGGAGTGTCGGCCAGAGTT
+GCCGCGCTGAAACGGGTATATGGCGGTATATGGCAGTTAAACAGATGACC
+ATCTACATTACTGAGCTAATACAGGCCTGCCTGGTAAATCGCAGGCCTTT
+TTATTTGAGGGGAGAGGGGAAAGTCATGAAAACTAACCTTTGAAATTCGA
+TCTCCAGCACATCACAAAACGCTTTCCACGCAGTAAAGCAAAGTCCTTCC
+AGACCCAACCAAACCAATCGTAGTAAACCATTAAGGAACGCAACCGCAGC
+TTAGACGCCAAAACAGGAAGCTATGGGCCTGCATTTAGGTGACGTCCTCT
+CGTCAGGTTGACATGGCATGGTCGCTGGCTGGATGCAGAAAGCTGGAAGT
+GTGTGGTTTACCGCAGCATTAAAGCAGCAGGATGTTGTTCTAACCTTGCC
+GGGAATTGGCTTTGTGGTAATAGGCCAGTCAACCAGCAGTGAATGCGTGA
+GGGAATTTGCGGAGCTATTTAGAGCTTATACCAGGCTTCGGTACACAGCG
+GTGGCGTTAAGTGGTCAGACGAAGCGAGACTGAGGCTCTGGGAGTGGGAA
+AGCTGAGATGGGGAGAGCGGGCTGCATGATTAAATGTCGTTAGTTTCCCT
+CCGGTGGCAGGACCGTCAGCATATTTGCTCTGGCTAATGGAGCGCAAAGC
+GACGGGCCCGGTAAAGTACGTGCATTACGTTTTCATGGGATAAGGTTGTG
+AACTCCAATGACATATCGGGTTTGTCAGGGAAGTTGTGAAGTTCTGGGAT
+ATACGCTCACCGTATTGCAGTTGATATCAACCCGGAGCTTGGGACAGCAA
+ATGGTTAATACGGTATGGGAACCAAAGATATTCAGACGCGAATGCCTGTT
+ACTGAAGCCATTTATCGATATGGTAAAGAAATATGGCACTCCATACGTCG
+GCGGCGCGTTCTGCACTGACACGATAAAACTCGTTCCCTTCCCAAATACT
+GTGGAATGACCATTTCGGGCGAGGGAAATTACACCACGTGGATTGGCATC
+AGAGCCTGATTGAACCCGAAGCGGCCTAAAGCCAAAGCCTGGAATCAGAT
+ATCCTTGGCTGAACTGTCCCAGACTTTGAGAAGGCAGATATCCTCGCATG
+GGTGGAGCAACAACATTCGATTTGCAAATACCGAGAACATCTCGGTACTG
+CATATTTCCTGCCTGCATTAAAAAAATTCAACGCAAAAAATTCGGACTTG
+CCTGCAAAGATGAG
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/45/0_2526
+GCATAGGCGGGTCAAGCATCCAGCGGCTCATTAAAGGCCATGCTGGCCAA
+TATGGCCGGGAGATTACGCGCTCAGCTCTGCTGTCCACTCTTCTCCTCCT
+CTGGTTGATTGTCGCAGCCGGATTCAAATGCTGCAGTCGCCCAGGCGGGC
+GGTTTACAGACCGGCCTGCACGGCGCTCCATCGTTTCACGGACTGCTGGG
+CAAAAACTTTCCGATAAAGTCGTCACCGCGTTTTGCGCACGTCTTTCTCG
+TAGGTACTCATCCGGCTTCTATCACATCACCTGCTTCCTGACCTTCTTTC
+AGACCATCGATGGCCATACGACCGGAGTCCTATCCAGTCCAGTTCCCCCA
+GGCACTGGCGCTCCTGAAAACGAAGCGGCGCTTTTGAAGGTAACGTCACC
+ACCGCGAACGAATGGCCTCTCCAGCCAGCTACAGAAACTCTGCTCGCCTG
+AACGGATGCGAACCGAATTTTCGCCGCCCATAAAGTCGCCACGACATCGT
+TCGCACTGGCCCGTGCCGTGAGTAGCTCATCTGGCGTAATTCCGGGAAAG
+CTGCCTCATGACGGAACACCCAGCCCGCAGCGATAGTACCCGCAGCAGTG
+ACTGCTCAACACGGAGCTAGCCGTTATCCGTATCCTGAGCCGTCTGCAGG
+TTCAGTGAGTCCACACAGGCATCAGGTGCGGTTACTTTTGCGCCTCCCAG
+CCGGACCGGCGCTGCGCGTAATACGCGGCAATTTCCACCAATCAACGCCG
+GTCAAGCCTTTCCCGCTGCTCCTGACTTGTTCGCAGCCCAGACATAAAAA
+TCCCATCGCTGACTTGCGTATCACAGCCACTCTCAATGGTGGCGCATACA
+TCCGCCTTCACAATGGCGCTCTGCAGCTGCGTGTTCTGCAGCGTGCGAGC
+ATCTTCATCTGCTCCATCACGCTGTAAAACAATTTGGCACCGCGGATCTG
+CCCGTCCTCCACGGTTCAAAAAACGTCGAATGAACGAGGCCGCGCCCGCC
+GGGTAACTGCACAGGGGTTATCCCATCGTCCAATTTCTGCGGCATCCAGC
+CAGATACCCGTCCTCGCTGACGTCAATTCCCAGCGCCGCACCCGCTGTCC
+CATTAATCTGCACACCGCACGGCAGTTCCGGCTGGTCCGCGGGTATTGAT
+TCGTGTTGCTGATGCGCTTCGGGCTGACCATCCGGACTGTGGTCCGGAAA
+GCCGCGACGAACTGGTATCACAGGTGGGCCTAACGACAGTTCACCGTTAA
+AGGCGTGCATCGCGCCACACCTTCCCGAATCATCATGGTAGAACGTGCGT
+TTTCGCTCAACGCTCAATGCCCGCAGCAGTCATCCCTCGCAAACTCTCTC
+CATGCCCGCTTCACCGTCGCGGAAAAAGGCACGGCCTTCTTCCTGCCCGA
+TGCCCCATGATAGCGCCAGCTTGGCGATGACTGAGCCCGAAAAAAGACCC
+GACGATATGATCCTGATGCAGCTGGATGGCGTTGGCGGCATAGCCCGTTT
+ATTGCGTAGCGCAGATCGTTCTGCGCGGGCGATGGGCCACGTAAAGTTGG
+GTCAACAGGGCTGCATCCACACTTTCACTGCGTGGGTTTCCAACCGCAAC
+GTGCCCCTCACAAATCTCGCTGCCACCGCCGTCCGATAACCGCATATTTC
+GCGCAGCGATGTCAAAAGCCGTCGCCGGCCCCGAAGGGGTGGGAAATAGG
+TGGGCGTTTCATACATAAATCCTGCAGGTCCCCCTGCGTCGCTGTGTCAT
+GCCGGTCTGCACTTCCAGCTCTGCAATATACTTTTTTCAGTCCAGAACAA
+ACGAAGTGCCCGTAACTCCACCCTTCCGTGTCGTCGTCTTTCTGTACTGT
+GCCACCCGTGTTACCTGTCATTCAGGCTCATGCAGTGCCGCACGGGCAGC
+GGCAAGTTCTTCCTGTCCGCGTCATTGCATCCTCTCCGATAAGGCCGGCG
+TAATCTGCCAGTGTTTTCTTGTTGTTGCTGCCACCATCCTCTTCCCTGCA
+GGCTCGCCAGCAGCGCACTGAGATCCGCAGCTGCCAGCGGAAATACTGAT
+GCCAGCGCCGCCAGCGCATAAACGAAGTCAGTGCCCGAGTGGCCTCATCT
+GCGTCCGCTTTTTGCTGTCCCACCAGTATTTTTTTCCTTGCCATCCATCT
+CCATTTTTCGACCTGCTCTTCGCGTCAGCTGCTGCGCTTCGTCAAATCAG
+AAAATATCTCGGTTAAGTTCCGGGAAGTGAACGGACCGGAACGGTTCATC
+CCCTTCCGGCGTCCAGTGTTGAAGGCGGGTTAAAATCTCTCTTCGGGTAT
+CCGTACCCGATTTTCGGTAAGGTAAACCCCGTTTTGGTTTTCGCTTACGG
+CATGCTGGCCACCGCTTTCCCGTAGACGGATGCCCCTTTAATGGGATCAC
+CACGGAACAGCCCAGTTTTTTCGAGCGGTCTACACATGGTCGGGTCAATC
+CCGCCAGTAATCCCAGCAGATACGGGATATCGACATTTAATGCACCGTTC
+CGCGGGTAATAAGGTTTCTATTGATG
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/47/0_1953
+GTCGATTTCCCAGAGCACCACGCTGGCCGACTGCTCCGGCACGGGTGCAT
+TCATTCGAATGTTTCTGCCGGATTCTGCATTCAGTTCCTACCACCTGTTC
+AAACTCTGCCTGAACTCCAACACGCAGCATACTTGACCCGCAGACGCACA
+TATTTGCGCAGGTCACCTTTATCTGCGCCACTCATAAGGCGGCGTCCACA
+GACAGGCATTTCCCAGGCCCCCCGTTGCTCTTCCAGAAACGACTACAAGT
+ACCGTGGCCTCTCACGGGGACAGAAAGCGTCACGCTGTTACGTTTTTCAG
+GTTGGCCATTCAAGCCCGGCAGGCGCTCGCTGAGAATAGCCATCACCAAA
+GCGCCACCTTTCTTACAGAAAGGGACCGAGCAACATCCATACCGGGTTTT
+CACTTTCCAGCGGAGGTTTCATCCGTCCACACTTCCGAGACAGGCCACCA
+TCACGCATCCTGTGTCTGAATTTTCAATCACGGGCACCCTTGCGGGCATG
+TCATACACCGCCTTCAGAAGCAGCCGTGACATATCTGCCCGTTCGTGCCG
+CTCGTTGTTAATCACCACATGGTTATTCTGCTCAAACGTCCCGGCACGCC
+CTGCGACTGGCTGTCTGCCATGCTGCCGGTTGCGTACCGACATAACCGCC
+GCGGTGGCATACGCGCGCATCAGCGGTAAAGATCCCAATACCCCAATCCG
+TGCTGGTTGACCTCCTTCGTGAAGCAAACTCACCACGGGTGGAACAATCC
+CCCGCTGGGAACGCTCATATTTGCCGCGGTTCCCCGTAAATCCTACTCGT
+CTGCAAAATGAGACATTTCCGCCCACGCGCGGCCCTGATCGGCTGTAACC
+AGCCTGACCGATGCGCCGCCACCAACCAGCCACGCCAACTGGCGACTGCC
+GATACTCCCGACAATTCCCCCACCCATTGCCTGCCTTAAGACCAGCATTT
+CTCGTCATCATGGAGCAGCACAGGACGGGTGAAGCCCTGCGCCAGGTCTG
+CTACTGCCGTCAGCATCGCCGCCATATTCTGTGCAATTACCATCAAAGGT
+CTGCGTGTGCACTTTTTACTGCGACAATACTGTCCGTGGCGCTCTCTTCC
+CACTCACTCCAGCCGGCCTTCAGGCTGCCCATCCAGTTCCCGCGAAAGCT
+GGTCTTCATGCCGCCAGGTCTTTTTTACTGCTCTGACATGACGTTATTCA
+GCGCAGCGGGATTATCGCCATACTGGTTCCTTCAGGCGCTGTTCCGTGGC
+TTCCCGGTTATGAGCTGCGGCGTCAGCCCCGCTTTTCGCATCAATGGCGG
+CCCGGATTTTGGCTCCGTTGCTGCTGTGCGAATTTTATCCCGCTGCTGCG
+CCAGCGCTTCAGGCGCTCCTGATACGTAACCTTGTCCGCAAGTGCAGCCA
+GCTGGCGTTTGTACTCCAGCGTCTCATTCTTTATGCGCAGCAGGGTTTCT
+ACTGTGCAGACAGCTGGCGACGTTGCGCCGCCTCCTCCAGTAACCCGCGA
+ACTGACTCCTCCCGCCTTCCACAAATCCCGGCGCTGCTGGCTGATTTTTC
+AATTTGCTCCGGCTGCTTCTTCTCAGCGTCCGGAGTTCTGCCTGAAGCGT
+CAGCAGGCAGCATGAGCACTTGTCTTCCTGACGATCGCCCGCAGACACCT
+TCACGTCTGGACTGTTTCGGCTTTTTCAGCGTCGCTTCATAATCTTTTTC
+GCCGCCGCCCATCAGCTGTGTGTAATCCGCCTTGCAAGGATTTTCCCGTC
+TTTCAGTGCCTTGTTCAGTTCTTCCTGACGGGCGGTATATTTTCCCAAGC
+GGCCGTCTGCAGCGTTCCGTAAGCCTTATCTGCGCCTCTTCGGTATAATT
+TCAGCCGTGACGCTTCGGTATCGCTCCTGCTGTGCGCATTTTTGTCCTGT
+TGAGTCTGCTGGGGCTCAGGGGACCTTCTTTCGGGCGCTTTCAAGCGCCC
+CCG
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/49/0_7870
+TTTGACTCATTGGAATATAGTCCATTCAAAGGCCAAATGTAAAAAGGATA
+TAAAAAAGGTTGCCCAGGATATTATTTTTAACCCGTCCCAGTCCATTTTC
+AGACATTAAGCCCTGCGGGCAAAAGAGAGACGGAGATATTTTAAAACAGA
+ACATTATCTATCAGAAAAGGCATCCTCTCAGACCCTCTGAAACAAGCGGG
+TCACCAATTGCTGAGATAAGCTGAAGAGATGCATATTGCTACGCAAGAAA
+TGAAAAGGTGATATTACTGGAAGCTTTTAAAAGGCAGGTGGTGCAAAAGT
+TAAGGATTAATTATCAGGAGTAATTATGCGAACAGAATCCATGCCTGGTG
+TTTACATAGTAATAATTCCCTTACGTCTTATCGAAAGCATTTGCCTATCT
+CTGCTTTTCCGCCACTACATTCCTGGTGTTTCCTTTTTCAGCTCATAGAA
+GAGGTCCTTGGGCGACATTGTCATCAATATCAGGAACCAATGATTGCAAT
+CCTGATTGCTCGCCTGACGTTTTCCTAAATCGGAAGCAGAAACGCGCCGA
+CTGGCCAAATTAGGAGAGTATCGGTATATGACATCGTAGGTTATTGTCTA
+ATGCCCTTAGTTTTGTTGAGCTTGGAGCTTGTTTTTCTGCGGGTTATTTG
+CTTCTTTCCAGCATAAGCGGCTACATGATACCACTATCGCCATCGGCATT
+GGCCTCTGCATCGTTCATTCTATATGCATCCTTGTTTTCCAACTATATAA
+TTTGACCAGAGAACAAGAATAACCCGGCCCTCAGCGCCGGTTTTCTTTGC
+CCCACATCGCCCCCCCAAAACACATACCAATTGTAATTTATATGAAAAAT
+AAAAGAGTACAACTCACTAAACATAGCAATTCAGATCTCCTCACTACCAA
+AGACAATGCCCCTGCCAAAAAATAAATTCATATAAAAGAACATACAGATA
+TCACCATCTGCGGTGATAAATTTATCTCTGGCGTGTTGAAATAAATACCA
+CTGTGGGGGCGGTGATACTGGCCATCCAAGCAGGGACGCAGGCTGACCAC
+CATGAAGTGACGCTCTAAAAATTAAGCCCTGAAGAACGGGCGCAATTCAA
+AGCAGAGAAGGCTTTGGGTGGGTGTGATCACAAACGAAAGCATTGGCCGT
+AATGGCGATTCCGGATTAGCTGCCAATGTGCCAATCCCGCGCGGGGTTTT
+CGTTCAGGACTACAACTGCCACACACACCACCAAAAGCTAACTTGACAGG
+CAGAATCCAGATGGATGCACAAACACTCCGCCGCGGAACGTCGCCGCAGC
+AAAACCAGGCTCAATGGAAAGCAGCAATCCCACTGTGGTTGGGGTAAGGC
+GCAAAACCAGTTAACCGCCCCTATTCTCTCGCTGATAGCAAACCGAAATC
+AAACGAGTAGAAAGGCGCACTAAATCCGTAAGACCCTTAACAGGTGCTGG
+CTGAATACCACAAACAGATTGAAAGCACCTGCACGTATTGAGCGCAAGAA
+TCAGCGCACATGGTACAGCAAGCCTGGCAACGCGGCATAACAATACAGGT
+GACGCCCAGAAAATTAAGGGAAAATCGATTCCTCTTATCTAGTTACTCTT
+AGATATTGCCTTGGCTTTATCTCAATATTAATATGGATCATAGCTGGCAA
+CTAATTCAGATCCAGTAAATATCCTCAATAGGGAATAATAATGCTTTTCC
+CATTCATCGGGAAAAAGTTTTGTTTCAACACACCAAGCTCAATCAACCCT
+CACTAATGTATGGGTAATTGTTCTTTGATGTAACCACAATACTTCCTGCC
+TTCATTAAGGGCTGCGCCCACAAAACCATAGATGCTCTTCTGTAAGTTTG
+AATTAACTGATCGCACTTTATCGTTGTTTGCAAATCTTAATGGCGTTTTT
+CTTAGCTAAATGCTATATCTTGGCGCTGGCAATAGCTGATAATCGATGCA
+CAGTTAATTCTAGCGAAAATGCAAGAGCAAAGACGAAAACATGCACACAA
+TGAGGAATACCGATTCTCTCATTAACATATTCAGGCCCAGTTATCTGGGC
+TTAAAAGCAGAAGTCAACCCCAGATAACGATTCATATACATGGTTTCTCT
+CCAGAGGTTCATTACTGGAACACTCGTCCGAGAATAACGAGTGGATCCAT
+TTCTATACCTCATCAAACTGTAGGGTGTAATAGTTTATCCGATTTTCCTC
+GCTGTAGGGGTACATCGAGAACCACCGAGCCTTGATGGTGGTTAAAAGAC
+AGGCAGCAATCTTTACTACCGCAATCCACTATTTAAGGTGATATATGGAA
+GAAAGAAAGAATTTGAAGGAGTTCGAAGAGCATCCTCAGGATGTGATGAA
+CAATACAGGACTATCCGTAATGACTACGACTATTGGGATAAAAATCAATG
+GTGGTGGACAATTCCAAGCGATGCAATGGATGCAAGCGCAATCGGAATGC
+ATGGTTACAGCCTGAAAGAAATGTTTTCCCTGTTAATGGAAGATGGGAAA
+GTATGTCGATAAATGGGCAATACGAACGCACGGAATGATGCCAGAGAACT
+TGGGGTAAACAGAACAAACAAAGCTGCTGATAGTGGTCCTTTATTTTTGC
+ATAAATAACCAAATAAACACTGCACTGGTATTTCATTCCAACGAGTGGAA
+ATACACGGAGCAATGGTCGCTTCGTAACTAAACAGGAGCCGACTTGTTCT
+GATTATGAAATCTTCTTTGCCTCCCAGTGGTGAGGAGCGGACTTTTTTAG
+CTGTGAGGATATGAAACAGATGTCAAACATCAAAAAATACATCATGATTA
+ACGACTGGAAAGCATCAATAGAAATTGAAAATCAGACCATGACGTAATGA
+CAGAGGAAAAACTTCACCAGATAATAATTTCTGGTCAGACTCTGAAACGA
+CTCAATAAACACGGCTCTGTATTAAATGACTGTATTAACATGCTGGGCGC
+CACAATGCTCTGCTTATAGCAATTTCAAGCTGACTTAAATGCATATGGGT
+TGGTTGTGGTGTGATTCGACTGAATGGATGGAAATGGGTCGGAAGATGGC
+CTCGCAATTGGATGGTAACGAAGGATAAGAATTACCGATATCGATACATC
+CAGGAATATTTGATTCAGATGATATGAACCTATCAAGGCCGGCCTGAGTG
+CGGTTTTACCGCATATCCAATAACCCGCGTTCCACTCGAGCGTTTTTCGT
+TATGCTATGAAATAAGGAAGCACACTCATGCAAATATGCCATTGCAGGGT
+GGGCCTGGTTGCTGGCCTCCCTTCGCGAGCGTTACTTGAACGAATCAGCC
+CGTAAATTACGTGACGGATGGAAACGCCTTATTCGACATACTTAATCAGC
+CAGGATCCCAAAGAAATGGATCAAACACTTATGGCTATCCAGACTAAATT
+CACTATCGGCGCACTTTTATGGCGATGAAAAGACGTGTTCGTGAATCCGT
+CGACGCTTATAAAAATGGATATTAATACTTGAAAACTGAAGATCAAGCAA
+AAGCATTCACTAACCCCTTTCCTGTTTTCCTAATCAAGCCCGGCATTTCG
+CGGGCCGATATTTTCACAGCTATTTCGGAGTTCAGACCATGAACGAGCTT
+ATTACATTAGGATCGTCTTGAGGCTCAGAGCTGGGCGCGTCCCTACCAGC
+AGCTCGCCCGTGAAGAGAAAGAGGCGAACTGGGCAGACGACATGCGAAAA
+AGGCCTGCCCCAGCACCTGTTTGAATCGCTATGCCATCGATCATCTTGCA
+ACGCCACGGGCCCAGCAAAAAATCCATTACCGTGTCGTTTGATGACGATG
+TTGAGTTTCAGGAGCTGCATGGCAAACACATCCGGTAACATGGTTGAAAC
+CATTGCTTCACGCACCCAGGTTTGATTTGATCAGAGGTATAAACAATGAG
+TACTTGCACTCCGCACGCTGGCTGGGAAGATGGCTGAACTGTCGGCATGG
+ATTCTGTCGACCCACCAGGAACTGATCACCACTCTTCCCCAGACGGCAAT
+TTTAAAGGTGATGCCAGCGATCGCAGTTCAATCGCATACTGATCGTTGCC
+AACCAGTTAACGCGCCTTAAATCCGTGGACGAAAGCAATTTACGCTTTCC
+TGGATAAGCAGAATGGCATCCGTTTCCGTGGTGGGCGTTGTATGGCTGGT
+CCCCGCATCATCAATGAACCAGCATGTTTGATGCCATGGACTTTGAAGCG
+ACAATGATCTGTACATGCCGGATTTACCGCAAGGACCGTAATCATCCGAA
+TCTTCGTTTACCGATGATGGCTGAATGACCGCCGCGAACCATTCAAAACT
+CCGCGAAGGCAGAGAAATTCACGGGGCCGTGGCAGGCCCACCGCACCCAA
+ACGGATGTTACGTCATAAAGCCATGTGATTCAGTGTGCCCCCGTCTGGCC
+TTCGGATTTGCTTGGTATCTATGGACAAGGATGAAGCCGAGCGCATTGTC
+GAAAATACCCTGCATACACTGCAGAACGTCAGCCGGAACGCGACATCACT
+CCGTTAACGATGAAAACCATGCAGTGAGATTACACTGCTGCGTCGTCCTG
+GATAAATAAAAATGGGAATGACGACTTAATTGCCCGCTCTTGTTCCCCAG
+ATATTCCCGCCGACATTCGTCATCGTAGAACTGACACGGCCGAAGCAGGT
+AAAAAGCTCTTGGATCCTGAAACAGAGAAGCCGCAGAGCAAAGGTGGCAG
+CATGGACACCGGACATTATCCTGCAGCGTACGGAATCGATGTGAGAGCTG
+TCGAACAGGGGGATGATGACGTGGCACAAATTACGGCTCGGCGTCATCAC
+CCGCTTCAGAGAGTTCACAACGTGATAGCAGAAACCCCGGCTCCGGAAAG
+AAGGTGCCCTGACATGAAATGTCCTACTTCACACACCCTGCCTTGCTGAG
+GGTTTTGCACCGGTGGCTCCGTGAAGTTAACGCTAAAGCATGCCTGGGGA
+AGACAGTACGAGAACGACGCCAGAACCCTGTTTGAATTCACTTCCGGCGT
+GGAATGTTACTGAATCCCCGATCTCTATCGCGACGAAAGTATGCGTACCC
+GCCTGCTTCCTCCCGATGTTTATGCAGTGACGGCAACGGCCTGAACTGAA
+ATGCCCGTTTACCTCGCCGGGATTTCATGAAGTTCCGGCTCGGTGGTTTT
+CGAAGGCGCATAAGTCAGCTTACATGGCCCAGGTGCAGTACAGCATGTGG
+TGACGCGAAAAAAATCCTGGTACTTTTGCCCAACTAATGACCCGCGTATG
+AAGCTGAAGGCCTGGCATTATGTCGTGATTGAGCGGGATGAAGAATACAT
+GGCGAGTTTTGACGAGATCGTCCGGAGTTCCATCGAAAAAAATGGACGAG
+GCACTGGCTGAAATTGTTTTGTATTTTGGGGAGCAATGCGATGACGCATC
+CTCACGATAATTATCCGGGGTAGGCGCAATCACTTCGGTGCTACTCCGTT
+ACAAAGCGAGGCTGGGTTTCCCGCCTTTCTGTTTATCCGAGAATCCACTG
+AAAGCACAGCGCTGGGCTGAGGAGAGTAAATAATAAACGAGGGGCTGTAT
+GCCAAAGCATCTTCGTTGAGTTAGAGAACGATTTCGGAGATGCACATAAG
+CCTTGCTCAATTGAATCAGGTTTGTGCCAATACACAGTAGAAACCAGATA
+CAGACGAAGAATTTCCATACTTTAGGCCGCATCCCCCTTTCCAAAAGCTG
+AAATGATGGTGGCGAAAGCAGAGCAGATGAGAGACAACCATGTATGACAA
+CCACGAATGCATGTTTTCTTGGCAAGCGGGCTTCATATTCTGTGTGCTAT
+GCTTGCCGACATGGGAGCTTGTTCAAATGACACCTCAGCCAGGTGAAAAC
+GCCCTTTCGGCAGCATTGCCGCTGCAGGCTAATTCTGAAATCAAAAAAAA
+GCCAGACAGCAGTTTCCGGATAAAAACGTCGATGACATTTGCGCGTAGCG
+TAACTGAAGAAGCCCGCGAAACGGTAACGCTGATGGATTCACACGACTCA
+TTAAGCCTGGCAATCGGCCTGTAAACGCGCGTCTTTAAGGACGATGAACA
+TGAAAAGCAAAATCATTCAGGGCAGCTACAGGCCTTCTCCTTTTTTAATT
+ATTCGCATCACTGCCTCAAGCCGTATTAAAACCAAACCAGTTCAGGGATT
+TAAGAAAGATGGCAGACATCCATTGATCAGCATCAGAAGATAGAAGAATT
+ACAGCGCAACACAGCAATAAAAATGCGGCCGCCTGACCAACCAGGCCCTA
+TATCGTGCCAACTCACAACAATGAGTGGCAGATATATGCCTGGTGTTCAG
+GCGGCGCATTTTTTATTGCTGTGTTGCGCTGTAATTCTTTCTATTTCTGA
+TGCTGAATCAATATGCTGCCCATCCTTTCATTTATCCCTGAACTGTTGGA
+TTAATACGCTTGAGGTGAAATGCGAATAATAAAAAAGGAGCCTGTAGCTC
+CCTGATGATTTTGCTTTTCATGTTCATCGTTCCTTAAAGACGCCGTTAAC
+ATGCCGATTGACCCAGGCTTAAATGAGTCGGTGTGAAATCCCATCAGCGT
+TACAGTTTCGGCGGTGCTTCTTCCAGTACGCACGGCAAAATGTCAATCGA
+CGTTTTTATCCGAAACTGCTGTCTGGCTTTTTTTTGATTTCAGAATTAGC
+CTGACGGGCAAATGCTGCGAAAGGGCGTTTTTCCTGCGAAGGTTCATTGA
+ACAGCCGCATGTCGGACAAGCATAAGCACACAGAATATGAAGCCCGCTGC
+CAAGAAAGAATGCATTCCGTGGTTGTCCAGTACCTGGTTCTCCTCACTGC
+TTCTGCTTTCGCCAACCATCATGTTCCAGCTTTTGTGAAAGGGATGCGCT
+AAACGTATGAAATTCTTCGTCTGTTTCTACTGTAATTGGCACAAACCTGA
+GTTTCCAATTTGAGCAAGGCATGTGGCATCTCGATACTCGTCTGTAACTC
+ACAGAAGATGCTTTTGTGCAACAGCCCCTCGTTTATTATTTAATGCTCCC
+TCAGCCAGCCGCTGTGCTTTCAGGGATGTTCGGATACAGAAAGGCCGGAA
+ATACCCAGCCTCGCTTGGTAACGAGTTAGACGAAAGTGATTGCGCTACCC
+CGGATGAATTATCGTGAGATGCGTCCCATCGCCATTGCTCCCCAAATACA
+AAACCAATTTCACCAGTGGCCTCGTCCATTTTTTCGATGAACTCCGCACG
+ATCTCGTCCAACTCCGCCCATGTACTTTTCTCCCGCTCATCACGACATAA
+TGCAGGCTTCACGCTTCATACGCGGTCATAGATTGGCAAAGTACCAGGCA
+TTTTTTCGCGCACCCACATCTGTACTGCACTGGCCAATGGTAAGCTGCAC
+TTTATGGCCCTCGAAACCACCGAGCGGAACTTCCATGAAATTCCGGAGGT
+AAACGGGCATTTCAGTGTCAGGCCGTTGTCCGTCACTGCATAAACCATAA
+GGGAGAGACAGGCGGTTATCGCATACTTATCGGTCGCGATAGATGATCGG
+ACTTCAGCTAACATTCACGCCGGAGTGAATTACAAACAGGGTTCTGGCGG
+TCGTTCTCGGGTACTGTTTTCCCCAGCCAGTGCTTTAGCGGTTAACTCCC
+GGAGCCACACCGGTGCAACCTCACAAGCAGGTGTGGAAGTAGGACAATCT
+TTCATGTCAGTTGGCCAACTTCTTTTCCGGAGCGGGTTTTGCTATCACGT
+TGTGAACTTCTGAAGCGGTGGATGACGCCGAGCCGTAATTTGTGCCACGC
+ATCATCTCCTCCCTGTTCGAACAGCTTCTCCACATGCGATCCGGTACGCT
+GCATGATAAATGTCCGGTGTCATGGCTGCCACCTTCTGCTCTTGGCGGCT
+TTCTGTTTCAGGAATCCAAG
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/53/0_1306
+GAAAGGAAGTGCATTAAGCAGCTCGGAGAGCGCGTTCAGATAGAGCACTT
+GATGAGGGAACCACCCAAGACCGGATGTTATGCATATGCATTTCATCGGC
+CGAACAACGGTGAAGGTAGAAGCCAAGCTACCCTGTAGTGTGGGCGATAT
+TTAAAGGTCTTAGGGGCAACAGATATTGGGGAAGGGGAGCTTTTTGACTC
+ATCTGATATAGATCATTAAGCCAAAATTGTAAAAAGGGATATACAAAAAG
+GTTGCCAAGGATATTATTTTTAACCCGTCACCCTCAATTTTCAGACGATT
+AGCCTGCGGGCAAAAGATGAGGCCCGGAGATCATTTTAACAGAACATTAT
+CTATCAGAAAAACCATCTCTCAGCGCCTCTGAAAAGGTCACCAATGCTGA
+GATAGGCGGAGAGATGTGGCATGTATTGCACGCAAGAAGAAAAGTGATAT
+AGCTGGAATGTTTTAAATAGGCAGGTGGGGCAAAGTAAGGATTAATTATC
+AGGAGTAATTAAATGCGGAACAGAAATCTGCCTGGTGTTTACATAGTAAA
+ATTCCTTCGTTATCGTAAGCATTTGCTACTCTTCTTTTTCCGCCACTTAC
+TTCTGGGTGTTTCTTTTTCAGCTCATAAGATGGTCTTGGGGCGACATTGT
+CATCCATATGCAGGAACCATGATTGCAATCTGATTGCTCCGCCTTGACGT
+TTCTAATCGGAAGCAGCAACGCGCCGGACCTGGCCCAAGATTAGAAGAGT
+AAATGGGTATATGACTCGGTAGTAACTTGTCTATGCCCTTAGTTTTGTTG
+AGCCTTGGAGCTTTGTTTTTCTGTCGGGTTTATTGCTTCTTCCAGCATAA
+GCGCTACATGATACCCACTTCGCCATCGGCATTGCATCTGCATCGTTCAT
+TCATATATGCCCATCCTTGTTTCCAACTATATAATTTGGAACCGAGAACA
+AGAATAACCGGCCTCCAGCGACGGGTTTTCTTTGCCTCACGATCGCCCCC
+CAAACACATAATCCAAATTGTATTTTATTGAAAATAAATAGATACAACTC
+CACTAAAACAAGTAGCAATTCAGATCTTCTCCACCTACCAAACAATGCCC
+CCTGCAAAAAATAAATTTCATATAAAAAACCATACAGATAACCATACTGC
+GCGTGATAAATTAATCTCGCGGTGTTGACATAAATACCACTGGCGGTGAT
+ACTGAGCCATCAGCAGGACGCACTGACCACCTATCCGGCTGAACGCTCTT
+AAAAATTAAGCCCTGGAAGAAAGGAGCAGCATTCCAAGAAGCAGAAGGCA
+TTTGGC
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/70/0_3728
+CGCCGTACGCATACTTCTCGTCGCGATAGATGATCGGGGGATTCGTAACA
+TCACGGGCCGGAAGTGAATTCAAACAGGGTTCCTGGCGTCCGTTCTCGTA
+TGTTTTCCCCAGGCAGTGCTTTTAGCGTTAAACTTCCCGGAGCCACACCC
+GTGCAACCGCTCAGCAAGCAGGGTGTGGAAGTAGGAAACAGATTTTCAAT
+GTCAGAGCACTTCTTTTCCGGAGCGGGGTATTTTGCTATCACGTTTTGTG
+GCAACTTTCCTGAGCGGTGATGACGCCGAGCCAGTATTTGTTGCCACGCA
+TCATTCCCCCCCTGTTCGACAGCTCTCACAATCGATCCCGGTACGCTGCC
+AGGATAATGTTCCGGTGTCATGCTGCCACTTCTCTGCTCTGCGGCTTTCT
+GTTTCAGGAATCCAAGAGCTTTTACTCGCTTCGGCTGTGTCAGTTCTGAC
+GATCCACAATGTCGCGGCGATATATCTGGGACAGAGCGGTCATAAGTCGT
+CATCCCTGTTTTTGTCCAGGGCGATCAGAAGAGTGTTTAATCTCTGCATG
+GTTTTCATCGTTAACACGAGTGATGGTCGCGTTCGGCTGACGTTCTGGCA
+AGTGTAAATGCAGTATTTTCCGCAATGGTCGGCTTCATCCTTGTCATAGA
+TACAAGCAATCCAGAAGGCCAGACGGCACACTGAATCATGGCTTTATGAG
+TAACATCCGTTCTGGGATGCCGACTGGCACGGCCGTAGATTTCTCTGCCT
+TGCCGAGTTTTGAAATGGTTTTTTCGCGGCGGATTATCCATCCATTCGTA
+ACTCGCAGATCGGATGATTACGGTCCTTGCGGTAATCCGGCATGCTCAAG
+GATTCATTGTCCCTGCTCAAGTCCCCATGCATCAAACTGCTGGTTTTCAT
+TGATGATGCGGGACCAGCCATCAACGCCCACCACCGGAACGATGCCATCT
+CTGCTTATCAGGAAGGCTACTTTCCTTTCGTCCCACGGATTAAGGCCCGT
+ACTGGTTGGCACGATCAGTAATGCGATGAACTGCGCATCGCTGGCATCAA
+CATTTAAATGCCGTCTGGCGCGAGTGGTGATCAGTTCCTGTGGGGCGAAG
+AATCCATGCCCGACACGTTCGCCAGCTTCCCAGCCAGCGTTGCGAGTGCA
+GTACTATTCGTTTTATACCTCTGAATCAAATCAACCTGGGGTGAGCAATG
+GGTTTCACCATGTACCAGGATGTGTTCTGCATGCGCTCAACTGAAATAAC
+ATCGTCTCAACGAACGGGTAATGATTTTTTGCTGGCCCCCAGTGGCGTTT
+GCAAATGGATCGTGCCATAGCGATTCAAACAGGTGCTGGGGCAGGCCTTT
+TTCCCATGTCGTCCTGCCAGTTCTGCCTCTTTCCTCTTCAAGGGCGAAGC
+GCCTGGTAGTGACGCGCCCAGCTCTGAGCTCAAGACATTGACATGTATAA
+GACGTTCATTGGCTGAACTCCTGAAATAGCTGTGAAAATATCGCCCGCGA
+AATGCCGGGCTGATTAGGAAAACAGGAAAGGGGTTAGTGAATGCTTTTGC
+TTGATCTCAGTGTTTCCCCCCCCAGGTAAAAAATTAAATATCCATTTTTT
+ATAGCGTCGACGGCCTTCACGAAACATCTTTTCATCGCCAATAAAATGGC
+GATAGTGACATTTAGTCTGGATAAGATAAGTGTGTTTGATACCCATTCTT
+TGGGACTCCATGGCTGATTAGTATCGTGCGATAAGGCGTTTCCATCGTCA
+CGTAAGTTCCCGGGGTGATTCGTTCAAGTAAAGATTCGGAAGGGCAGCCA
+GCAACAGGCACCCTGCAATGCATATTGCAATGGTGGTGCTCTCATCTTAT
+ACATAACGAAAACGCCCTCGGAGTGAAGTCGTTATTGGTATCGAGGTAAA
+ACCGCACTCAGGCGCCTTGGATAAGTCCATATCATCTGATCAAATATTCC
+TGAAGTATCGATATACTGTAATTCTTATTCCTTCGCTACCATCCATGTGG
+AGGCAATACCTTCTGACCATTTCATCATTCAGTGACTCACACAACACCAT
+ATGACATTTAAGTTCGTTTGATTGCCTATAAGCAGAGCATGTCTGCGCCA
+GCATGAATCTAATACCAGATTTAATACAGAGCCGTGTTTATTGAGTCCGG
+CTATTACAGAGGTCTGACAGAAATTATTAATCTGTGGAAGTTTTTTCCCT
+GCCATTAAACGTACATGGCGATTTCAATTTCTATTGATGCTTTCCAGCGT
+AATCAATGATGTATTTTTGATGTTTGACATCTGTTCATATCCTCACAGAA
+TAAAAAATCGACCTCACTGGAGGCCAAAGAAGATTTCCAATATCAAGAAA
+AGTCGGCCCTGTTTAGTTAACGAGCGAATTGCTCCGTGTATTCCTTCTTG
+GAATGAATACACGTGGCAGTGTTTATTCTGTTATTATGCCAAAATAAAGG
+CAACTATCAGCAGCTTTGTTGTTCTGTTTACCAAGGTTCTCTGGCCATCA
+TTGCGTCGTTCGTATTGCCATTTATCGAACATATTTCCCATCTCCATAAA
+AGGAAACATTTCTTCAGGCTTAACCTGCATTTCCGATTGCGCTTGCATCA
+TTTGCATCGCTTTGAATTGTCCAGACATTGTTTTTTTATCCATAGTCGTA
+GTCTACGGATAGTCCTGGTAGTTGTTCCATCACATCCCTGAGGATGCTTC
+GAACTATCCCAACTTCTTCTTCCATATATCACCTTAAAATAGTGGATTGC
+GGTAGTAAAGATTGGTGGCCCTGTCCTTTAACCACATCAGGGCTCGGTGG
+TTCCTCAGTGTACCCCCTACAGCGAGAAAATACGGATAAATATGTAAACC
+CTACAGTTTGATGAGTATAGAAAAATGAGATCACTCGTTTCTCGGAACCG
+GTGATTCCAGTAATGAACCTCGGAGAAGAAACATGTCTTATGCATCGGTA
+TATCTGGTTCGGACTTCTGCTTATTTAAGACCCATGATAACTGGACCCTG
+ATATGTTAAATAGAGAGAATCGGTATTCCTCATGTGTGCATGTTTTCGTC
+TTTGCCTTGCTTTTCGCTAGCATTAATGTGCCATCGATTATAGCTATTGC
+CAGGGCCAGATATAAGCGATTAAGCTAGAAAGCATTAAGATGCAAACGAT
+AAAGTGCGATCAGTAATTCAAAACCTTTACAGAAAGGCAATCTATGGTTT
+TGTGCGCAGCCCTTAATGAAGGCAGGGAGTATGTGGGTTACATCAAAACA
+ATTCCATACATTAGTGGAATGTTGATGAGCTTGGTGGTGTTGAACAAAAC
+TTTTCCCTGATGGAATGGAAAGCATACTATTATTCCTATTGAGGCTATTT
+AGCTGGACTGAATTAGTTGCCAGGCTAATGATCCATCATAATATTAGAGA
+TAAAAGCCAAGGGCCAATATCTAAGTAACTAGATAAGAGGAATCCCGATT
+TTCCCTTAATTTTCCTGGCGTCCCAATGCATGTTATGCCGCGGTTCGCCA
+GGCTGTGCTGTACCATGTGTGCCGCTTGATTCTTGCCGCTCAATAACGTT
+TGCGGTTGCTTTCAAATCTGTTTGCTGGTATTCGCCCCAGACACTGAAGT
+CTATCGGATTTAGTGCGCCTTTCTATCGTGATTTCGGGATTTTTGCGATT
+CGACGAGAGGAAATAGGGCGGTTAATGGTTTTGCGCTTACCCTGCCAACA
+CAACAGGGGATTTGCTGCCGTTTTCACC
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/105/0_2152
+CTAACATTTATCTGTCATCATACTTCCGAGCATTTATTAGCATTTCGCTA
+TAAGTTCTCGCCTGGAAGAGGTAGTTTTTTCCTTTGGTACTTTCACCTGT
+TCATCCTCTGTTCACGTTATCTATCGCTTTTAAAACGGTTCGACCTTCTA
+AATCCATCCTGATCCATTAAATATATTTTTTAGAATGGTTCATCAAGAAA
+GCCCTCTGAATCAACGACTTGCATATTAAAGTGGTGTATGCGCAGATTGT
+CCACTTCAAGTAAAACACCTCCAACCGAGTTAAAACACCTTAAGTTCACC
+CGAATGTCCTCAATATCCGGACGGATAATATTTATTTGCTTCCTCATTGA
+CCGTAGGACTTTCCACATGCAGGATTTGTGCGAACCTCTTGCAGTACTAC
+TGGGAATGAGTTGCAATTATTGCACACATTGGCGTGCATCCGAGTAAGTC
+GCTAATGTTCGTAAAAAAGCAGAGGAGCAAAGGGTGGATGCAGATGAAAC
+TCTGGTTCATTCGAATAAAACTAATGACTTTTCGCCAACGACATCTACTA
+ATCTTGTGATAGTAAATATAAACAATTGCATGTCCAAGAGCGTCAATTCG
+AAGCAGATATTTCCTGGATATTGTCATAAAAACAATTTAGTAGATTTATC
+ATCGTCCACTGAATCTGGTGGTGTCATTTACGTCTTAACTCTTCATATTT
+AGGAATGAGCACTGATGAGTTCCATATTTGAAAAGTTTCATCACTACTTA
+GTTTTTTGATAGCTTCCAAGCCAGAGTTGTCCTTTTTCTATCTACACTCT
+CATACAACCAATAAATTGCTGAAATGAATTCTAAGCGCGAGAACGCCTAG
+TGATTTTAAACTATGCTGGCAAGCATTCCTTTGAGTCGCAATATAAAAGT
+ATTGGTGTACCATTTTGCTGGGTCTGAGGTTGTTCTTTAGGAGGAGTAAA
+AGGATCAAATGCAAACTAAACGAAACGGAAACAAGCGATCGAAAATATCC
+CTTTGGGATTTCTGGAACTGCGATAAGTCTATTTAAAGTTTTCAGAGAAA
+AATATTCATTGTTTTCTGGTTGGGTGATTGCCACCAATCTTCCCATTCAG
+AAATTGTTGTTTTACCACACCATTCGCCCGATAAAAGCATAATGTCGTGC
+TGGGCATAGAATTAACCGTCACCTCCAAAAGGTATAGTTATAATCACTTG
+AAACCGGAGAGGCACTTTTTCTATTAAATGAAAAGTGGAAATCTGACCAA
+TTTCTGCAAAATCCATTTTACACCCGTGCGAACTGTCCATGAGATTTCCT
+GAAGAGTTACCCCCTCTAAGTAATGAGGTGTTAAGGACGCTTTTCATTTC
+ATGTCGGCTAATCGATTTGGCCATACTACTAAACCTGAATAGCTTTAAGA
+AGGTTATGTTTAAAACCATCGCGTTAATTTGCGTGAGATTAACCATAGTA
+GTCAATGCTTCACCATAAGGAAAAAAACATTTCAGTGGATTGACTGTAAT
+TTTTTATCTATTAATGGAATAAGTGCTTACTCTTCTTTTTTGACCTACAA
+AACCCAATTTTACATTCCGATATCGCATTTTCACCATGCTCATCAAGACA
+GTAAGAATAAAACATTGTAACAAAGGAAATAGTCATTCGCAACCATCTGC
+TCGTAGGAATGCCTTATTTTTTTTCTACTGCAGAATAATAGCCCGCCTCT
+TTCAATAAACAACAAAACTCCAACATATAGTAACCCTTAATTTTATTAAA
+ATAACCGCCAATTTATTTGGCGGCAACACAGGATCGTCTCTTTTAAGTTA
+CTCTCTATACATACGTTTTCCATCTAAAAATTAGTAGGTATTTCGAAACT
+TAAACGGGCATCGTATTGTAGTTTTTCCATATTTTAGCTTCTGCTTCCTT
+TTGGATAACCCACTGTTATTCAATGTTGCATGGTGCACTTGTTTATACCA
+ACGATATAGTCTATTAATGCATATATTAGTATCGCCGAACGATTAGCTCT
+TCAGGCTTCCTGAAGAAGCGTTTCAGTACTAAATAAGCCGATAGAGAGCC
+ACGCGACTTCGTAGCTCATTTTCCATAAGTGTTAACTTCCGCTCCTCGCT
+GCTATAACAGACATTCACTACAGTTATGGCGAAAGGTTGCATGCTGGGTG
+TT
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/115/1304_3321
+CGTGCCTTTTGGAAGGAGGATCATGAAATGGGAAGAAGGCGAAGTCATGA
+GCGCCGGATTTAACCGCGCTAACCCTTTTATATACGAGACACAATGATAT
+TAACTGCTACAGGGACCCAAGGACGGGGTAAGAGTTGGATTAGGCAGAGA
+CAGGCGAATCGAGCAATCACTGCACGCTATACAGAGCCAACATTGAGTTA
+TTTTCAGGACACAACACAAGCCTCTGACCAGCGGAAATCAACAGGAAATT
+CGTTACGTTACATTCATCGGCTTGATCGCTACGAAAAAATCCTGGCCAGC
+AGAGGAATCAAGCAGAAGACACTCATAATTACATGAGCACAATTAAAGCA
+ATAGGAGGGGTCTGCCTGAGCTCCACTTGAGACCATCACCACAAAAGAAT
+TGCGGCAATGCTCAATGGATACATAGTACGAGGGCCAAGCGGGCGTCAGC
+CAAGTTAAATCAGATCAACACTGAGCGATGCATTCGAGAGGCAATAGCGA
+ATGGCCATATAACAACCAAACCATGTCGCTGCCACTCGCGCAGCAAAATC
+AGAAGGTAAGGAGGATCAGAGACTTACGGCTGACGAATCCTGAAAATTTA
+TCAAGCAGCAGAATCATCGCACCATGTTGGCTCAGACTTGCAATGGAACC
+TGGGCTGTTGGGGGGGGGGGGGGGGGGGGGTTACCGGGCAACGAGTTGTG
+ATGTTATTGCGAAATGAAGTGGTCTGGAATCGTAGATTGGATATCTTTAT
+GTCGAGCAAAGCAAAACGGCGTAAAAATTGCATCCCAACAGCATCTGCAA
+TATTTGATGCTCTCGCGGAATATCCATGAAGGAATACACTTGATAAATGA
+CAAAGAGATTCTTGGCGGAGAAACCATAATGCATCGTACTCGTCCGCGGA
+ACCGGCTTTCCATCGGCACAGTATCAATGGTATTTATGCGCGCACGAAAA
+GCATCGGTCTTTCTTCGAAGGGGGATCCGCCTACCCTTTCACGAGTTGCG
+CAGTTTGTCTGCCAGACTCTATGAGCAAGCAGATAAGCGATAAGTTTGCC
+CCTCAACATCTTCTCGGGCATAAGTCGGACACCATGGCATCAACAGTATC
+GTGATGACAGAGGCAGGGAGTGGGACACAATTGAACATCAAATAATGCCT
+TCTTCTAATTTGACTGATAGTGACCTGGTTCGTTGGCAACAAATGATAAG
+CATGCTTTTTTTATAATGCCAACTTAGTAATAAAAAAAAAGCTGAACGAG
+AAAACGTAAAAGATATAAATATCAATATGATTAAAGTTAGATTTTGCATA
+AAAAACAGACTACATAAATACTGTAAAACACAACATATGCAGGTCACGTA
+TGAATCAACTACTTAGAGAGTATTAGTTGGACCTGTTAACAGAGATTAGC
+GCAAGGTGATTTTTGTCTTCTTCGCGCTATTTTTCTGTCATCAAACTGTC
+GCACTCCCAGAGAAGCACAAAGCCTCGCAATCCAGTGGCAGAAGCTTTTG
+TGTGCACCCACTACGACCTGCATAACCAGTAGAAAGATAGCAAGTGATGT
+CAAACGACGCCAGCTGACTTCTTTGTCTTCACGACTTCCCCACACCCAGC
+ATGCATACCTTTTCCGCCATAACTGTAGTGAATGTCTGTTATGGGAGCGA
+GGAGCCGGAAGTTTCTAACACTATGGAAAAATGGCTACGAAAGTCCGTGC
+TATCTATCGGCTTATCTAGTAGCTTGAAACGCTTCTCAGAAGCCTGAAGA
+GCTAATCGTTCGGCGATACTATATATGCATTAATAGACTATACGTTGGTA
+TAAACAGTGCACCATGCAACATCGAAGAACAGTGGGTTTATCCAAAAGGA
+AGCAGAAAGCTAAATACTGGCAAACTACAATACGATGCCCGGTAAGTTCA
+TACTACGTAATTTTTAGATGGAAAACGTATGTACAATAGGAGTAACTTAA
+AGAGAGATCCTGTGTTGCCGCCAAATAAATTGCGGTTATTTTAATAAAAT
+TAAGGGGGTTACTATAT
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/115/3365_7852
+ATATAGTAACCCTTAATGCTTATTAAAATAACCGCAATTATTTGGCGGCA
+ACACATGGATCTCTCTTTTAAGTTACTGCCTCTATTACATACGTTTTTCC
+ATCTAAAATTAGTAGTATTGAACTAACGGGGCCTCGTATTGTATTTTCCC
+ATATTTAGCTTTTCTGCTTCCTTTTTGGAATAACCCACTGTTATTCATGT
+TGCATGGTGCATGTTTATACCACGATATAGTCCTATTAAGTGCACTATAT
+AGTATCGCCGAACGATTTAGCTCTTCAGGCTTCTGAAGAAGCGTTTCAGA
+CTAATAAGCCGATAATAAGCCACGGACTGTCGTAGCCATTTTTCATGAAG
+TGTTAACTTCCCTCCTCGCTCATAAAGACATTCCACTACAGTTATGGCGG
+ACGGTATTGCATGCTGGTGTGGGAAGTCGTGAAAAGAAAAGAAGGTCAGC
+TGCCGTCGTTTGACATCACTGCTAGTCTTCTTACTGGTTATGCAGGTCCG
+TAGTGGGGTGGCACACAAAGCTTTGCCACTGGATTGCGAGGCTTTGTCGG
+CTTCTTCTGTGAGTGCCGACAGTTTGATGACAAAAAATTAGCGCAAGAGA
+CAAAAATCACCTTGCGCTAATGCTCTGGTACAGGTCCTACTACCATCTCA
+AGTGTTGATTCTAGTGAGCTGCTATGTTTGTGTTTTACAGTATTATGTAG
+TCTGTTTTTTATGCAAATCTAATTTAATATATTGAATATTTATATCATTT
+TTACGTTCTCGTTCAGCTTTTTTTATACTAAGTTGGCATTATAAAAAGCA
+ATCTGCTGTTATCAATCTTGTTGACAGACGAAAGGCACTATCAGTCAAAA
+TAAAATCATTATTTGATTTCAATTTTGTCCCACTCCCTGCCTCTGTTCAT
+CCACGATACGTGATGCCATGGGTGGTCCGACTTATGCCCGAGAAGATGTT
+GAAGCAAACTTATCGCGTTATGCTGCTTCTCATAGATGTCTTGGCAGACA
+AACTGCGCAACTCGCTGAAAGGTAGGCGGATCCCCTTCGAAGGAAATGAC
+CTGATGCTTTTTCGTGCCGCGCATAAAATACTTGATCCTGTGCCTGATGA
+AAGCGGTTCGCGACGAGTAGATGCAATTATGGTTTCTCTCGCCAAGGAAT
+CTCCTTTGCATTTATCCAAGTGTGTTCCTTCATTGATATTCCGAGAGCAT
+GCAATATGCATGTCAAGCTGTTGGGATGGCAATTTTTACGCCTGTTTTGC
+TTTGCTCGACATAAAGATATCATCTACGATATCAGACCACTATCATTTCG
+CATAAATCACCAAACTCGTTGCCCGGTAAAACAACAGCCAGCTTCCATTC
+AAGTCTGAGCCAACATGGTGATGATTGCTGCTTGCTTGATAAATTTTCAG
+GTATTCGTGAACAGCCGTAAGTCCTTGATCTCCTTACCCCTTCTGATTTT
+GCTGCGCGAAGTGGCAGCGACAATGGTTTTTGTTTATATGGCTTCAGCTA
+TGTGCCTCTCGGAATGCATCGCTCAAGTGTTGATCTGGAATTAACTTGCT
+GACGCCGCCTTGCCCTCGTCTATTATACCATTGAGCATTGCCGCAATTTC
+TTTTGTGGTAATGTCTTCAAGTGGAGCATCAGCAGACCCCTCCCCTTAAT
+TGCTTTAATTTTGCACATGTAATTTAATAGTGTCTTCTGCTGATTTCCTC
+TGCTGGGCCAGGATTTTTCCCCGTGTAGCGATCAAGCATAGGAATGTAAA
+CGTAACGGGAATAATCACTTGGTTGACTTCTCGCTGTCAGAGGCTTGTGT
+TTGTGTCGCTGAAAAATAAGCTCAATGTGGCCTGTATTAGCTTCAGGTGA
+TTGCGATCGCTGTCTGTCTCTGCCCTAATCCAAACTCTTTACCCGTCCTT
+GGTCCCTGTACAGAATATCCATTGTTTTCTTAGGTATACAGGGATAGGGG
+GTTAAATATCCCGGCGCTCATGACTTTCGCTTCTTCCCATTTCCTGATCC
+CTCTCAAAAGGCCACCTGTTACTGGGTCGATTTAAGTCAAACCTTTTACC
+GCTGATTCCGTGGAACAATACTCTCTTCCATCCTTTAACCGGAGGTGGGA
+ATATCCTGCATTCCCGAACCCATCGACGAACTGTTCAAGGCTTCGTTGGA
+CGTCGCTGGCGTGCGTTCCACTCCTGAAGTGTCAAGTACATCGCAAAGTC
+TCCGCAATTACACGCAAGAAAACGCCATCAGGCGGCTGGTGTTCTTTCAG
+TTTTCTTCAATTCGGAATATTGGTTACGTCTGCATGTGCTACTGCGCCCA
+TAGTCATCAAGTGTGTTCGTAGCAGTCGCTTATGTTCCTCCGCTTCGATA
+GACTCTGGTTGAATGGGTCTCATTCCATTCTCATGTGTGGACTCGCGAAG
+TGCATTTATCATCTCATAAACAAAACCCGCCGTAGCGGAGTTCAGATAAA
+ATCAAACCCCGCGAGTGCGAGGATTGTTATGTAATATTGGGTTTGAATCA
+TCTATATGTTTTGAGTACAGAGAGGGCAAGTATCGTTTCCACCGTACCTC
+GTGATTAATAATTTTGCACGGTATCAGTCATTTCCGCACATTGCAGAATG
+GGGATTTGTCTTCATTAGACTTATAAACTTCATGGAATATTTGTATGCCG
+ACTCTATATCTATACCTTCATCTACATAAACACCTTCAGTGATGTCTGGC
+ATGGAGACAAGACACGATCTGCACGACATTGATAACAGCCCAATCTTTTG
+CTCAGCACCTCTAACTCATTATACTCCATTTATAAACTCCCTTGCAATGT
+AAATGTCGTTTCAGCTAAACGGTATCAGCAATGTTTATTAAGAAAAGTAA
+GTAATACGTCAACCCGATGTTTGAGTACGGTCGATCATCTGACACTTACA
+ATGACTCTGGCATCGCTGTGAAGACGACGCGGAAATTCAGCATTTTTCAC
+AAGCGTTATCTTTTACAAAACCGATCTCACTCCTCCTTTGATGCGAATGC
+CAGCGTCAGACTCATATGCGATACTCACCTGCATCCTGAACCCATTGCCC
+TCCAACCCGTAATAGGCGATGCGTAATGATGTCCGTAAGTTACTAACGGG
+TCTTGTTCGATTAACTGCGCAGAAAACTCTCAGGTCACAGTGGCAGTGCC
+TTGATAACAAGGAGTCTTCCGAGGGATGGCGAACAACAAGAAACTGTTTC
+CCGTCTTCCCGGACTTCGTTGCTTCAAGTTTTAGCAATACGCCTTCCTCC
+CATCCGAGAGTATCCACCTTCGTATCTCACGCTGCCGTTGAGTTTTGACT
+TTTGCTTGTTTCAAGCTCAACACGCAGTCCCTACTGTTAGCGCAATACTC
+CTCGTTCGTCCTGGTAGCGGCGTTTGATGTATGGCTGGTTCTTTCCCGTT
+CATCCAGCAGTTCCAGCCACAATCGATGTGGTTGAGCCATTCATGAAAAG
+GTCTGCGTCAAATCCCCAGTCGTCTGCATTGCCTGCTCGTGCGCTTCACG
+CAGTGCCTGAGAGTTAATTTCGCTCACTTCGAACTCTCTGTTTACTGCAT
+AAGTTCCAGATCCTCCCTGGCATTGCACAAGTCCGGAACAACCCTGACGA
+CCAGGCGTCCTTCGTTTCATCTATCGGATCGCCACACTCACAACAATGAG
+GTGGCAGATATAGCCTGGTGTTCAGGCGCGCATTTTTATTGCTGTTGTTG
+CGCTGTATTCATTCATTTCTGATGCTTGAATCAATGACTGTCTCCATCTT
+TCATTACCCGGAACTGTCTGGTTAAATACGCTTGAGGCGTGAATGCGAAT
+AATAAAAAAGGAGCCTGTAGCTCCCTGATGATTGTTTGCTTTTCATGCGT
+TCATCGTTCCATTAAAGAGGCCGTTTAACATTGCCGAGTGCCAGGCTTAA
+ATGAGTCGGTGTGAATCCCATCAGCGTTACCGTTTCGCGGTGCTTCTCTC
+AGTAACGCTACGGCAAATGTCCTCGACGTTTATTATCCGGAAAGCTTGCT
+GTCTGGACTTTTTTTGATCTTCCGAAATTCAGCCTCGACGTGGCACTGCC
+GCGCAGGGCGTTTTTCCTGCTGAGGGTGTCATTGAACCAAGTCCCTCATG
+TCGGCAAGCATAGGCACACAGAATATTGAAGACCGCTGCTCAGAAAAATG
+CATTCCGTGGTTGGTCATGAACCTGTTTCTCTCATCTGCTTTCTGCTTTC
+GCCACATCATTTCCAGCTTTTGTGAAAGGGATGCGGCCTAACGTATGAAA
+TTCCTTCGTCTGTTTCTACCTGGTATTGGCAACAAACCTGATCCCGATTT
+GGCAAGGCTATGTGCCATCTCGATACTCGTTCTTAACTCAACAGAAGATG
+CTTTGTGCATACAGCCCTAGTTTATTATATTTATCTCCTCAGCAGCCCAC
+TGTGCTTTCCAGTGGATTTCGGGATAACAGAAGGGGCCGGGAAAATACCC
+GCTCGTTTGTAACGGAGTAGACCGAATGAATTGCGCC
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/115/7896_11181
+GGCGCAATCACTTTCGTCTACGTCCGTTACAAGCGAGGCTGGGTATATTC
+CCGCCTTTCTGTTAGCCGAATCCACTGAAAGCACAGCGGCTGGCTGAGGA
+GATAAATATAGGAGAGACCGAGCGGCCTGTATGCACAAAGCTCGTTTCTG
+TTGAGTTAAGAACGAGTATCCGGAGATGGCACATAGCCTTGCTCAAATTG
+GAATCAAGGTTTGTGCCAATACCTAGGTATGGATAACAGACGAAGAATTT
+GCTACGTTTAGCCCGCATCCCTGTTTTCACAAAAGCTGGAAATGATGGAT
+GGCGAAAGCGCCCCCCAGAAGCAGATGAGAGAAACCAGGTATGACAACCA
+CGGATGCCATTTTTTCTGGCAGCGGGCTTCAGATTCTGCGTGTGCTTATG
+CTTGCCGACATGGGAGCTTGTTCAATGACACCTCAGCAGGAAAACGCCCT
+TCGGAGCATTGCCCGTCATGGCCTAATTCTGAATCAAAAAAAGCCAGGAA
+GCAGTTTTCCGGATAAAAACAGTCGATGACAATTTGCGTAGCGTACTGAA
+GAAGCGCCCGCCGAAACGGTAACGCTGATGGGATTCACACGGACTCATTT
+AAGCCTGGCAATGCGGCTGTTAGAGATGGAGTCTTTAGGAACGACTGAAC
+GAGTGAAAAGCAAAGCATCCATCAGGGAGCCTAAAGGCTCACTTTTTTTA
+TTATTCGCATTCACCCTGCAAAGCGTATTAACCAACAGTTCAGGGATTAC
+TGAAAAGATGGGTCAGACATCATTGATTCAGCATCAGAAATAGAAGAATT
+ACAGCGCAACACAGCAATAAAAATGCCGCTGAACCCACCAGTCATATATC
+TGCCACTCATTAGTTGTGAGTGGTGCGATCCGATAGATGAACGAAGACGC
+CCTGGTCGTTCAGGGTTGTCGGAACTTTGTGGCAAGTTGCCAGGAGGATC
+ATGGAACTTATCTGTAAACATGAGAGGTTTCAAGTGAGCGAAATTAACTC
+TCAGAGCCTGCGGTCAGCGGCAGAGCAGGCGAATCGCTGACGACTGGGGA
+TTTGACGCAGACCCTTTCCATGAATATGGTAAACACCATCGATTGTGCTG
+GAACTGCTGGATGAACGGGAAAGAACCAGCATACATCAAACGCCGGCGAC
+CTAGGAAGACGAGGATATTTGCTGCTAACAGTAGGGAAAACTGCGTGTTG
+AGCTTGAAACACGAAAATCAGAAAACTCAAACGAGCAGCGTGAGTATTAC
+GAAGGGTGTTTATCTCGGATGGGAGTAAGCGGTATTTGCTTAAAACTGGA
+AAGCAACCGAAGTCGTGAAGACGGACCAGTTTCTTGTTTTCCCATCCTGG
+GAAGACCTCCTGTTATCAAGCACTGCCCTGGTGCCTGGAGAAGTTAATGC
+GGCAGTTAATCGAACAAGACCCGTTAGGTAACTATCTGACATCATTAACG
+ACATCGCTATTTACGGGGTTGGAGTCAATGGGTTCAGGATGCAGGGCGGA
+GTTATCTGGCTATGAAGTCTGACGCTGGCATTTGCATCAAAGGCGAGTGA
+GGATCGTTTTTGTAAATATAACTGCTTGTGAACAATGTGAATTCGCGTCC
+GGTCTTCACAGCGGATGCCAGAGTCTGGTAGTGTCAGAATGATGACCGTA
+CTCAAACATCGGGTTGAGTATTATCTTACTGTTTCTTTACATAAACATTG
+CTGATACCGTTTATGCTGAAACGACTACATTGCAATGGAGTTTATAAATG
+AGTATCAATGAGTTTGAGTCTGGAGCAAAAGATTGGGGTCGTATCATGTT
+GTGCAGATGCCGGGTGTCTTGTTCTCCATGCATGACATCACGAAGGTGTT
+TATGTAAGATGAAGGATAGATAGAGTCGGCATAACAAATATTCCATGAAG
+GTTTATAAGTCTAATGAAGACAAATCCCATTCTGCAAGTGCGAGAAATGA
+CTGATGCACGGTGCAAAATTTATTATCACGAGTACGTGTGGAAACGATAC
+TGTGCCCTCTCTGTACGAAAACATATAGATGCAATTAAACCCAATAATTA
+ACATAACAATCCTCGCACTCGCGGGGATTGTATTTTATCTGACTCGCTAC
+GGCGGGCTTTGTTTTTATTGATGATGATAAATGGCCTTCCCGAGTCACAG
+GAGACATGGAATGGAGAGCCATTCAACGAGTGGTATCCGAAGCGGGAGAA
+CGATCAACGACTGCTAACGAACACTGGATGATATTGGCGCAGTAGACCAT
+GCAGACGTAACCAATATTGAATTGAAGAACTGAAAGAAGCACCAAGCGCT
+GATGGCGGTTATTTTCGTTGCGGTATTGCCGGAACTGTTGCGGATGGTAA
+CTTGACACTTTCAGGGTGGTAAACGACGCCAGCGACGTCCAAGGAGCCGT
+TGAAACAGTCGTCCGCGCCCTTCAGCGGAATGCCGGATCTCCCCAACTCC
+CGTTAGAGGATGGAAGAGAGTATCTGTTCCAGCGAATCAGCGGTAAAGGT
+GACTTAATCAGACCAGTTACAGGTGGCCTTGTTGAAGAGGATCAGAATGG
+GAAGAAGGCGAAGTCATGAGCGCCGGATTTACCCCCTAACCTTTTATATT
+AAGAAACAATGGATATTATGCTACAGGGACCAAGGACGGGGTAAAAGGTT
+TGGGAATTAGGCAGAAGACCAGGACGAATAGCAATCCTGAGCTAGTACAG
+GCCAACATTGAGCTTATTTTCAGGACCACAACACGCTAAGCCTCTGACAG
+CGAGAATCAACAGTGATAATTCCCTGTTACGTTACATTCATTCGGCTTGA
+ACGCCTACGAATAAATCTGGCAGCAGAGGAATCCAAGCGAAGCACTCATA
+AATTACATGGCAAGAAATTAAAGCAATAAGGAGGGGTCTGCCTGATGCTC
+ACTATGAAAGACATTCACCACAACAGAATTGCGGCAGTGCTCAATGGATA
+AACAGTAGACAGGGCAAGGGCGGCGCTCAGCCAGTTAGAATCAGTATCAA
+CACCTGAGCCGATGCATTCCGAGAGGCAATAGCGAAGCGCCTATAACAAC
+AAACCATGTCGCCTGCCAACTCGCGGCAGGCAAAATCAGAGGTAACGAGA
+CAAGAGACTTACCGGCTTGACGGAATAGCTGAAAATTTTATCAGCAGCAG
+AATCATCCCATGTTGGCTCAGACTTGCAATGGAACTGGCTGTTTGTTACC
+GGGCAACGAGTTGGATGATTATATGCGAATGAAGTGGTCTGATATCGTAG
+ATGGATATCTTTTATGTGCGAGCAAAGCAAAAGCA
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/147/0_6711
+CGTGGCCTCCTCACGGGGACAGAAAGCGTCCCACGCTGTACGTTTTCAGT
+TGGCATTCAGCCCGGCAGGCGTCGCTGAGAATAGCCATCACCAAAGCGCA
+CCTTTCTTACGAAGGGACCGAAGGCCACATCCATACCGGGTTTCACTTTC
+CAGCGGAAGGTCTTTCATCGGTCCACCTCCGGAGAAACAGGCCACCATCA
+CGCATGCTGTGTCTGAATTGTCATCCACGGGCACCCTTGGGCGGCCCATG
+TCCATACCACCAGCCTTCAGAGCGCCGGACTATCTGCCCGTTCGTGCCGT
+CGTTGTTAATCACCCATGGTTATTCTGCTCAACGTCTCCGCGGACGCTGC
+GACGGCTGTTGCCATGCTGCCCGGTGGTACCGACATAACCGTCCGGTGAC
+ATAAGCCCGCGCATCAGCCGGTAAAGATTCCCCACGACCAATCGCGGCTG
+GTTGCCGTCCTTCGTGGAAGACCAACTCACCACTGGTGAACAATCCCCGC
+TGGCTCATATTTGCCGCCGGTTCCCCGTAAATCCCTCCGGTTGCAAAATG
+GAATTTCGCCGCAGCGGCCTGAATGAGACTGTACCGCCTGACGCGATGCC
+GCCGCCACCAACAGCCCCCCGCCAATGGCGCTGCCGATACTCCGACAATC
+CCACCATTGCCTGCTTAAGCGAATTTCTGTCATCATGGACAGCACGGAAA
+CGGGTGAAGCTGGCGCCAGTTCTTGCACACCTGCCCGTCAGCACTCGCCC
+GCACATACTTCTGTGCCAATACCTTCAAAAGGTCTGCGTGGCTGCCCTTT
+TTACCTGCGAACATACTGTCCGTGGCGCTCTCTTCCCACTCACGATCCAG
+CCGGACTTCCAGGCCTGCCATCCAGTTCCCGCGAAGCTGGTCTTCAGCCG
+CCCCAGGTCTTTTTCTGCTCTGACATATGACGTATTTCAGCGCCCAGCGG
+ATTAGTCGCATACTGTTCCTTCAGGCGCTGTTCCGTGGCTTCCCGTTCTG
+CCTGCCGGTCAGTCAGCCCCCGGCTTTTCGCATCATGGGGCCCGTTTTGC
+CGTTGCTGCCTGTGCGAATTTATTCCGCCTGCTGCGCCAGCGCGTTCAGG
+CGCTCCCTGATACGTAACCTTTGTCGCCAAGTGCAGCCCAGCTGCGTTTG
+GTACTCCAGCGGTCTCATCTTTATGCGCCAGCAGGGATTTCTCCCTGTGC
+AGACAGGCCTTGCGACGTTGCGCCGCCTCCTCCAGTACCGGCGAACTGAC
+TCTCCGCCTTTCCCACAATCCCGGCGCTGCTGGCTATTTTCTCATTTGCT
+CCCCGGCAATGGCTTCTCCAGCGTCCGGAGTTCTGCCTGAAGCGTCAGCA
+GGGCAGCATGAGCACTGTCCTCCTGACGAATCGCCCGCAACCACCTTCAG
+CTGGACCTGTTTCGGCTTTTTCAGCGTCGCTTCATAATCCTTTCTTTTTC
+GCCGCCGCCATCAGCGTGTTGTAAATCCGCCTGCAGGATTTTCCCGTCTT
+TCAGTGCCTGTTTCAGTTCTTCCTGACGGGCGGTATATTTCTCCCAGCGG
+CGTCCTGCAGCCGTTCCGTAAGCCTTCCCCTGCGCCTCTTCGGTATATTT
+CAGAGCCGTGACGCTTCGGTATCGGCTCTGCTGCTGCGCATTTTTGTCCT
+GTTGAGTACTGCTGCTCAGCCTTCCTTTCGGGCGGCTTCCAGCGCAAGAC
+GGGCCTTTTCCAGATCATCCCAGTAACGCGCCCGCGCTTCATCGTTACAA
+ATAATCATCCTTGCGCAGATTCCAGTATGTCGTCTGCTTTCTTATACGCA
+GCCTCTGCCTTAAATCAAGCATCTCCTGCGCGTATCAAGGACGACCAATA
+TCCAGTCACCGCATCCACATGGATTTTGAATGCCCGCGCAGTAACCCTGT
+CCTGCCCAGGTCTCCAGCGGTGCCCATGTTCTCTTTCAGTGCGGCGGGTC
+TGGTCATCAAACCCTTTCGTTGCGGCTCGTCCGCCGCCTTGCAATGCCCC
+GGCTTCATCGCCGGAACGCATGCACTGAGGCACATACGCAATCTGCTCCG
+CCGACACGTTATGGGAAACTGGCGAGCCATCGCCCGTCAGCCCCGACGTC
+GGGTCTGTGGTCACTTCCCGAAGGCTTCAGCGACCTTGTCCACCTCCACG
+CCGGATTGCAGAGGAGAAAACGCGCCACACTCTGGCCTGGTGGACTCAAT
+CCCCTCGAGCTCACTCGCTTACCCCAGCCTTAACCAGTGCGCTGGAAGGT
+GGACTCGCTGGTCCTGGTTAAACGTCAGCCCTGCGCCTGCCCGGCTCTGG
+ACAGCCAGCATACGATCTGTTTGCCGTCAGTCCCGCTGATTGCGGAAAGG
+GACCAGCGTTTGGTTGAATCGGACAGGGGTTGAGTTGCCCTGATACCAGC
+ATTACCCAGCGCAACCGGGTCGCCACGCCAGGCGAGGTGGCCCCCCCATC
+GGCAGGGTGATCGCAACCGGCAAGCCCTGGAACCATGGGGATCATCCCGC
+CGAAGGAGTCCTTCACCTGCCCCCCTGTTGCAGAGGATTCAGCCACGGAC
+TTTGCCCGCCTGGCAAGCTGCCGTGGCCACGGTCGGTGAACTGTGCAGGC
+AGCATACGCATGGCGGCTTTATACTGCCCCGACGGAAATCCCCTCCCCCG
+CTTTCTGTGCAGCAGCGCCTGTCCCGGCTCAGCGACTGTTCAACGACCTG
+CCGCTGTATTTTTTCGCATCACTTTCCGTACCCTAGAAAAATGACGCCTG
+ACTCTGGCCTCTGCCTCGTTCAAATCTGGCCGCATCCAGACTCAAATCAA
+CGACCAGATCGCTACCGGTTCAGCCATACCGACTCCTCCTGCGATACCTT
+CTGATACTGATCATAAGATGTACGTCATCCTCCGTCATGTCGGCCACCCT
+CCGGGGAAGCGGGGATAAACGTTCATTCCCGTCCGGGCCCAAAGCGGACC
+TTCCGGAGCCTGCCAGCCTTTCTGCATCAGCCATCATCTTCAGGTCTTCG
+TCCAGCCCTCGCCCGGTTCAAGCAGACTGAAATCGCATGCGGCTGCATAT
+CCGGATCGCTGAAAACAGGCTGGAGCACGGTGTACGTAGCCCGGAAAAGT
+GCATATCCATAGCAGAACATCATGAAAATAATGGGTACTGTAAAGCGGGC
+CAGTCGGCATACTCCGTGGATGACATCCCGGCAAGCATGGACGCCAGTCG
+GGTCGCCCATCTCACGCGGCCAGTTTCAGGGCAAAACTCAGCTCCCGTCG
+AACACTTCCCGCAGAAACAGGCTCTGCGGGCCCCGAGCGTCCTCTGTCTG
+TCTCAGGGGCATAATTTCACCAAAAACTTCCATACTACCAGACAGCCGGT
+ACACCACGTTTTCAGCATGAGAAATTGCCCTCGTGGGCCAGGTTGGGTAA
+GCACTTCCTGTCTCAATCGTTTAACGGCTTCATTCATGGACGGCATCCTG
+CGTCTTCTGCGGATGGTTATGCACAGGGACAGTCGCCACCAGAAACGCGC
+CGGTTCCAGGCGTCCTTACCACAGTAACGTTCCCGGTTGCTGTCTGATCC
+GCCTGTTTGCCTGCGTTTCATCAGGGCGAGATGCTCAATGCGCTGCAGGG
+CCTGACAGGTTCAGAAAGGCGTGACGGTTCACACCCCCCCGGTTATGTTC
+AAATGATTTCCGGGTTTTCAGCGAACATGCTGGACTCTCACGATTAACTC
+GGTGACGGTAATTTCTGCAACCGGCAGCAACTCACCATTACCGGTACACC
+GGGAATGTTGACCTTGCCTGCGCAACGCCGTTCAACGGTGATTGGTCATA
+CAACTGACCGACAACGGTGCTTTGTTTTTATACGCAGACACGCACCGAAA
+GCTCTTGTTCGGTTACGCCCTGTCCGGCTGGAAGGGCAACGGTCAGCGTG
+GTGCTCTGCTTTCACCACCGAGGTGCTGGCAGTGCGTCAGGTCCATTGCC
+GCGTTTGCCGCTGTTACCGTGCTGCGATCTTCGCCATCGACGGGACGTTC
+CCACATTGGTGACTTTCCACCGTGCCGGGGTGAATCACTTCACCTTCGCG
+TCACCGCCTTACCGGATACTGCTGACCCAGCCACGGAACACATCGACCGT
+GCGTTCGGGAAGCGATTTTTATAGGCACGGGTATCGCCTTCATTAAACAC
+GCCGCAGCGCCTGCTGCCCCTGCTCTCCGGCATCCACGCCCAGCGTGAAA
+GCTGGTATCTCACGGCAGATTTCTGCACTGCCCGGTCGCAGTCCAGTCTG
+CATCTTCATCATCGAGAAGCTGTCGTCATAGGGACTCAGCGGTCAGTTTC
+GCCGGGCGTCAGGTCTTTCAACTTTGCCGACGCGACCAGGTCAACGTCTG
+AAAGCGGATTCGCGTAGGGTCACCGCTCCCCTATATAAACCCACAGGGTG
+GTCCCGGCACCTTTTCCCGGCATTTGTAGGATTTGGTACAGGCATAGCGT
+CCTCACATTCATAGGTAATGACATAAGTCAGGATCGGCTGAACTCACAGC
+CCGCATCATCGTCGCGCCGGTAGTCAATAGCCGCTGGCTCACCATACTGG
+TGATCAAATTCTGCAGTGCGGGATATCGTTCATCACCGGATAAATTCGGG
+GACCCCATCCACGCATCAAGCTCTGAACTCGGCACCTGACAGGCAGGAAA
+ACTTCGATATGCAGCTCCGCCTGCCAGGTATCGCTGTCCAGCTTTCGCCC
+GTGTATCAGCGCCGTGAGATAAACGGCAACTGCCGGAAAATCCGCCTCAT
+CAAAAACAGCGGGGGCGACATCAAAAACGTCGCTCCGTGTCATGCTTCTC
+GTGCATCCGTACGGCTGCAGCGGAGTTCAGTATGTTTCATCGCTTTATTA
+CCATCCTCAGTTTGAGTGCTGCAGCGCATAGCACAGCTTTCGGAAGACGT
+TCACGCCGTATCCGCTCATATTTGTTTAAACGCCGTGGTCAGCGGCACCG
+CATCGATTTTCCACCACATCAATGGGGTAACGGTTTTTTCCCAGCCACAC
+GCTGATGACATGCCACCGGCCATTTTTCAGATTGCTGAATAAACCGCCGG
+GAATACGACGGTTACCACCAAAACACCTGCCGGCCACCTTTCAGGGATGA
+ACGCTGCCCCTTTTTACGACCTGCGGCGCGAAAGGACACCCGCGCTTACC
+CCAGCTTGATTACGGGCAATCCCCCGGTTAACTTTTGAACTCTGGCCTGC
+GGAATTTTTGACCGTGGCCCTTTTCACCTGGCCCTTTCCTTTACCAGTTT
+TCCGGCGTACCTTTGTCTCACGGGCACCTTGTGAACGCCGACCTGCGGAT
+ATCGCAGGGATGAAGCCAACGCGGTTAATGCATTGCGGCTGGCACCAGGA
+ACCCGCCGTTTTTGCTGATAGGCTGAGGTTTTCAACGGCTCTGCTCAAGA
+CCTTTTATGGCCATACCATCCCCTTTCAGCGGCGACGGTTAAACGCGCAG
+GCGGGTACGCCCGTCCAAGCCAGAGATACAACTTCCGCCATCATCCGGCG
+AAACCCGATATACCCATGAATTTTTCCTCACCGATGGTCCCAGCGTGTCT
+CCAGCGCCGCAGCTGGCCTCCCTCATCAGTCCGGCAACAGGGACGGGCTG
+GAGCCTTCAACGCGCACGCCCTGTCCCGGCTAGCTGATAATTTTCAGGGT
+CATCAAAAACACCACGTATCACCGCACCTGACTGCTCACCGGATGTAAGT
+GGTGGCTGACGTTTCCCATTTACCCGCGTATGTTTTTCATCGGCCGCGGG
+CATGGCAGCATCGAACAGGTTATCGAAATCAGCCACACCGCCTCCCGTTA
+TTGCTTCTGGCCAGGCCGCGCTCTGTCATTTCCGGCTGCCAACCGGCAGA
+GACACGAAACGCCGTTCCCGGCGCTACAAATGCCACAGGTTCATCCGCTC
+GTGGCGTGAAGTGCATCAGTATGCAGTTCAACCAGTGCCACGAACGTGAA
+CAGTTCAGACGTATCCCAGATCACGGTATCCGGCTGCGGCTGATCCCACC
+TCATGTTCCATGTGCCGGTCAGCACATTTTCCGGGCTGAGAGGGGTGTCC
+CTGACCGGCGTTTCATGTCCGTAGTCCTCAAGCCCTCTTTCAGCTCTGCC
+ATAACGGGAGCGCCAGTTTCTTTCTTCGTCCCGTCAGGCTGACATCACGA
+GTTCCCCAGTTTGTTACCCAGCCGAGCGGGAGACGGGCAATCAGTTCATC
+TTTCGTCATGGACATCCCTCCCACAGAGGAAAACAATGGCCCGAAGGGCC
+ATGATTAACGCCAGTTGTACGGACACGAACTACATCAGGGTCAGCCAGCA
+GCATCAGCGGGTGCTGACTCGATCATGGTGAACTCACGCGCCGGGATTCT
+GCCGGTGGTCACCAGTTTTTTCGGGTACGGGCAAGAGGGTTAATGCCTTC
+GCGCTGGTGCGTCTCGCATCAACCTGAAATGCAGCCATAGGTGCGCAGAC
+CGCGTGGCCTGAGTGGTTCCCCAGCACCATCGTGTTGTCCGGCAGGAAGT
+TCTTTTTTGACGCCCGTTTTTCCCACGTACTGTCCGGAATACACGACGGA
+TGGCCACATCGCCTACATCCCCTTATAGGACCGCCGCTTTGCCCAGGTCT
+TGTCACCGCTGTCTCACCAGCTCGAAATTAGAGACCCGACGGGTATCTCC
+AGCTTCTCCTTGACGGCTTTGAAGGGAACGGAAAAGCGCCAGCCTTTTCA
+GGTCGAACACG
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/171/2019_3396
+GCCGTAAACCTATGGGTGGAATAAAACATGGGACAGAATCACCGATTCTC
+AACTTAGCGAGATTACAAAGTTACTGTCCAAACGGTGCAATGAAGCCAAG
+TTAGAACCTCCCGTCCAGAATGAAAATATTACAAGCCAGCAAGGCGGCAT
+GTTGGGGACCAAGGGTAAAGAACATCTCAGATGGTGCATCCCCCTCAAAA
+ACCGAGGGAAAATCCCCTAAAACGAGGGGATAAAATCCCGTCAAATTTGG
+GGGATTGCTATCCCTCAATAACAGGGGACACAAAGACACTATACAAAGAA
+AAAGAAAAGATTATTCGCCAAGAGAATCTGGCGATCCTCCTGACCCAGCC
+AGAAAAAACGGACTTTCTTGGTGAGATCGGAATGCTTGGCAATTCGAGCG
+GCAGCAGAGGGAACAGCAGAAGACCTGGACCCGCCGAGCAGAGTGGATCG
+TTTGACATGGTGAAACTATCGCAACCATCTCAGCCCAGAAAACCGAATTT
+TGCTGGGTGAGGCTAACGGATATCCGCCTATGCGTGACGGACGTGACCGG
+ACGTAACCACCCTGCGACAGTGTGTGGTGACGTTCCAGTGGGCATTGCCC
+CCAGGACAACTTCTGGTCGGTAAACGTGCTGGTAGCCGCCAAACTTTCCG
+CGATAAGTGGACCCAACCCTCGGGAAATCAACCGTAAAGCACAGGCACAG
+AGGCGGTGACAGCAGCAAACCAAAAAACCGACCTGCCCCACACAGACTGG
+ATTACGGGTGGATCTATGAAACATCCCGCCGCACGATGGTTAACCTTTGA
+CCCTGAGCAGATGCCGTCGATCGCCAACAACTGCCGGAACCAGTACGACG
+AAAAGCCCCCCGCAAGGTACACAGGTAGCGCAGATCATCAACGGTGTGGG
+TTCAGCCAGTCTACCTGGCAACTCTTCCCCCCGGCGACCTGGCTAACCGT
+GGACCGAACGAAAGTAACGAAAATCCGTCGCCAGTGGGTTCTGGCTTTTT
+CGGGAAAACGGATCACCCACGATGGAACAGGTAACGCGATGCGCGTAGCC
+GTCCGGCAGAATCGACCATTTCTGCATCACCCCGGCATGTTGTTGATGGT
+GCCGGAAGGAGCATCCGTTAACCGCCGGACTGCCAAACCGTTCCAGCGGA
+GCTGGGTTGATATGGTTTACGATTATTGCCCGGAAGCGAGGCCTGTATCC
+GGAATGCCTCGGAGTCCTCTTATCCGTGAAACAAAACGCGCCCACTATTC
+CTGGCTGGTTAACCAACCTTGTATCAAACATGCGGGGCCATGCGCTTACT
+GATGCGAATTACGCCCGTAAGGCCGCAGATGAGCTTTGTCCATATGACGG
+CGAGAATTACCCGTGGTGAGCCGATCA
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/180/0_2599
+GGCCGCAGAAAATGAGCTTCGTCCATATGGACTGCGAGAATTAAACCGTG
+GTGAGGCGGTATCCCTGAAACCAGTAAAACAACTTCCTGTCATGGGGGCG
+GTAGACTCTAAATCGTGCCAGGCTCTGGCCCGAAGATCGCAGAAATCAAA
+GCAAGTTCGATACTGAAATGGAGCAAGTGTTGACGGGCAACGAGAAGGCA
+ATTATTCATTACGCCCGTGGGGACGAACCGATAATGAGCGCCATTCTGTG
+CGCCGGACCGTTTGCCAGCGCTAACAGCGCAACACGTAACCGCAAACTCA
+GGCAGGGCCGCGGCTAAAATGGCCACGGGCAGGGTTCTTCTGGGTGACTC
+GAAGGTATGGCTGGCGAACGGTGGTATTACCGCTTTGCTACCAGGGAACC
+AACGGAAGGCCGCTCGACGCCCGAACTTGGTTTTTAAGGAGTGTCGCCAG
+AGTGCCGCGATGAAACGGGGTATTGGCGGTAATGGGGAGTAAAAGATGAC
+CGATCTACATTACTGAGCTAATAACAGGCCCTCTGGTAATCCGCAGGCTT
+TTTATTTGGGGGAGAGGGAAGTATAAGAAAAAACTAACCCTTTGAAATCA
+GATCTCCAGGCATCAGTCAGCAAATACAGCTATTTGCCAACGGCAGTACG
+ATTGGCAAAATCCTTTGATTTTACCAGAACCAACCATACCATAAACCTCG
+GTAGTAAACTTCCAGTTAACGGTTTTAAACGCATCGACAGCCGCAGCTTT
+TAGCCCTGGTCAAAACACCTGATTAGCTATTGGGTCCTCGCTTTAGGTGA
+CGTCTCCTCGTCAGTTGAATGGCAATGGTCCCGCAGAGGATGGGCGATGC
+CAGCTATGCAAAGCGCTTATGTCGGTTATGTTTCAGCGCGCACCTTAACG
+CCACGGCCATCTTGATAGCGCAGATGTTGTTCCTAAGATATGCGGCGATG
+TCTTTTATAGGTAATAGGCCAGTCACCAGACATAGCGAATGCGTTGCGAC
+TGCCTGCGAATTTGCGGAGTATTAGAGCTTATACAGGCTTACGGTACAGA
+GCGTGGCGTTAAGTGGTCATACGAAGCGAGAACCTGGCTCTAGGAGTGGA
+AAGCCGAGATGGGGAGAACAGGGCTGCATGATAAATGTCGTTAGTTTTCT
+CCGGATGGCAGCGACGGTCCAGCATATTTGCTCTGCTAATGGGAGCAAAA
+GGACGGCCAGGTAAAACGTGCTTACGTTTTCATGGATACAGGTTTTGTGA
+ACATAAGTGACATATCGGTTTTGTCAGGGAAAGTTGTGAAGTTCTGGGAT
+ATACCGCATCACCGTATTGCAAGGTTGATATCAACCCGGAGCTTGGACAG
+ACAAATGGTTATACGGTATGGGAACCAAGGTCTCATTCAAAGCGAATGCC
+TGTTCTGAAGCCATTTATCGATATGGTTAAAGAATATATGGCACTCCATA
+ACGTCGGCGGCGCGTTCTGCACTGACAGATAAAAACTCGGTTCCCTTCAC
+CAAATCAAATGTGATGACCATTTCGGGCGAGGGAATTAACACACGTGGAA
+TTTGGCTACAGAGCTGATGAACCGAAGCGGCTAAAGCCAAAGCCTGGAAT
+CAGATATCTTGCTGAACTGTCAGACTTTGAGAAAGGAAGCTATCCTCGCA
+ATGGTGGAAAGCAACAACCCATTCGATTTGCAAATACCGGAACTCTCGGA
+ACTGCATATTCTGCATATAAAAAATCAACGCAAAAAATCGGACTTCCTGC
+AAAGATGAGGAGGGATTGCAGCCGTGTTTTTAATGAGGTCATCACGGGGA
+TCGCCATGTCGTGAACGGACATCGGGAAACGCCAAAGGAGATTATGTACA
+GAGGAGAATGTCACCTGGCCGGTATCGCGAAAATGTATTCGAAAATGATT
+ATCAACCTGGTATCGAGGACATGGTAGAGCTAAAAGATTCGATACCGGCT
+CTTGTTCTGAGTCATGCGAAATATTTGGAGGTGCAAGCTTTTGATTTCGA
+CTTCGGGAGGGAAGCTGCATGGATGCCGATGTTATCGTGCGGTGACTGCA
+AAGAAGATAACCGCTTCCGACCAATCAACCTACTGTAAATCGATGGTGTC
+TCGTGTGAAAGAACACCAACAGGGTGTTACCACTACCGCAGGAAAAGGCG
+GACGTGTGGCGAGACAGGACGAAGTATACGACCCATAATCCTGCGAAAAC
+TGCAAATACCTTCCACGAACGCACCAGAATAAACCAAGCCAATCCCAAAA
+GATCTGACCGCTAAAACCTTCAACTACACGGCTCACCTGTGGGATATCCG
+GTTGAGCTAGACGTGTGGCGAGGAAAACAAGGTGATTGACCAAAATCGAA
+GTTACGAACAGAAAGCGTGCGAGCGAGCTTTAACGTGGCGCTAACGCGGT
+CAGCAGCTGCATGTTGCCTGGAAGTTCACGTGGGTAGCCACTGCTGCGCA
+GAACTGAATGAGCGATCCGAATAGCTCGATGCACGAGGAAGAGAATGATG
+GCTAAACAGCGCGAAGACCGATGTAAAAATCGATGAATGCCGGGAATGTT
+TCACCCTTGCATTCGCTAATCACGTGGTGGGTGCTCTCAGAGTGGTGAA
+>m120619_015854_42161_c100392070070000001523040811021231_s1_p0/180/2645_6512
+TTCCACACTCTGAGAGAGCACACCACTGATTAGCCGGAATGCAGGGTGAA
+ACATTCCCGGCATTATCCGTTTTTTACAGCGTCTTCGCGCTGGTTTAGCC
+ATCATCCTTCTTCTCGTGCAATCGAGCTATTCGGATCGATCAGTCAGTTC
+TAGCGCAGCAGTGCTCACACACGTGAACTTCCGCACATGCCGCTTCTGAC
+CGCAGTTAGCAGCACGTTAAAGCTCCGCTCGACGCTTTCTCTGTTAGTAC
+TTCGGATTTTGGTAACACCTGTTTTCCCTCGCACGACTCTTAGCCATCGG
+ATATCCCACAGGTGAGCCGTGTAGGTTGAAGGTTTTTACGTAGATCTTTT
+GGGATTTGGACTTGGGTTTATTTCAACGGTGCGTTTCGTTGGACGGGTAT
+TTCAGTTTTCGCAGAATTAATGTCGGCTGATACTCGTCGCTGTCCCTCGC
+GCACACGTCTCCGTTTTTCCTGCGGTAGTGGTACACCTGTTGGTGTTTCT
+TTCACACCGGAGACCCATCGATTCCAGTAGGTTGATTTGGGTCGGAGCGG
+TATCTTCTTTGCTCACCGCACCGATACCATCGCATCATGCCGCTTCCTCC
+CTGAAGTCGCAATCAGCTGCCTCCAAATATTTCGCATGACTCAGACAAGA
+GCCGTATCGAATCTTTTAGCTCGTACCAAATGTCCCTGATACAGGCTGAT
+TAATCATTTTCTGAATAACATTTTTCGCGAATACGCGTCCCAGCGACATT
+CTTCCTCGTACATAATATCCTTGGGGCGTTTCCCGATGTCCGTCACGTCA
+CATGGGATCCCGTGATGACCTCATTAAAACACGCTTGCCATCCTCTCATC
+TTTGCAGGCAAGTCCTGATTTTTATGCGTCTGATTTTTTAATGCAGAATA
+TGCAGTTACCGAGATGTTCCCGGTATTTTGCAAATCGAATGTGTTGCTAT
+CCACCATGCGAGATTTCTTCCTCTCGAAAGTCTACAGTTCAGCAGATATC
+TGATTCCAGGCCTATTGGCTTTAGCCGGCTTCGGTTATCAGCTCTGATGC
+CAATCCACGTGGTGTAATTCCCCTCGCCCGAATGGTCATGCACAGTATTT
+GGTGAAGGGAACGGTTTTTATCTGTCAGCTGCAGAACGCGCCGCCGACGT
+ATGGAGTGCCATATTTTCCTTTACCATATCGATAATGGCTTCAGACAGGC
+ATTACGCGTCCCTGAATAGTCCTTTGGGTTCCCATACCGTATAACATTTG
+GCTGTCCAAGCTCCGGGTTGATATCAACCTGCAATACGGTGACCGGTATA
+TCACCAGAACTTCACAACTTCCCCTGACAAACCGATATGTGCATTGGATG
+TTCACACTGTATCCATGAAACGTAATGCACGTCTTTACCTGCCGTCGCTT
+TTGCTCCATTAGCGCAGAGCAAATATAGCTGACGTCTGCACCGGAGAAAC
+CTAACGACTTTATCATGCAGCGCCTGTCCTCCCCCATCTCGCCTTTCCAC
+TACAGAGCATATCTCAGCTTCGTCTGACCACTTAACGCCACGCTCCTGTT
+ACCACGAATGCCTGGTATAAGCTTCTATAGCTGCCGCAATTCCCCTACAC
+GCATGCCTGCTGGTTTGACTGGCCTATTACCACAAAGCCATTCCCGGCAA
+GCTTAGGAACAACATCCCTGCTGCTTTAATGCTCGGTAGAACAGCACACT
+GCTCCAGCTTTCTGCCTCCCAAGCAGCGACCATGCCATTCAACCTGAAAC
+GAGAGAGACGTCACCTAAGCAGGCCCATTAGTTCCCTGTTTTGGTCTAAG
+CTCGCGGTTGCGTTCCTGAATGGGTTACTACGATTGGTTTGGTTGGGATG
+CTGGTAAGGATTTGCTTGTACTGCCGTGAATAGCGTTTTGCTGAGTGCTG
+GGGATATCGAATTCCAAAGGTTAGTTTTTTTTTCATGACTTACTTCCCAT
diff --git a/tests/data/test_bas.fofn b/tests/data/test_bas.fofn
new file mode 100644
index 0000000..dd962ae
--- /dev/null
+++ b/tests/data/test_bas.fofn
@@ -0,0 +1 @@
+/mnt/secondary-siv/testdata/BlasrTestData/pbalign/data/ccs_P4-C2/m130328_211423_ethan_c100499512550000001823070408081371_s1_p0.bas.h5
diff --git a/tests/data/test_ccs.fofn b/tests/data/test_ccs.fofn
new file mode 100644
index 0000000..1352ec4
--- /dev/null
+++ b/tests/data/test_ccs.fofn
@@ -0,0 +1 @@
+/mnt/secondary-siv/testdata/BlasrTestData/pbalign/data/new.ccs.h5
diff --git a/tests/data/test_filterAdapterOnly.fofn b/tests/data/test_filterAdapterOnly.fofn
new file mode 100755
index 0000000..62697c8
--- /dev/null
+++ b/tests/data/test_filterAdapterOnly.fofn
@@ -0,0 +1 @@
+/mnt/data3/vol57/2820011/0006/Analysis_Results/m130302_124313_42130_c100502672550000001523078308081365_s1_p0.bas.h5
diff --git a/tests/data/test_leftmost_query.fasta b/tests/data/test_leftmost_query.fasta
new file mode 100644
index 0000000..520bad1
--- /dev/null
+++ b/tests/data/test_leftmost_query.fasta
@@ -0,0 +1,50 @@
+>ref000001|gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655 chromosome, complete genome
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
+TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
+TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
+CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
+ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
+CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
+AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
+GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
+GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
+ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
+ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
+GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
+ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
+CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
+TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
+GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
+TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
+AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
+CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
+CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
+CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
+TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
+GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
+GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
+TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
+ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
+CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
+GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
+GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
diff --git a/tests/data/test_leftmost_target.fasta b/tests/data/test_leftmost_target.fasta
new file mode 100644
index 0000000..35916f4
--- /dev/null
+++ b/tests/data/test_leftmost_target.fasta
@@ -0,0 +1,301 @@
+>ref000001|gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655 chromosome, complete genome
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
+TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
+TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
+CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
+ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
+CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
+AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
+GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
+GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
+ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
+ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
+GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
+ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
+CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
+TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
+GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
+TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
+AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
+CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
+CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
+CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
+TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
+GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
+GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
+TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
+ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
+CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
+GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
+GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
+TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
+TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
+CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
+ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
+CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
+AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
+GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
+GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
+ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
+ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
+GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
+ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
+CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
+TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
+GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
+TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
+AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
+CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
+CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
+CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
+TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
+GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
+GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
+TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
+ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
+CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
+GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
+GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
+TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
+TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
+CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
+ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
+CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
+AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
+GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
+GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
+ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
+ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
+GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
+ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
+CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
+TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
+GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
+TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
+AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
+CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
+CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
+CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
+TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
+GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
+GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
+TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
+ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
+CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
+GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
+GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
+TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
+TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
+CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
+ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
+CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
+AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
+GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
+GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
+ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
+ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
+GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
+ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
+CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
+TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
+GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
+TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
+AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
+CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
+CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
+CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
+TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
+GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
+GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
+TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
+ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
+CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
+GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
+GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
+TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
+TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
+CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
+ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
+CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
+AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
+GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
+GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
+ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
+ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
+GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
+ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
+CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
+TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
+GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
+TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
+AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
+CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
+CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
+CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
+TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
+GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
+GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
+TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
+ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
+CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
+GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
+GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
+TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
+TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
+CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
+ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
+CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
+AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
+GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
+GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
+ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
+ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
+GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
+ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
+CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
+TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
+GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
+TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
+AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
+CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
+CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
+CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
+TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
+GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
+GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
+TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
+ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
+CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
+GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
+GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/tests/data/test_pulseFile.fasta b/tests/data/test_pulseFile.fasta
new file mode 100644
index 0000000..7543e32
--- /dev/null
+++ b/tests/data/test_pulseFile.fasta
@@ -0,0 +1,695 @@
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/7/0_1165
+GAATCGTCGTCAAATACTCGCCATGTACCCTCTTCTTCCCATCCCGCTCA
+AATCCGACATCAATGCAGGCCTTCATCGCTTCTACGCGGGTCCATAGTTG
+GCAAGTACCACGCATTTTGTTCGCGCGTCACCCACGGACTGCCTAGTTAC
+TGCTACCCGGCCATCGAAGGCTGACTTTATGGCCTCCGAAACCACCCGCA
+GCCGCCCGGCAACTTCCATGAAATCCCGGAGGCTAAACGGCATTTCAGTT
+TCAAGGACTCGTTGCCACGTCACTGCAATAAACCATCGGAGACAGCAGGC
+GGGTACACGCATACTTTCGTCGCGATAGATGATCGGGGATTCGTAACAGT
+TCACACCGAGCCCGCGAGATATGAATTCAAACAACGGGTTCCTGACGTCG
+CTCTCACGCTTACTCGTTTTCCCCAGGCCAGTGGCTTTAGCGTACCTCCG
+GGACCACACCGGTGCAAACCTCAGCAAGGCAGGGTGTGGAAGTAGGAACT
+TTCATGTCAGTCCACTTCTCCTTCTCGCCGCGAGCGGGTTTTGCTCATCC
+CGTTGTGACCTCTGAAGCGGTGATTGACGGCGAGCCAAGTACCGATTTTG
+CCACGCATCATGCCCTGTTCGACCAGCTCTCCATCGATCCCGGTACCGCG
+GCCCTGGCAGGATATCGCTCCGGTCGTCACTGCCTGCCACCTTCTGCTCT
+GCGGCTTTCTGTTTTCAGGACTCCAAGAGCTTTTACTGCTCGCCTGTGTC
+CAGCCTTCTCGCGACGATGCACGAATGTCCCGCGGCCGAAATATCTGGCG
+ACCAGAGGCGGCAATAAGTCGCGTCATCCATGTTTGTTATCCAGGGCCGA
+TCAGCAGAGTGTTAATCTCCTGCATGGTTTCATCGTTACCCGGACGGATG
+TCGCGTTCCGGCGGACGGTTCTGCCAGTGTATTGCAGTATTTTCGTACAA
+TCGCTCGGCTTCATCCTTGTCATGCAGATAGCCCAGCAATCCGAAGGCCA
+GACGGGCCACACTGAATCAATGGCTTTATCCGTCAACACTGTTCTGGGCT
+GCTGACTGACACGGCCCCGTGATTCCTCTCTGCTCTTTCGCGAGCGTTTT
+GAATGGTTCTCGCGGCGGCATTCATTCCATCCATTCGGGTAACTCGCGAT
+CGATGATTTACGGTC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/8/2069_2682
+CGGTGTATCAGGCAAGGCCACTCATATCAGGTGCAGCTTGACTGTCATCA
+ACACGGCCTTTCAGCAACACCCGATACTTCTTCCAGGGCCTTCCAGCAAC
+GAGGTGTGCCTTCCTTCGTTGCAGTTTCCAGATCTCAGCATCCTGAAGCG
+GCCGCGATATGCTCACTGGGCTACCTTGCATCAGGCCTTTTTTTTGCTTT
+TCTTCAAAAAAAAGAAAATGATGTTGCCATCGTAGAGAACATGCTGCTAA
+CGTGAGAGAAGAAGAGATTGAATCTCAGAGAGAGAGACAGAGCGGTCATA
+CAGCAGCTTAACAGTGCGGGACCAGGTGGGTTAGAGAGAGGTTCTGGATT
+AGCATCGAGAGAGAAGCGCGATATGCTGCGCTGCTGGCATCCTTGAATAA
+GAGAGACTACGCACGCTTTCTCGCAACTCTCCCCACAGCTTCTGTTTTGG
+GCAATATCAACCGCCGCTAGTACCATGGCAATCTCTGCTCTTGCCCCCGG
+CGTCGCGGCACTCGGCATATCCGCATAAGCGAATGTTGCGAGCATTGCGT
+ACCGTTTGCCTTAGTATTTCCTTAAGCTTTGGGCCACACCACGGTATTTC
+CGATACCTGTGTG
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/8/2724_3021
+CACAAGGTATCGGGGAAATCACCGATGGTGTGGCAAAGCTTGAAGGAATA
+CTAGGCAAAGGTACTGGCAAGTGGCTCGCGACATTCGCTTATGCGGATTA
+TTGCCGTAGTGCCGCGCGCCGGGGGCAAGATGCAGAGATGCATGGCTAAA
+GGCGTGCGGTTGAGATTGCGAAAAAAGCTGTGGGGTAAGTTGTCGAGAAG
+AGTGCGGAGATGCAAGGCAGTCGGCTAATTCAAGGATGCAGCAAGCGCAG
+GGAATATCGCGCTGTGACGATGCTAATACCAAACCTTACCAACCACT
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/13/0_278
+GTATAGAAATGGATCCACTCGTTATTCTTCGGGACGAGGTGTTCAGTTGA
+CCTCTGGAGAGAACCATGTATCATGAATCGTTATCTGGGTTGGACTTCTG
+CTTTTAGCCAGAATACATGGCCTGATATGTTACATGAGAGAATGGTATTC
+CTCATGTGAGTGGCTGTCTTTCGTCTTTCTCTTTGCATTTTCGCTAGCAA
+CTTATGTGCATCGATTATCAAGCTATTGCCGCGGCCAGATAGTAAGCGAT
+TTCAAGCTAAGAAACACCGACCATTAGC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/13/327_954
+CTTAAGCGATTTATCTTCAAGAATTAATACAGCTATAATCTGGCGCTAGG
+ACATAAGCTAAATAAATCCGATGCACATTATATGATACGCGAAAATGCAA
+GAGCAAGCAGAAAACATAAGCCACACATGAAGAGAATAACAGATTCTCTC
+CATTAACATATTCAGGCCAGTTAAAAAACAATCATGAGAGCTTAAAAGAC
+AGAAGTCCAACCCAAGATAACGAAATAATATACACTGGTTCTCTCCAGAG
+GGTTTCATTACTGAACACTCTCCGAGAATAACGAGGGATTCCATTTCTAT
+ACTACATCAACTGTAGGGGTTGTAATAGTTTATCCGATTTCTATCGCTGT
+AGGGGACACGAGAACCACCCGAGCCTGATGTGGTTAAAAGACAGGAACAA
+TCTTTACTACAGCAATACACTATTTAAGGTGATATATGGAAAAGAATTTT
+GAAAGAGTTCGAAGAAGCATACCTCAAGGATGTGATGGAACAATACCAGA
+GACTATCCGTATGACTAAACGACTATTGATAAAAATCAATGGTGTGGACA
+ATTCAAGCGATGCAATGGAGCAACGCTGCCCATCGGAATGCATGGTTAAG
+CTGAACGAAATGTCTTCCTTGTACATC
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/13/1004_1580
+TACGGAAACATTTCTTTCAAGGCTTAACCATGCATTCCCGATTGCAGCTT
+GCATCCATTGCCATCGCTTGAATTGTCCACACCATTGATTCGTTTATCAA
+TAGTCGATAGTCTACGATACGGTCTGGTATCTGTTCCATCACATCCTGAG
+AGATGCTCTTCGAACTATCTTCAATTCATTCCTTCCATATATCACCTTAA
+TAGTGGATTGCGGTAGTAAAGATTGTGCCTGTCTTTTAACCACATCAGGC
+TCTGTTCCTCGTGTACCCCTACAGCGAGAAATCGGATAAACTATTTACAC
+CTACAGTTTGATGAGTATAGAAATGGATCACTCGTTTATTTCGGACGAGT
+GTTCAGTAATGAACCTCTGGAGAGAACATGTATATGGTTATCTGGGTTGG
+ACTTCTTGCTTTTGCCAGATAACTGGCCTGATATGTTAATGAGAGATCGT
+AATTCCCTCATGTGTGGATGTTTTTCGTCTTGCTCTTGCATTTTCGCTAG
+CCAATTAATGTGCCTCGATTATCAGCTATTGCCAGCGCCAGATATAAGCG
+ATTTAAGCTAAGAAAACGCATTAAGA
+>m121004_000921_42130_c100440700060000001523060402151341_s1_p0/13/1625_2202
+CTTAATGCGTTTTCTTAGCTTAAATCGCTTATATCTGGCGCTGGCATAGC
+TGATAATCGATGCACATTATTCTAGCGAAAATGCAAGAGAAAAGACGAAA
+CCATGCCCACATGAGGAATACGATTCTCTCATTAACATATTCAGGCCCAG
+TTTATCTGGCTTAAAAGCAGAAGTCGCAACCCAGATACGATCATATACAT
+GGTTCTCTCCAGAGGTTCATTACTGAACACTCGTCGAGATAAGCGAGTGG
+ATCCATTTCTATACTCTCAAACATGTAGGGGTGTAATAGTTTATCCGATT
+TCCTCGCCTGTAGGGTACACGAGAACACTCGAGCCTGATGTGGTTAAAAG
+ACAGGCACCATTTTACTACACGCAATCATATTTTAAGGTGATTAATGGAA
+GAAGAATTTGAAGAGTTCGAAGAGCATCCTCAGGATGTGATGGAACCAAT
+ACCAGGCACTCATCCGTATGCACTACGACTATTGATAAAAATCAATGGTG
+TGGACAATTCCAGGATGCAATGATGCAAGCCATGCAATCGGAATGCATGG
+TTAAACTGAAGAAATGTTTCCTGTAAT
+>m130406_011850_42141_c100513442550000001823074308221310_s1_p0/5/0_14503
+AAAGAGAGAGATAGAGAACAACTGATCAAGTGATTTCTTTGATTTTCCAG
+ACCTGCCACGTGTTGCACGCCGCTGTTCCAGACGATCAACGCCCCGATAT
+CATCCGGACAGAGCCGTCCAGCGGTGACAGATGCCCCCTCAACACCAAAA
+TAAACGACCTGCAAAACTGCCCGTCTGCTTCAATGCGAGATGTCCCGAGT
+CGCGAACTCTCCACACGAGCAGCGCTTCATCTTTGTATCGCGTTTTTTAT
+TCTCTCGGACGCCAGCGGACGTATCGGCGCGCAATCCCGATACACAGAGG
+TAGAGTACTGAGACACAAGACTTCCTCGCTCGGGTGATAAGTGCGGCAAT
+CGGCGCAGTGGCCGATTCCCCACCAAACACGCAGCCGCAGCACACGCCGG
+CATTAGCCGCGCGACGACCGCACGCGACTCCCAACCGTTAACGGACTTCT
+CGCTTTCTGAATCTAGCGTACATACAGTAACTGCGTTACAGCCCTTCGGC
+CAACGACCCTCGGACAGGACACTTTCTGTGTACTTCCTCAGCCGCGATGT
+GCCTATCCTACTGCTGGCAGACAGCTGCCGTTCCCCAGCGGCCTGGTGGG
+TTGGCAATCAGAACCACAGGCCATCCTGTACAATGCAAGCGACGCGCTGC
+ACTCCTCTCTGAGCCAATCATCACAGGCAAGACCGAGAGCTTTTGCGCTT
+ATTATCGCATCGACAGACATATTACTTTAAATAGACGCCTGCTAGTCGTC
+GTGCACAGATCCTGCACCCACCAGCGGGATCTGATCCCGCGATACAATCA
+TCACTCGAGTCGTTAACGCCTCACAGCCAGCGCGTCGGACAACCGCCTAC
+TCCCTGAAGCGACGGTGGTGCGTGCTCGCTACTCGAATCATGGTGCACCG
+CGGTTAATAGGCCACAACTTTACCAGACCCTGCGCCAGAATTCTCGACAG
+GCACGCCTGGACTTACCTCCGCTGCGCGATCTCGCTTCCGTCTAAGCACG
+CGTGCATTTCACTCTAGCCGATGCTTCCCAAGACTGAGTCAGGATCAACC
+TGCCACCAGTACTCGCTGGCTTGCCGCGAATCCAGCTGAGCATTCGCTCG
+AAACAACATGGTGACCAATAGAAAACTGACGATAGAGCCTAACCAAAACA
+CCACAGTAGGGATTACTCCTCTCCATCAAAAGCCTCATATCGGGTACGTA
+ACCGAGACTGACCGAGTACCACAGCGCGATTACTTACGCTCCAAAGACGC
+GAGCAGCCCCTTGAATTCTCCACCATCCTCAGCTCCGCACTATCGAGGAT
+GAATCACGACGCAGTCGTCTTGATTAATACGGGCAAAATCCATTTTCTTA
+TCCACAGCCAATGACACCACGCAGCCTGGCCCATTCGTTCTTCTCCGAAC
+CTCGCCACGACAGACAGCGTACCCAGCGGCGACACCTCCCGTCGCGACTA
+CCAACATCACCGTATTTCTATAGGCCAGCACGCATCAGTCCCTGAACACA
+TACCGTTTGAACCGTCTGTAACATTTGACCACAGCACGACCGACATAGGT
+CAGTGTCTATGCCTATGCACGCGGCGCGGGTGTTCCTCCAAAGCAATAGC
+CCGCACGAGCAGGAGGCGCCAAAGACATGGCAGACACTACGTGCGTTGTC
+GCTCGCGCGAAGCCTCTTCTGCCAGAACAATACATTAAACCCGACGACCT
+GTGTATCCCACGGAGGAGATCGCAAGTTTTGGTAGCGAATTGCTTCCCCT
+GTCTGCACCAGCCCTACGTGGTATTCGCGCACCCTAACAAATGGCATGTA
+AGGGTGCACGAGAGCGGGGGGGGGGTGCCGCTAGCTTCGCCGCCAGTTCC
+GGCGTTTTTCCATGTTCCAGCGCGCGTTGTTGTTCGTCAGGAGCAGCTTC
+CGCGACAGGCGACACACACCCGATCGGAAGATAGCGCTGCACCATCTCCG
+CAGTTGGTCCGAGTCCACGCGATTACACGCAGTGCGTGTATTCTTTGCTG
+CGCCAGTCGCGTTCCCTCACGCAGAGGTGCGCACCCGGAGCGCGCCTGAA
+CGCGAAGTTGATCCCAGACCTCGAGCCAGGACCGCGCAGTCTTGGTCCAG
+CGCTAGTCTAAACACCGGCCCTGCGCGATATGATCTGCTCCAGGTTCACT
+CTCACTCACCTTTCTAGCGTGGTCATCACACCTCCTGTCATCCGCTGAGC
+GAACTGCCTGGCGCGCCCGCAGCACCTCACGCAGCAGCACGCGGGAACCA
+TCCTGAGTCTGTCACTTTTCGCGGAGCTTGGTTTTATGGTCCGGATAGCC
+TCTTCAGTAGCTGGCGTCACTATCGCGATTCTGCGTCTGACGGCGGCCCT
+GGGTTGAGCGTACATTACTGAGGCCGTAAGTCTGCTTGCGCACGTGGTCA
+CCAAGCCGTGCGACCGTGCACTATCCTCGCTCAGCAGCGGCATACGCGAA
+GTCGCGGAACATCGGCGCGCACACACGCGGTCGCGAGGCCGTTCATCGCG
+TCAATCGCATTGGCGGTAGACATCAACCGGCGTTAGCGCTGGAACGTCCA
+GCGCTATTACCCTGTTCCAGCTATCAATCGGTCTCATGCCAGATACCTGC
+CAAACAGCGACACAAAGTAGATCGAATCCGAACAGAATCTGATCATTCCG
+CCGGTATGCGACGCTCGCGGACCAGTTACACGCCAGAGCCTGCAAGCTGC
+GGCGATCTGGCTGTCCATCATATTCGCCGCCACGTAAGCGGGATATCCTC
+CCTGCGCGATCGTTTGGCCTATCCCGAGAGCTAGCAGGCTGAAGAGATTA
+ACCACACCGCACCATATCCATACAACGGAAATGGCGACTGAGCTGAGTGT
+CCTCACACATCTCTCACACAGCACCTGCTCCGACTGCGATAGAACCTACG
+TCTCGTCGCTTCATGCGGACAGTCAACGGCAGCTTCTGCCAGCATGCACG
+CCGTGTTTTGGTTTGCACCCCATTCAGCCCTGCTCAACACATCCGCACAC
+GCCTATGTGAGCGCGAATCTCGTCGAACAGGGCACGTGACGCATGGCATC
+GCACTTCGAGCGTCTATGGGTTGAACACTGCGGCGGGAGTTCACCATCGC
+TAGCGGCAAAGACGCCTGTTCAGCACATACCTATGGTAGCAACTCGCGAG
+GAGCTTACCTCGAGTCGTCGAGCGTGTGCCCAGCGAAATATGCACGTCGC
+TCGCAGCCCGTCTTGTCGCAGCACGCGATTAGTGTTTCGCATCATTCGAG
+GAAGCCGGGCGTCAGCAGGCGGAGACAGAATTGCTCGCAGTCTAACTTCC
+AGCGCCCTGGAATGACCGGCGGTGCGAGCATCGTCTAGGAATAAAACTTC
+TGCGCACCGCAGTTTGAGGAACAAATTTTCGCTCGAGACCCCCCTTCTGC
+GAACAGCTATGATCGAGACAGCAGATAGACAATTAACGTGTTCATTCTCA
+CGCAAAAATCGGCGATCTCGCCCTGAAAGCGAGACAATCTATCAGACGAG
+TGCGTTACCGGTGCGTTCATACGTCGGTTGTCAGCAGAGCCAGACATAAG
+ACTTGGACTGTTCAGGCTGAGCACCGCTTGCGGCTTGCTGGTTATTACAG
+CGGTAACTTCCTGTGCTTTTACCCACTTGCGTCCAGAACCAGGACGCATC
+TCAGTCATGTAAACTCAGCCTCTTGAACACGTACCTATTACTACGCGATC
+GCCTGGCCGCCGATGCCGAGACTCCGTACTTCTGTCACCCAGCCACGGTT
+TCAACCTCGGTCATCAACCAGCTCTTGCCGAGACTTGCGTGTGCGCGCGG
+CGTCGCGTCAGCAGTCTATACCGACATTCTTAAAAGCTCGCCTCATGCTC
+CGACCGCTGCCAACCTCCACCCACCGTAGTATTACACCACAGTGGCCGCA
+CCCTGCGTCGAGCGTCGAGACAGTACCCGGGTGGATTTCGCAGTTTAGCC
+CCTTCGCCCCAGCAGCTCGGCGTGATTGACGGACTAAAATTAGCCGTTTC
+CTGAGAGCAGGCCCGGTATCATTAAGCAGACCTGACGCATAGTCCGAACA
+TAATACGCCCTCCACAGACAGGAACGAATCGGTACTCGCCTACACAGGTG
+CCGGCGTCGAGAGAGATCAATGTTCCTGCGCGGCCAGAGCGGATAGACCG
+CCCACAATTATCAAGGATTGTGCGCCATTTCATACCGTGCATAAACAGAT
+TCAGGAGATAATATCCACCATGGCAGTGACGCTCCTCGCGAACGGGCATG
+ACATGTAATTGCGGCCAGTCACTGAAGGGGTATGGCAACACAGCCCCCGT
+CAGAACGGCGAGCTGAATGCACATCTTGGCGTCCGTAGCGTGGGCAGCAC
+AAGACGGCGATTAATCAGTATAGTACGAGGCCCGCACTGTGTACCATTGA
+CGGCTTGCGCTACGGTAATGCCCTGTTTTTCTCGTATGATCCGAGCGCCT
+ATTCGTCTGCGCCCAGGTATCTCTGATACAGCAGTGCGCAGGATGACGTG
+CTCGGAGCAGCGTGCCAACACATCCAATCTCGACCACCGCAGACGACCGT
+ACCAGTTATTATCAAACCGCTGCGCTGCACTGGTTCCTCCGACTGAGCAG
+CGCGGCGTGCCCGCTCGGTCCGCTGCTACAGCCTGTCCACCACCGCGCCT
+TCACAGATCACGTTTGTCGCCCGGTTTGATGGCATCAACGTGGAGTCTCT
+CACGCTGATATACATAGGTGCCTGCGAGCCCTATTGCTAATCCAGCGGTC
+GTAAGATGGCACGATGCTATGTGGTCGACGCAGGACCAGGTCCTTAGGCC
+CGGTTTAGACGGACGGTACAATCAGCCACACACACGCATACCTCAACGGC
+CCAGCTTATTCTGCCCGCGAGTGAACGCGCCAGCAACCATAGTTAAGCCA
+CCCGCTTGCAGTCGCGACTCCAGCCAGAAGCACACATTTGTACAGATACT
+CTTCCGCTCATTATCGATAATCGCTCAACCAGCAAGTCGAACTTCTGAGT
+ACCAGAGCCGTAAGTTTCGGGGTCTCTCAGTAAAGCTGTGGCAATCGCGG
+AAAGAATGCCGGTTTTGGGTAGTCCTGAATGCGTATGTCTGTGATGTCCA
+TTGTATTAGTGAGCAGTAATTATCCATAGCTGCTGTGCACGTCAACGCGT
+CCATAAGTGCACTGATATGCCTGCCTGCTGTTAGCGGCGTGGACGCACTG
+CTGTCGTCTCACAGTAACAAATAGCTAATCCCAGTTTTTATACGCCACCT
+TGAGCCGCGGTCCTGCAGCCTGCCTGCGCTGCGTAAGATACTGCCTACAC
+AGAATGGAAGTATCTAGGACTGGCACTGGCAAGAGAAGACAGCCTGCTCC
+GAATTCTGCGGTCAACACCTGGCGATTGTTGTGCTTCAGTGGCTTTCTTG
+CTTTTCCATCTCTAATCTACCCTTCTTGAAATTACGCTTCAGGATAATCC
+CGCTAACTGCAGGACACTTCCTGCGATCCGGTAAGGCCACTGGTGCGACC
+CGGAAGCTCGGTGGTGACTGCAGAGGTCTCAGTTTTGACTGTTACCTACG
+CCCAACGGCGGGCATCCTGCTGGCCACCTGGTAGATCCCGGCCTATATGT
+CGTCACATATTCCTAGTGATAAGGAGCTAAACTATGGCCGAGAGAGCATT
+ACCCAGAGACGACCAGCCATAGAGAGGCCGCTACACACCTCGTCGTATCT
+GTAGTAAACCACAATGAAAGAAAAACCTGGCAAACGTGAGAAATTACAGA
+GCCGTAATCCGCGCCTCTGGTCAAATTGGTCAACCGCGCGGCATCCATGA
+TGTTTCTGTGCCAGACACAACCGAAGAATAAGGCTGAGCCAACATGCACG
+CTGTGACACAGCAACGCGTTATATTATCGTCGTGCTACTGGTACATACAT
+TCACCAATGTATGTAAATCTAACGCCTGTAAATTCACGAACATATGCAAG
+AAAAACCAAACAAGAACGCGCAAGAAACGCGCCAACACCATCCTCGATGT
+GGCTCTACGTCTTTTCCACAGCAGGGGGTATCCATCCACCTCGCTGGGCG
+AGGATGCAAAAGCAGCTGCGTTACGCGCAGTGCAAGCTACGGCATTTTAA
+GAGACAACTCGGGATTTGTTTTCAGTGGAGAATTGGGAACTTGTCTAGAA
+TCCAATATTGGTGAACTAGAGCTGAGTATCAGGGCAAAATTCCCTGCGAT
+CCACTCTCAGTATAAGAGAGATATTAATTTTTTCAAAAAAATTCCGTTTC
+TTGAATCCACGTGACAGAAGAACGGCGTCGATTATTGATGGAGATTATAA
+TTCCACAAAATGCGAATTGTGTCGGAGAAATGGCTGTTGTGCAACAGGCA
+ACAAACGTATCTCTGTCTGGAATAGTTACTGACCGTATAGAACGAAACGT
+TAAAACATGATTGAAGCGAAAATGTTGCCTGCCGGATTTAATGACGCGTC
+GCGCAGCAATTATTATCGCGGCTATACTTTCCGGCCTGATGGAAAACTGG
+CTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGT
+TCGCCATCTTACTGGAAGATGTATCTCCTGTGCCCCAACGCTTTTCGAAC
+TCCTGCCACTTAACCGAATAACCCTGAATCTGACATCCAGTGATTTCTTC
+CCTGGACATTTTCGTCGTTGCTATTCTGGTTCACTGCGTCGTGATATTCA
+TTAGCGGTTTTGACTTTTTCAGGTCGTTCTCAGGTTCGAAACCTTCATCC
+TCATCATGACTATGTTCCAGTTATTACAAACGATCACGAGCATTTTGTTT
+TTTCCAGCATTTATTGCTTTTGTTTTTGTCTGTTATGCCAGAACACGGCG
+TTTGCGCGGCGTCATCGAATGGTGATCTGCCGCAAAAGCGACCTGCCAGG
+CGCAACTTGAACTCCAACTAAATTGAACAAAAAAGAGTCTTTCTGCTCAG
+GACAAACTTGGTGCAGCAGATCTGACAGAACATTCAGCCACCCTCGATAA
+AATCGATCGCATAAAAGAAGAGACATTTCAGCTAACGGCAAAAGTCGCTG
+AAGCGCCGGAAAAAATGCGCCAGGCGACCGCCGGCCGTTAAACAGCACTT
+AGCGATGTCGATAACGGAGAAGAAACTGCGCAAAATTGTCTGAGCCACGC
+GTCCGTGTGCCGCCAAGCTGGAAACTCGCGTTGCCCCAGGCGCTGGACCG
+ATTGCAAAAACGCACAACAACGATCATGCGTCTTATAACAGCCAGCTGGT
+TTCGTTTACAGACGCAGCCCCGAAACGCGTGCAAATGCGAGTATAACGCT
+TCGCAGCAAGCTGCAACAAAATTAGCAAGTCGTCTGGATGGGACTGTTCG
+GCGAGACCAGCCTTACGTCCACAGCCCAGAAAGTGCTTAAATGCAGGCCA
+GCAGGCCGTTTCTGAACGGAGATTGACCAGCAGCGTAAAAGCCTGAAGGG
+AACCCACCGTCCTGCAGGATACCATTGCAAAAGCAACGTGATTACGTGAA
+CGGCGAACAGCCGCTCGTCTGGTAGCACCAGTTACAACTGTTGCAAGAAG
+CCGGTAAACAGCAAACGCCTGAACTTTAACCGAAAAAACGGCGCAGGAAG
+CCGTCTCCCCGGATGAAGCCGCGCTATTCAGGCTAATCGCGCGGTGAAGC
+AGAACTGGAAATTAACCAGCGTTAAGTCAGCGTCGATACCCGCGACTGAA
+AACGTAATCAGTGATGCAGCAAAACATTAAAGTCAAAAACTGGCTGGAAG
+CGGGCGCTGCAAATCGAACGCAATATTAAAGAGCAGATTGCCGTGTCCTG
+AAGGGCAGGCCTGCTGTTGTCTCGTATCCTTTACCAGGCAACAACAAACG
+CTGCCCCTCGGCGGATGAACTGGAAACATGACCCAAACCGCATCGCGGAT
+TTTGCGTCTCGAAACATTTGAAGTTAACCAGCAGCGTGATCACTCTTTCC
+CAGAGCGATGCGTAAACATCAACAAAACTGGAATGAAGGTCCTACCAACC
+GAAGCACAGCGAAGGTTCACGATCGTTATTGCAAGTGGTTGATATGCGCG
+CGAATGCTGGATGTCAACCTTCAAACAAACAAGGTTGGGTAACCAGCTGA
+TGATGGCCCATTAACCTGCAAATCAACCAGCAAGCAGTTAATGAGGTGTC
+GAAAACACCTGAAAATCCATCCTGACCAGCAAATCTTTTGGTGAACAGTA
+ACCGTCCAATGGAGGGACCTGGAATCAAAAGCGTTCCCGAAAGCCTGGAA
+AAGTGAATTTAAGTACAAGAAAACACGGTGAACTGGCAAAAATGGCCCGC
+CGTTTTTATCGCTTTCCTCGCTGGTTGCCGCTGCTGTTGATTGCCGGGCT
+GATCCCACTGCCGTCTGGGCTGGCAATGAAAGCGTATCAACAAAAACTGG
+CTTTCCGCCTGTGGGTTCCCTGCGGTAACGACCAGCCAGCTCAAAACTCC
+AAAAGCGATCCTTATCAGACCTGACTTCCGTGCGCCTGCGGTGTGCCTGA
+TTATTCTCGCGGTTGGCCTGATTCTGTTGACCATGCAGCCTCAACAATCC
+AGGAACTGCTATGCGTCGTTCCAGTCAAAAAAACTGGCGCATATTCGGCT
+GGTGGTTGCCTCGTGCGGAAGGTAGCTGGAGAAAAACGGCGTTGCGTACG
+TCACTTGACTCGGCATGCCGGAACAGCAGACCAGCCACTGGCGTCGGCAA
+ATTGTCCCCGCATCAGTCTCGCATTGCTGCCTATCCATTTCGTCTGTGGT
+GGCAGAACTTTCCCCGCTGCACTCTGATGGAGAGTGCTGGGGCAAGCGAT
+GATTTTCCTCAACCTGCTGCTGATTGCCCTTCCTGGTATGCCGATGTGCG
+CGAAAAGCTGGCGTGATAAAGAGTCGCAGCCCAATGCGACTGTCCACCAT
+TACAGTGCTGTCGATAATCCCGATTGCGCTGATGGTGCTGACTGCTACAG
+GCTAACTTCTACACTACGCTCTGCGTCTGGCAGGAGCTGGATAGAAACCG
+TTTATCTGGTGATCATCTGGAACCGGCTGTACCAACGTTTACTGCGTGCG
+GCCTTAAGCGTAGCGGCGCGGCGCGTATCGCCTGCCGTCGTGCGCTGGCG
+GACCGTCGGCAGAATCTGTGAAAGAGGCCGCAGAAGGTGCTAACCGCCGA
+AGAACCACCATTGCACCTGAAAGCCAAGTTAACCAGCAGACGCTGCGTAT
+TACCATGTTGCTGATGTTTGCGCTGTTGCGGTGTCATGTTCTGGGCAATT
+TGGTCGATTTATCACCGTAGTTTCCAGCCTATCTCGACAGCATCACGCAT
+CTGGCATTACACACGGCAACGAAGCTGGCGCTGCGGTGGTTGAAAAAAAC
+GTCACCACTGGCAGTCCCTGTTGTTTGCGATTATCGCCCTCAATGGGTGG
+CCTGGGCGTTGATTCGCAACACCTGCCTGGTTACCTGGAAGCTGGTGCTC
+TCCGCGACTGAATATGCGCCACGGGCGCGTCGTATGCCATACTACTCACC
+CATCCATTAACACAATCATTATTTGCTGTTGGTGCAGAACCGGTGTTCGG
+ATCGACTGGCCGTCTCTGGGATAACCCAGTGCTGGCCGCAAGCATTATCC
+GTAGGGTCTTGGTTTTGCGTTTACAAGACAATTTCGGTAACTTCGTCCTC
+CGGTTTGATCATGTCTATCCGAACACAGCCGCTCGCGGTGCGTTATTGGC
+GATACGGTAACCATGGTAGCTTCTCGGGGGAACGGTAAGAAGACCGTATT
+CGTGCGACAGACGATTTACCGATTTCGATTCGCAGAAGTGATCATCGCCG
+AACAATAGCGTTTGTTACCGAGCGTCTGATTCAACCTGGTCGTTGACTGA
+CACTACTACGCGTCTGGTGAATCCGTCGTCGGCGTGGCCCATGGCTCCGA
+GTCCTGGAAAAAGTGCGTAAAGTGTTACTTGAGGCGCGACTGACCAACCC
+AAGGGTGATGCACAACCAACTGCCGAAGTCTTCTTTACGCGCATTTGTGC
+CAGCACGCTTGGAGATCATGAGCTGCGTCTGTATGATGCGTGAACTGCGG
+ACCGTAGTCGTACTGTCGATGAGCGAACCGTATTATCGATACGCTGATGC
+CGTGAAACCGACATCAACATTGCCATGTTAACCAGCTTGAAGTGGACATC
+TGCACAAACGAGAAGGGCGATGAGGTGCCCGGAAGTAAAACGCGACACAA
+AGGCGATGACCCGACCGCCAGCGGTAGGGTAAAAACGAAGGGGCAACATT
+TAGTTGCCCCGAGATTGCTAACAAAGGTGCGCGTTGTTCATCGCCGATGC
+GGCGTGACCAGCCTTATCCGGCCTAACGAAACGCAAGAATTCAATATAAT
+TGCAGGAGCGGGTGTAGGCCTGATAAGCGTCAGCGCATCATGCAGTTTTG
+CGTTTGCCCCAACCTTAGGGGACATTCACTACGCCGACCCCAATTTATCT
+TCTCACTTTCCGCCTCATCATCGCGCGTTAATTTCCTTTTCATAATCACC
+GCTTTACAATAATCCTAGCGCGCGCAGCACGGTACTGGCAGGGATTGATT
+TTCCTCCCAGCAGCACAATCAATCGGACAGCCAGTTTGACATCGTCAGGG
+GCCATGTTTCCAGTGCACAATATTCTCTCCATCTTGCTAGCGGGTTAAAC
+GCGCCTACCTGTTTTCGATTTTTCCTAGCGCATGGCGGCAGCGTGGCCAG
+GCGCGCTTCATAGGCTTCCACTTCAACGACTGCAAGCGTTTGCTGTTCCA
+CGAGATCGGCTCAACAACCTGCGCTCAGACGGGCTCTGCGTCGGCAACGC
+ATCTCCACGCTCAGCCGCCCGCTCCAAAATGCTGACTGCTGAATACGTTT
+ACGCTGCCAGCGGGCCATCTTTTCGAGGGTGCACTGTCCCACTCGCGCAT
+GACCAGGCGGGAGGCTTCACGCGCGATGCTTCCAGTTTGTTGCCGCCAGA
+TGTTCCGCCAGCCCAGGCCAACCTGCCGGCAGCTGTCTGCTGCTCAACTG
+CATACGAAGCGCAGCCAGATTATCGCCCGCCCTCGTCGAGACAAGCCTGT
+AGTGTTGTCGCACGAAGTCTGAAAAAGATGCCGTCGAAACGAGCACTCAC
+TACGTGGCGAACTGTGACACCCGGGGACAACAGACGCTGGACGCAGCGTA
+GCGAGCTTGTCCTTCCCAGTTTTTCCAGCAGCCCCAGGGGCGTTTTCCGA
+TAAGACCTCAATGCAACCATGATAATTGTCTATGCTCAAAGTACCACTCT
+CGTATAGCTGACACACTCAATAGTGCTAACGAATCATTTTAACATCATTG
+GCTGGCTGGCGGTAGTGCTGGGTACGCTGGGCGTTGGTAATTACCGTTAT
+TACCACCCGACGCGTTATCCTGCTGGCGGCCTGGTGCTTTGCCCGTTCTT
+CCCGCGCTTTCACGCCCTGGTTGCCTGTACCCGCTCATGGTTTGGCAGCC
+TATCTACGTTTCCTGGCAAAACATCATGGATGCCGCGCGGCGTGCCAACG
+CGGGCGATTTTTTGCTTATTTTGCTACGTTTGCCATGTTCTCTGTGGTCG
+TCCAGAGTGCCATGGTGCGCATCATGTTGCTGGTAATTCTCGCCTGTTTG
+CTTTTCTATATGTGGCGAATTCCGGTGATTGATGAAAAAGCAAGTAAAAG
+CACTGAAGCACAACAATCCGCAGTTGCAATTATTGCGACAGCCAGTACAT
+TCTGGCGTTTTCGAGCACAGGCCAGGCGGTCAACAGGTTAAACAACTGTT
+ACTTTTGAACGTTTTTAAAACCGCCGTGAGTAACCCACGCGTAACAAGCA
+GGCATACACTTAATGACCGCGACTGCAACAGCAGTTGAGTATCTCAAAAA
+ATTAGCATCAAAGCATTCAGGACACCCAAACCCGCATTCTTTTCCGCGAT
+GATCACCAGCTTACTGGAAGACCCGAAAGGCTTACGCTCTCAGCATCGAC
+TTGCTGGTTGAGCGTTACCAAAAATGCGGGCATTACCCAAAGTTGGTCGG
+CACCGAGCGCGTGGTCTTGTTGGGCCGGCTCCGGTAGCTTCTGGTCTGGG
+CGTTGGCTTGTACCGGTCCCGTAAACCGGCAAACTTGCCGCGTGAAACCA
+TGCAGTGAAACTTACGAGCCTGGAATACGGCACCGATCAGCTGGAGAGTT
+CCACCGTTGATGCCATCAAACCGGGCACAAAGTTCTGGTGTGGCGACTGC
+TTGGCAACCGGCGGCAAACTATCGACAACGACGTTAAACTGATCCGCGTC
+TGGGTGGTGAAGTGGCTGACGCTGCGTCATATCAACCTGTTCGATCTCGC
+GGCGAACAGCGTCTCGAAAAGACAGGGCATTACCAGCTCAGCCTTGTCCC
+GTTCCACGGGCCATTAATTATCCCAGTCTGTGCTCCACGCTACGGACAGC
+ACAAGAATGTGCATTCAGCCTCGCCGTTCTGACGGGGCCTGTTTAGCATT
+ACCTCCTTCGTGTAATCCACCTTCCAGCGTTTCAGTAGCCTGGCCAATGA
+GTTATCAGGTCTTTAGCCGAAATTGCGCCACAAACTTTGCGACGATCGTC
+GGCCAGGAACATGTGCGACCGCACTGGCGAACGGCTTGTCCGTAGGCGTA
+TTCATCTTGGCCTTATTTTTTTCCGGCACCCGTGCGTCGGAAAAACCTCT
+TTCTGCCCGACCTGCTGGCGAAGGGTAAACGCGAAACCCGCATTCCGCGG
+ACCCCCGTGGCGGCGTGGTGCGATAACTGTCGTGAAATGCGAGCAGGGGC
+GTGTCCGATCTGATTGAAATCGACGCCCGCCTCGCGCAACCAAAGTTGAA
+GATACCCGGACCTGCTGGATTAACGGTCCAGTAGCTCCGGCGCGTGTCGT
+TTCAAGTTATCTGATCGCGACGAAGTGCATATCTGTCGCGCCACAGCTTT
+TAACGCACTGTTAAAAACCCTTGAAGAGCCGCCGGAGCACGTTTAAGTTT
+CTGCCTGCGACGACCGATCCACATGAAATGCCGGTGACGATTATGTCCGC
+TTGTCTGCATTCATCTCAAGGCCGCCGGATGCGAGCAATTCGCCATCAGC
+TTGAGCACATCCTCAACGAGAACATATCGCTTCACGGAGCCGCGGGCCGC
+CTGCAAATGCTGGCACGCGCCCGCTGAAGGCAAGCCTGCGAGTATTGCCT
+TGAAGTCCTGACCGACCAGGCGATTGCCAGAGGGTGACGGCCAGGTTTCA
+ACCCAGGGGTCAGTGCGATGCTGGGTACGCTTGACGTACGATCAGGCCCG
+CTGTCGCTGTAAGCGATGTCGAGGCCAACAGGCGAGCCGTATGGCGGCTG
+ATTAATGAAGGCCGCTGCCCGTGGTTCGAGGGGAAAGCGTTTGCTGGTGG
+AATGTCGGCCTGTTGCATCCGTATTGCGATGTACAACTTTCGCCTGCTGC
+ACTTTGGCACGGACATGGCCCGCCATCGGAGCTGCGGGATGCGTGAACTG
+GCGGCGGCACCATACCGCACCGGATATCAGCTTACTATCAGACGCGTGTT
+GATTGGTCGCAAAGAATTACCGTAATGCGTCCGGACCGTCCGCATGGCGT
+TGAGATGACGCTGCTGCGCGCCGCTGGCCCATTCCATTCCGCGTATCCCG
+CTGCCTGAGCCAGAAGTGCCACGACAGTCCTTTTGCACCCGTTCGCGCCA
+ACGGCAGTAATGGACGCAACCCAGGTGCCCGCCCAACCGCATATCAGCGC
+CCGCAGCAGGCACCGACTGTACCCTGCCCCGGAAACCACCAGCCCAGGTG
+CTGGCGGCGCGCCAGCAGTTGCAGCGCAGTGCCAGGGAGCAACCAAGCAA
+GAAAAGAGGAACCGTCAGCCCGCTAACCTGCCGCGCGCCGCGGTGGACAT
+AACGCTGCGCTGGAAAGACTGCTTCCGGTCACCGATTCGCGTTCAGGCGC
+GTCGGGCCATCGGCGGCTGGAAAAAGCGGCCAGCCCAAAAAAAGAAGCGT
+ATCCGCTGGAAGGCCGACACTCCGGTGATGCAGCAAAAAGAAGTGGTCGC
+CACGCCGAAGGCGATGAAAAAAGCCTGGAACCAGAAAAACGCCGGAACTG
+GCGCGAAGCCTAGCGCAGAAGCATTGGGGAGCGCCGGACCCGTGGGCGGC
+CACAGGTAGCCAACTTTCGCTACCAAAACTGGTCGAACAGGTGGCCGTTA
+AAATGCTGGAAAAGAGGAGAGCGACCAACGCAGTCATGTCTGCATTGCCT
+CCTCCTCAGCGGCATTTGAACAACCCCGGGTGCACATGCAAAAAACTGGC
+GAAGCGTTGACATGTTAAAAGGTCAACGTTGAGACTGCTATCGTTGAAGA
+TGAAATCCCGCGTGGCGTACGCCGCGGGAAAGTGGCGTCCCAGCGATATA
+CGAAGAAAAAACTTGCGCAGGCGCGCGAGTCCATTATGGGATAATAATAT
+TCAGACCCCTGCCGTCGGTCCTTTCGAGCCGGAGCGGATGAAAGAAAGTT
+ATCCGCCCCCATTTGATTCGAACACAGCTTACGTTCGTCATCCTTCACAA
+CCC
+>m130406_011850_42141_c100513442550000001823074308221310_s1_p0/6/0_5194
+AAAAAAGAAGAGAAGAATTCCCGGTTCAAAAATTAGTGACATATACATCA
+TATAGACTACTTCATCGAGATTAATAAGAAAATCACAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAGTACGAATCCAATATTCATCTCCAGAGCCATG
+ACGAAACGAAAACAAAAAAAAAACGGAATAGAATACAAAAAAAAATGCGT
+CGGGAATAATACAGCTATCAGAACGAACTTATCAACTAAGACAAACTAAC
+AGAATGGGGGAAAAGGACAAATTAATATCAGAGCCAAAATATTAGAAATG
+AAAAAACCGATACAAATACAACTAATCGCGCGCGGCAATTAAGCACAATA
+TGCTTAACATGACCGGATATAAAAAAAAAAAAACTCAGTAAAAGGATGAT
+AAAACGCCGCATTAAGAGAAAAATCGAATAGCCAGACGGTGCCCATAAAC
+AAAATATATAAATCGAAGGTGAATGCTCGAAGGCATAAAAAATATCATAG
+CCAGTTTGACCGTAGAAATGAGGACGAATATTATTTGACGAACGTATCCG
+CTGGCATACAGAGAATAGAATTATAGTAATCGTATACAAAAAAAAAACAG
+AATTCGGCAATAAGCGCAATTGCGAAAATAATGACAAGGACGTTAAATAG
+AGAATCATCACCAAAAAAGAAATAGATAAAGTTAATTAAAGCAGAGAGCA
+GAAGGGAAACCATAACTAGCAAACAGATACATAAAAGCCAGCATCAAAGA
+TGATCGAATCGCCATACCAATAAGAGAGGATAAAACAATAACGAACAGCA
+ATATCATGCAATCAGATCTTTCATATGTGGGAGATATAGATAGAAAGTTA
+GTATATATGATACGATAGGGCGGAAAAATAGAGAATATCACTATTTATTC
+ACAACCCAATAACGCCATAAAGAAATAACAGAATGACAGAGATTCCAGCA
+TGTTCCAAGAAATAGACCAAGAAAAAAAAAAAATCTTTAGCGAATGGTTG
+TGCCTGTGGTGTACAAAGATAATATGCGCAATTCTCACCAGAACAATAAA
+TAATAACAACTAGCTATTATAATGCAGATAACTCCAGAATGGGCTGCCGA
+CAAAGAAGGTTTCATGAGAGCGTGAAATTAACCCTGATTTAAAAGGTATA
+TACAAAATGAATAAACATCGCAAAGACAAAGATAACAATATCAACAAAAA
+AAAACGATATAAATACACAGTATATACAAGATAATTAAGCGACACAAATC
+GATAAGAAGACAATATTGTGAATAGATGGAAATATAGGGGAAAGAAAAAA
+TCACATCGGGACATAAATTGTAATCACCGCAAAAATGCATAACGAGTAAT
+ATAGCGAAAGGATTATATATATAGACGGTACGGAACAAAACAGCAAGCGG
+GATTCAGAATCCTTTACATAAACAAAAGTGTACGACGAATAGACACATTG
+CTGATCGAATGCAGACGCGAATGGCGACAGAACGACCCGCGGTTTAAAGA
+GCCAGCATAGGAACGAAGCCCACGCAACCGCCCTTAGCAATAGAGCCTGA
+AGTAGTAGTCGAAAGGCACGTATAAAAAAAAACGAGAAATATGCCAGACA
+GCACTAAAGGCCAAGATAATTAGACAAAGAACACAAGGCGATAACAGAAG
+CGACGAGATGATGAAGTGCGGTTAAACACAATAAAAAAAAAAAAAAAAAC
+ATATTAATCATATAATATACAGAAATGGCGAGAAGTACCTAGTATAGACC
+ATGAATGAAGAACCGTAAAAAGCGCATCAGGAATTCTAAATAAAAAAGAT
+ACTTCAACGGAGAAAAAATCCTTAAATGAGATCTCCGCTGTTGAAAAATC
+GACATCACCTGACAAGCAGTGTGTCTGTATAATGTTACATGTCCGGTGCA
+AAAGTACGAACGCCTATAGAGACTGAGCGAAGAAAACAGCAGCAATATAA
+TACAAGCACAAATCTGATACTCGCAGCCGCAGTAAATATAGAGCGGATTA
+CATAAAAAATTGAATCGAATGTAAAAAAAATACATGCATCGCACTATAGA
+AATCCGAGAATATATATGAATACCACAGCTAATAGGTCGCAGTATATGTG
+GCAACAGATGACTAAGGAAAACAATCGCAGAAATTCAGACAGAGAAATTA
+ACCAAAACAGAGAGCAATACCGTGAATAGACACGAAAATAGACGGATACT
+AAAACACACAGAAATCCAGACAGACCAGATAGATTGAGTCAGCCGACGCA
+CACACAAAAAATAAAATCAGCTGCGCTGTAAGACCAGAAGTATGTGTATG
+CTAGCAACCTTATGCGGATATTCGGAGTATGTACTGTAATAAAAAAATGC
+GCCACTAGAAATCACCAGTCAGCGGAATTACAATCAACAGCGAAAAATAT
+ACACGCGCACAACAGGAAATAACCCAACCAGAATTCACCATGATACGAAA
+CGGTCAAAAAATCGCCTAAAGAGCTGAGCAGATCAGCTGAATAAAACAGA
+ATCCTTTATGCTATTACCGGAGCTGTAAAAGACCCAAAGCAAAAATCCAC
+GCGACAAAAAAAGATTTCAATCTACCCACGAGAGCGCAGAAAAAAAAAAA
+AAAAAAAAAAAAAAAGCTTTGACATCGCTAAGTGGCGTCAGCCCAAAAAC
+AAGATACGCATGACTAATATCACCATACTTGACGAGAGCTTAATTCTTGT
+GCACATTTGCGGCTTTGTCGCTCTGAATATCGACAACCGCGACGCGATAA
+CCCCATACGGCAGCCAGACCAGATGGCACAAAGGACAGCGCCATAGGTAA
+TTAGCCCACCACGACTGACAACGCAACCTGAATTCATTTTTTACTCCTTA
+ACAGATTCAAACTTCAAACCGAAAAAATCCCGAGCGCGATATCGATCCGA
+GAGACAGGGCTAGCCAACAAATGGACAGTGCCGGAATTCCGCCTTCGTTT
+ACCTCGAAGACGGAGGAGAATGACTGAACCAACAGTTCGCGAGGTTGTCT
+TCCAGCACGAACTAAGCACCAAGCGGAGATTCCACCGGATAGCGAATGCA
+TGCCCAGAGTTGAAAATTTGCAACCAGGAGTTAAGGATTAGCACCTTTCA
+AACAATCGCCGATGGCAAAAAATGAAATGAAGCAAAAATACATACATTAC
+GAGGATCCGCAAAAAAAAGGACAGCGCTTCACGGAACAGGTGATGAGACA
+TACTAGTACAAGGGGCGTCATTGGCACTCGCGCCGATACGGGTGAAATGG
+ATGTCTGATAAATAAAAAAAACAGGATCATAAAAAGTTATCAGCCTCTAT
+TGATAGAATAAAAAACACAGGAAGAAAACCAGAGCGATCAGTCGATAACG
+AGACGCGGACGATATAGAGGCTCACCAGTAAAAAAGAAGAGAGACACACA
+AAAAGAAGCGAACAGTGTCCATGCGGGCTTACCGCCAAGCAGACAAAAAC
+CAGACCGAGAGAATGAAGAATACGCAGAAGCCGCACTGCAGGCGATATGA
+TGGAAAAAACAGTGCCGGATAAGCCAGAAGCGGCAGGAATATTTGCGAGA
+CAAATCTGCAGCGAACATACAAAATACAGAACCCGATACCTGTGCGAATA
+AACTGCGCCTGGGCCCGAGGAAAAAAGGAAGAAAAGCAAGATGGGAGAGA
+CGAATGAGCAGAGCATAGACCAAAAAAGACCAAGAATGAAGGCATTCGCC
+AGCGGAAGCAAGCCGTGGAGCAATACCAGATCACAAGGAAGAGCATAAAA
+TGAATGCCAAATGAGCGCCAGAGACGAAAAATACCATAACAGGCAAAATA
+GATATTTTTAATACAGATAGGAATCGAATGGTGTCACGCACCAAGATTGA
+ACAGCACAGCAACGTGCCAAACAATGCCCATTACCACCTTTACCGCCAGG
+TAAAACCAATTCCGCCTTGATATCAGAGAAATGATTTTCTTACTGGATAG
+TCTAAGTACAGAAGCCAACATGAAGAGGTAATGATGGGTGTCAAGCATCA
+CATAACTACAAGTGATGTTTCTTCTATATACGCCAAGACAATTAAAAAAT
+ATCTTAATCCACAAATGTAAACTAGCGCCAGCGACCAGGACTATGCAAGT
+CGAGTGGATAATTAAAATGGTAGGGAAATAACGTATAAAATCCGTATATC
+GGATAAGAATGCCGCAGCGTAATTAGATGGCCGCACAGTCGATTACAAGC
+GACAAAACAATTCCGCTCCGCGGGATATCCATTCTATATAAATCACAGAA
+TCAATAGCCTGCCAGCACACCGTGCTGGATGCCAGTATGATCAAATCGCA
+GGCCAGAGGTCCAGAGCGGTGAAATATAGACGATTTTAATTTTCCCACGG
+GACGTAAAAAATAAGAGAGCTATATCAAGCCTAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAACAAAAACAACAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAACAAAAAAAAAAAACAAAAATAAAAACACAAAAACCCC
+>m130406_011850_42141_c100513442550000001823074308221310_s1_p0/7/0_2243
+AAAAAAAAAAATCAAAAAAAAAAAAAAAACAGAAAAACAAGAAGAAAAGA
+AAAAAATAACTGAAAAAAAAAAAAAAGAAGAAAAAAAATAAACAGACAAT
+AAGAAAATAGCAAAAAAAAAAAAGAGAAAAAAAATAAGAATAAAAAGACA
+AAAAAATAGCAAAAACAACAAAAAATTAATAAAAAGAAAAGAACAGAACC
+AATAAAGATAAAAAGATAAATAAAAGAAATAAAAAAGAATATAAAAGAAA
+CAAACAAATAAAAAAGACAAAAACAAAACAATAAAAACAATAAATATAAG
+ACACAACATAAATAAATAAAAGAAATACAAAATTACAATAAGAAAAATAA
+ATAAAAACAATAAAGAAAAAAAAAAAAAAAACAAAAAAAAAAAAACACAA
+AAAGAAACAAAAGAAAAAAAAAAAGAAACAAAAACATAATACAAAAACAA
+AAGAATAAATACAAAGAAAAAAAATAGTCATAAAAGAAAAGAAAAAGAAA
+AAAACAAACAAAATAGTAAAAAAAAAGAAAAAAAAAAAAAACAGAAAAAA
+AAAAAGTAAAACAAAAAATTAACAAACAAAAGAGCAAATAAGTTGAAAAA
+AAAGAAAAGAAAAAAAAAAAAAGAAAAAAAATCAGAAAAAATAAAAACAA
+ATAATAAGAACGAATAAACATAATAAAAAAAAAAGAAAAAAAAGAAAAAA
+AGAGAATAAAAAAACAAAATAAAAAAAAAAATAAAAAATAAAAGAAATAA
+AAAAAGTAAATAAACAAAGAACAAAAAATACATAAAAAAAACAATAAAAA
+AAGAACAAAAATATAAGAAAAAATAAAACAAAAAAAAACGAAAGAACACA
+AAGTACTAAAAATAAAAACATAAAAAAGCAACACAAAAAGATAACAAATT
+AACACAAAAAAATAGAAAAAAAAACAGAAGTAATAAACAAAAAAATAAAG
+AAGGTAAAATAAAAGAAAAGAATGAAAATAAAACAGAAAAAACAGATATA
+GACATATAGAATATAAATAAAAAAATACATAATAACAAGAATAAAAAAAA
+GAAAGAAAAAAAAGAAAACAAAATACTAATAAAAAAATGAAACAACAAAG
+AAGTAATACAAAATATAAATAAGTGGAACACGCAAAAATAAAAAAAAAGA
+AAAAAAAAACAAAAAAAAGAAATCGGCAAATAAATTAATAAAATCAGAAA
+CGAGAACGAGAAATAAAAAACAACTAAGGAAGAAACATCAAAAACAACAA
+AAGAGTAAATCAAAATAAGAAGAAGAGTAAAAAATTCACGCAAAGAAACA
+AAATCAAAAGAACAACAAGAAAAAATAAAAAAGAAATATGCAAATAAACA
+AAAATGTTATTAGAAAAAGTATAATAAATACAATAAGAAAAAAAAAACAC
+AAATAGAAGAAAAAGAGAAAAAAAGAAAAGAAAAAAAATTAAAAAAAATA
+AAAAAAAAACAACAAAAAAAAGGAGAGAAAGATAAACAAAATAGAAAATA
+GAAATAAACAGAAAAAGAGAAAAAAACAAAGAAAAAAAACAAATAAAGTA
+AAAAGAAACAAAAAAAAAACAAAAAACAAGAGAAAAAAAATAAATACAGA
+AAATAAAAGAAAACAATACATAAGAATAACAAAAAATAAAAACAATAATA
+TAAGAATAAGAAATAGAAAAAATAAAGAAAAAAGTAAAAAAAAAAAGAAA
+GAAAAAAAAAAAAAAGAAAAAAGAAAAAAAGAAGAAAAAAAATATAATAA
+TAAAAGATAATAAACAAATAAATAACATATAAAGAAAGAGAAGCAGAAAA
+AAAAAAAAAATAAAAAAACAGAAAGAAAAACTGCAAAATAAGAAAATCAA
+ATAAAAAAAAAACAATAAAAAAATGAATAACAAAGAAAAATATAAAAGAA
+ACAAAAACAATAAAAAAAACATAAACATAAAAAGAATAATAAGAAAAAAA
+AAAAAAATAAATGAAATGAGTATAACAAAGAAAGCAAAAAACAAAAAAAA
+AAAAAAAAAAAAAACATTAAAAAATAAATAAAAAAAATAAAAAAAGAAGG
+AAAAAAGAAAAATTAAAAAAAAAGTAAAAGCACAAGTCAGAAGAATAACG
+TAAGAGTGAAGAAAACTAAAAAAAAGAAGAAAAAAAAAGTAAAGATAAAG
+AAAAAAAAAAAAACAGTAAAGAAAAACAAATAAAAGAAAGGAGAAAAAAG
+GTCCTGTGGTTTCAGCTGAGTTTGCAGTGTCAGCATTCCTTTC
+>m130406_011850_42141_c100513442550000001823074308221310_s1_p0/8/0_7878
+AAAAAAAAAGAGAGAGGAATGAGTCAGAAGGCACCCCTGATAAGAAAATC
+TTCGTGGAGGCTGGCGCGAATTTTAGCATTTGTTCAATGGCGTAAACGAA
+CGTATCCATTTGGGTATGACCTCCATTAATTTCAGCCGATATAGTAACGC
+AGTGACAAATAAAGTAAATGTAATTGTTTTAGAAAAAATGATTCTTGTGG
+TATATAATCGCCATCACTTCCAGGCAGCCCATAAGGCCAGCGCACTAAGC
+AGTGTTGGGATGATAACGCTGCGTGTTTTAAGAAACTGGCACCCAGCTCC
+GCGAAGCCAACCACAGCGTGGGCACGAAACGGCGTGTAAATCGGCATCAC
+TTCTGGTGCGGTAGAGACAACAGCAGGAGCCGCATATCGAGGCATGCCAA
+TGGTGTCGAGCAAAATACCTACCGCGCCACGTTTGGTTGGGCGGGCATTA
+CCCACACAGCAGGCGCAGCGGCAAATAGCGGAAGCAATAATTCGCCACGC
+CAACTAGTAACCCAAGCACAGAACCTCATAGCTCCATCGGGCGCCCTTTG
+CCAGAATGCCTGGATTAACGCCAGTGAGGCAGCCACAAGACAATGCCTGC
+CAGAATTGCCGACGAATTAGAAAATCAGCGTTACGCCTGCAAGGGCACCA
+ACTAACCTGCGGTAAACGCAAAGAGATGTTTGCGCTGAAAGAGGCCGGCA
+GGAAACTCATAAAGAGTGGGCCGGAAGCATAAAACCTAATGCAGCTTCAA
+CGGCGGGATAAACCTTGCAGCAAGCCGCTGCCGGAGAATGCCCCTATTAC
+CCGTACAAATAATCCCACGTGACCATGAACTGAAAGGCATGCGATATCCC
+CAGTTTCTCGCTCCGAGCGGCCGATTATTTGCGTACAAGTTTTGCGGTTG
+CGAGCGGCAAAAAACCCTCATCCGTCCAGGCAAACGCCCACAGGGCGGTT
+TTCGATTTTTTGCAGACGCTGAATAATACGGCTACGCAGTGACGGGCCAT
+ACAACACATGGCGAACATCCATTGCCATGACGGTCAGTGCAGCAATCCCC
+ACAAAACTACCCCGGCACTGCCCAGCATCGCGTAAGACCGAAACTGGCTC
+GCGCCTGCATAATGATGCAGGAGAAAAAAACGCTTTCGAGAGGAAGAGAA
+TCCCAGACCGGGTCCGCATTTCAGACGAACGCAAAGGCCACCGGAATTAT
+AACTAATAACAATCGGTAAACTGTCCTTTGCAATCCTTCCATGAAAGGTC
+GCCGAACCAGGAGCAGCTGTGGAGTAGGGCTTTCCATAGAGATGTACGCT
+ACCGATTGTTAATATTATAAATAGACTGAATGAATATCCTTAACCTTATC
+AGACTGAGGCTTCTTTAACACCACTTATAAGTGTAAAGCCACGAAAACCG
+TTGTGATTGCTTAATTTTGCGGGCTTCCTGAACGATGAAACCTCGCCACC
+CAGACCGTAAAAGTTAACCAGGGCAATCGGTCGCGCCAGCCAGACAAACC
+AGGCCCAAACCGCCATGTTGCCAGGCTGAGGCTAATTAGCCGAACCGGCG
+GGCACCGCCAATAAAGTAGCTAGTCATGTAACCTGCGGTCAGGCGATTGC
+GCGCATCAGGATGTATCCGATAAATTACCGTCTGGTTTAGTGATATGCAC
+GCCCTGCACGGTGAGATCCAGCACCAGGATTCCGATAAATCAAACGCCAG
+TACGGAAGTGTGACCAAACCAGATCGCCAGCCATGAAATAATAGCAGCAG
+CAGACCGAAAGTTGTGGTGTGGTGCGATTTGCCCTTATCGCAAACCGCCC
+GCCGGACGAGCGCCCATACGCTCCGGCAGCTCCCGCAAGTCTCAAACGAC
+CAATGACACCATCCGCTGTAGTTAAAAGGTGGAGGCGGGCAAGCCAAAAA
+GGCCCATTGAGGTCCAGAGAATGCTGAGAATGGCAAGGTCAGGCAGCCCA
+GCAACGCGCGGTACGCAGAATTTTATCGCTGATAACTATGAAACGGAACC
+CAACAACTGTGGGTAGTTGAGGTGGGTTTCGATTCATTTGTGGCAGACCA
+CGCCATAATGCCAGCGCCATTCAGTGCCGATTAACGACCCGAAGCAACCA
+AAAGACGGTGCGCCAGCCGCCGAGATTCGCCAAGCAATCCGGCAACTGTC
+CGTGCAATGCAAGAATCCCAACAGCAGACCGCTCATAATAGTGCCAACCA
+CCTTTGCCGCGTTTACCCGGTGAACCAGCGTCGCTGCCAGCGGAACAGAA
+TTTGTGCCACGACTGAGAATAAAACCGGTTAATGCCGGTACCGAGGATCA
+TCATCGCCAGCTGACGACTTGCTGGCGGGTAATCAACATGCCGCCAGTAA
+GGTATCGAGACAATCAGGCGGCGGCCGTTCAAACATATACCGAGGGGAAC
+AAGAAACAGTAGACCTGCCGGCATAGCCCAACTGCGCGGCGGTAACAATA
+AAGCCTGCGAACTGCGGAAAGAGGAAAAGTTACGCGAGATGGTGTCGAGC
+AATGGCTGGGCGTAAATAGTTACTGGCTACCAGCCAGACCGGTGGCGATA
+GACATCAGCACGATCAGCGCCGGGCAAGCTCAATGATTTAGGTTTAGTCA
+TTAATTTTTGTTCATCAGGTGATGATTAAGCTGGAAATCCAATAATAGCG
+GATGGTTGATGAATATGGGATGAAAGATAGATTGTTGAAAGTGCGATGTG
+GTTTGTTAGGATGATTAAGACGCGCAACAAGCGTCGCATCAGGCATTGTG
+CACAGAACGGCGGAATGCGGCAAAAACGCCTTATCGCGCCGAATAAAAAT
+TAACTTCTGCGTGCCAGCGCCTCCATTCACCCCAAGCCATCGAACTGCCT
+GCTGGTGGGCTTTGATCCAACATCAACCGTTGTCCCTGAAATATCGCCCT
+TCTGAGGCTTTGCCGTCATGCATAATGGCGTTCTGGGCCGTTAAAATCTG
+CCACTGGCAACCTGCATAATGGCAACAGTTTCGCTGCTGCCGGGTTTTTC
+TGCGGCCCAGGCTTTGTTGGCAACGATATGCATGGTGCTGACCCGGGAAG
+CCATAATTCCGCAAACCATTCAGGCAGTTTTGGTACGGCGTTTTTATCGC
+ACCCGGCCAGTGCGGAGATACGGCACCTGCAACCAGACGAAACCATCTTT
+TTTGCCCGGCTTCATTCGTAACTCACCCAGTACGGCGTCCAGGTGAATAA
+AAACACCGGTTTGCCCTCTTTGGTACGACCTGATGGTGTCGGCCATCATC
+GCTGCGTAGTTCCCCTGATTAAATGCGTCACGGTGTTGGTCAGTTCATAC
+GCGGCAAGCGGTGGTTGATCGCACCTTTCGCAGGCCCCAGCCAGGGTTAC
+AACCGGTAAATCAGCTTTTCCGTCGCCGTTGGTATCGAACCAGTTTGGCG
+ATCTTCGGATCATTTCAGTTGTGCGATGTTGGTGATTTTGTACTGGTCGG
+CGTTTTTCTTATCGATCAGGTAACCCTGTCCGCGCGTTAACAAATACCCC
+TTCACGATAAAATTTCTTATCGCCACCGCAGCTTCGTACATGTTGTCATG
+CAGTGGCGTCCAGTTCACGGCGTGAAGGGTTCATCGCCGGAAGCAACGAG
+GTGTACCAACGTTGTAAATCTATCGCTTGGGTTTGTTGACGGTATAACCT
+AAAATTCTCAGCGCACGACTGACAGCAGCGTCTGGAAGGTTTCTTCAGTG
+GATGGTGCTCTGAACTGGATTAACAGTAATGCTTTGCCCGGCAGATCGCA
+GCAAAAGTTTGTGTAAGAGATAAGCGTGGCAACGCTGTCGCAAAAAGTAC
+CGCCTATGTCGCATTGTTATTCCTTTTTTTGGCAGGGTGAATAATGCCGC
+GTCACCGGGCAAGTGCCAGAGTTATTAAGAATGGGCGGGTCAGCAGACCA
+ACAGGGCCAAGTTGGTGTACCAGCGACGGTTGCCGCGACTGGCGTGAGTC
+GCGCCCAACCGGCCTGCGTCAGACGATCGAGGATAATGGCGAGGATCCAA
+AATCCCGACCGCCGCCCAACGGTGGCAAGCCCCATATCCAGACGACCGAT
+ACCGCGAAGAAAAACTACCATCTGACCACCCGCCGACGGCAAATCCATCG
+AGGCGATGACCACCATAGAAAGGGGCCAGCATCAGCGTCCTGGTTAACGC
+CCGCCCATAATGGTCGGCATCGCCAAGCGGTAACTGAAACTTTGAACAGC
+ATCTGGCGCGGGCTGGCACCTGAATGAGCGCGAGGCTTCAATCCAGATCC
+CGCCGGAACCTGGTTAAATCCCCAAATGGTCAGACGGATAATCGGCGCAG
+AGCAAAGAATTGATCTCACCACCACGCCCCGGCACGTTACCGATACCAAA
+TAGCATGACGATGGCACCAGATAAACAAACGCTGCGTGGTCTGCAATGGC
+CATCAAGCAAGTGGACCGAATAATTTTTCGCCGCTCGCGGACTTCTCGCC
+CAGCCATATCCCAACGGCAAACCGAATGACGATTACAGAACAGCAGGGCG
+GTTAACACCAGCGCCAGAGTCACCATTGCCTGCGACCAGGCACCGATTGC
+GCCCGATGGCAATCAGCGAAACCAGCGGTCGCCACACCCCATTCCGACCC
+CCGGAAATCTGCCAGGCGATGAGAAGTCGAAAACGATAATCGCCACCGGT
+GCGGCATACCAGCAGCAATTGCTGGAAACCGTTGAAGGATATAATCAACC
+GGAACGAGCCGCCCTGGAAGACTGGGACGGAATGGGTAACGACCCAGTCG
+ATCCCTTCAGTGACCCAACTGTCGATGCGGGATCAAGGTTTTTGGAACGG
+AATGAGAATATTAAAATGCTCTGCGTTTGGCGCAGGCGTACTGGTCAGCC
+AGTCAGCACCACCGCCGCAGTCGGTGCAGTCGTTCGGTGTACCCCAGGCG
+TCTGCGGTATTGCGCGGCACTGTCCCGCCGCTGGCGTGGTATCCCACGGG
+ATTATTTTGATCAGACCATTATTTACCCCCTCAACGATCTAAAGCGCGCA
+TGCAGCATTCCTTTCGAAATGATGCCGACATACTGTGGTCCTCCGTCGAC
+CACGGGCACCGCACAGGGTGCCTGTCCCGAACATGAGAGAGCAACTCGCT
+AAGAGGCGTTTGTGCATCGACTGCTAACGGCGCCATCAAATCAGCGCCCG
+CATCAAGACCTTGCGGCTGCGTTAACGCGGTTTTAAAGCGAATCGATGGA
+GACTGCGCCGACAAACTTTATTACCGGCGTTCGATAACGTAGCCATATTT
+CGCGATCTTCATCCCTGCAATAATTTCAGTGCCGAACGTGGCCGAAGCCA
+GGGGTTTTACGAAAATAAGCCATATCGGTGTCCGGCGGGCAATATCTTTC
+GCACTGATACCTGACTAATATCCAACGCCACGGAAGAAGTACGGAACATA
+ATCATTCGCCGGATTATGAGAATTTCATCCGGTGTGTCCGACCTGTACAC
+TTCACCATTTTTATAATGGCAATCGGTCGCCAATACGCATGGCTTCATCA
+AGATCGTGGAAAATAAAGACAATGGTGCGCTGAATGTTTCGCCTGTAATT
+TTCCAGCTCATCCTGCATCTCGGTGCGAATTAAATGATCGAGCGCCGAGA
+AGGCTTCGTCCATTAATAATATATCCGGATTATATCGCTAACGCGCGGGC
+TAATCCCACACGTTTGGACGCCATCCCGCCAGAGAGTTCCATCCGGGTGA
+CTGTGGGCATAATTTTCCACCCGACCTGACGCAGTGCATCAAGGGCTTTT
+TCCCGGCGTTCTTCGGCATTAATCCGGCCAATTCCATACCGAAGCGCAGT
+ATTGTCCAGCATCGGTCATAAATGCGGCATTAAGGCAAAGGACTGGAATA
+CCATCGCAATCTTTTTCTTGCGCACCTCACCGGGTTCGGCGTCGGATATT
+TTGGCAATATCCACACCATCAATCAGTCCACTTGCCCGCGGGTGGGTTCA
+ATCAGGCGATTGAGACAGCCGTACCATTGTGGATTTACCAGCCGGATAAT
+CCATTGGATGACAAATATACTCGCCTTCTTCAATGGCCAGACTGGCGTCT
+TTTACGCCAAGCGATAGCCCAGTTTTTTCCCAGAATTTGGTTCTTTTGAA
+AGTCCTTGTTCGATATATTTGAACGCTCGCTGTGGATGCTCGCCAAATAT
+TTTATAAAGAATTTTTAATTTTCTAATTTAATTGCATGCAATAGAAAGAT
+TCCTTTATTTGTCTATGTCGATATATTACCCAATGGAAATAGTCACTTTT
+TTCTAACCCTAACATACTGAGAATAACTGAGGGCAACCCCTGATGGCAAA
+TGGTGGCATGAATATTTGATGCGAGCAAATCGCCGGAATTTCCCGTGATA
+TAAAGGGCTGGACAATATCGAGAAAGTTGGATAATTTTTTGTCAAAGATA
+GCGAAAAAACGTCCTGAATATTGTGGTTTCAGCGAATCAATGCAACAGAG
+TATCAGTGTAGATCACCACAAATTAATTTGCGTGATAAAAAGCTATTTGG
+CGGATTATTTCCCTGCTGCGGGTAGTGATATTTTTGGAAAATAACACCCT
+CAGAAATTCCAGTCTTCATCTTCTGTTTCAACCGCTTTCCCCAATCACAA
+ATAAGAGGAGCCTGAACCGGAAAAAGAATCGTGATTTTCATCGGCATTCG
+CGAAAGCGCGGCGAGGATTGCCGGATTCACTTCCGCATTTTCGGGAAATA
+AACGGTTCGTAGCCCAGATTTCCCCCCCAAAAATCCCAAAAAGCCTTATT
+GGCGTTGTAACAGAGAAACGCTTTTCCACATCGTCACCGACGGGGTTTCG
+GCGTACAGCTCCATCGGTGTATGTGAACTCCGTTGTTCGTAGAGTTCCAG
+CAACAAATCGAAGGCGAAACTCTCAACTTCCTCACGTTGTCCAGAGATAT
+CTTTTCCCATGTTTTTCTGATATTTAATAGGCCTATGTAGTAACCGTGAC
+TGCTTCATCGCGGATAATCAGGACGGATTCAGGTTCCGCGGTATTGGTCA
+GCTTTCCGCGGCTGGAAAAATACAATCGGCAGCCAGAAACCGGAATAGAA
+TCAAAAAAGATTCAAGAACAACTGGCGATTTTCTTTTTCAGCGGATCATC
+AACCGCGATAATGTTTGCTGAAATAATCTGAGCTTTCGCTGCAACGGTGC
+GTTTTCTTCACTCCAGGCGTAGCGGCATCGACATCTTTTGGTCTGGCAAT
+AGCGTCGAGAAAATCGAACCTGTAAGAGCGGCATGAACCGCTTCGCATAA
+AGCTGATATTCGAATAATCCGCTTCTTTCATGAGGCGTGGAGTGCAATCG
+GGCAATCAGAGAAGGGCGCGCCGTAACATTTTGCAGCGTGTCGAGCAGCG
+TCAGGCCAGTAAAAACGCGCATCGTCCAAGTTGTTGTTCTACGACAGTTA
+AATGTCTGCCCAAGGCAGGAAATATCGTTCGACAGCGGCACCTTTTTCTG
+GTAGCCAGAATGCCTGGTCAGGCGATTCCACACCTCCAGATCTTTATCGT
+ACAGATTCTTTGTTCCAGTTTTGATGGGCGCTGATACGTGAAGTTTCATA
+GATATCCCTTAAGTGCACAGGAGGACGCCAGCCTTCAATTTCAGTGCCTT
+CCAGCGCCATCTGACGCAGGCGGAATGTAATAGAGCGTTTTGATACCCTT
+GGCGCCAGGCGTAAATCTGCCGCTTTGTTGATATCGCGAGTGGTGGCGGT
+ATCGGGGAAAAAAAGCCGTCCAGCGACAGCCCCTTGACGACAATGGCTGA
+GTCCGCCTTCCGCGTAGGTTCGTGATACTTTTCTGCGCCAATTTCGTAAG
+GCCGTCCTGATACAGCGCAGATTCCGTTAGTCTAATAAACGGCAGGGTAG
+TAAACCGCGTCCTGTTTTGCCCCGCCCC
diff --git a/tests/data/test_pulseFile.fofn b/tests/data/test_pulseFile.fofn
new file mode 100644
index 0000000..7f4e3da
--- /dev/null
+++ b/tests/data/test_pulseFile.fofn
@@ -0,0 +1,4 @@
+/mnt/data3/vol57/2650250/0001/Analysis_Results/m121004_000921_42130_c100440700060000001523060402151341_s1_p0.bas.h5
+/mnt/data3/vol53/2450496/0001/Analysis_Results/m130406_011850_42141_c100513442550000001823074308221310_s1_p0.1.bax.h5
+/mnt/data3/vol53/2450496/0001/Analysis_Results/m130406_011850_42141_c100513442550000001823074308221310_s1_p0.2.bax.h5
+/mnt/data3/vol53/2450496/0001/Analysis_Results/m130406_011850_42141_c100513442550000001823074308221310_s1_p0.3.bax.h5
diff --git a/tests/out/readme b/tests/out/readme
new file mode 100644
index 0000000..8606a09
--- /dev/null
+++ b/tests/out/readme
@@ -0,0 +1,2 @@
+# This directory saves output files generated by pbalign's
+# unit tests and cram tests.
diff --git a/tests/unit/test_fileutil.py b/tests/unit/test_fileutil.py
new file mode 100755
index 0000000..d6d89ff
--- /dev/null
+++ b/tests/unit/test_fileutil.py
@@ -0,0 +1,131 @@
+"""Test pbalign.util/fileutil.py"""
+
+import unittest
+from os import path
+from pbalign.utils.fileutil import getFileFormat, \
+ isValidInputFormat, isValidOutputFormat, getFilesFromFOFN, \
+ checkInputFile, checkOutputFile, checkReferencePath, \
+ real_upath, real_ppath, isExist
+import filecmp
+
+
+class Test_fileutil(unittest.TestCase):
+ """Test pbalign.util/fileutil.py"""
+ def setUp(self):
+ self.rootDir = path.dirname(path.dirname(path.abspath(__file__)))
+
+ def test_isValidInputFormat(self):
+ """Test isValidInputFormat()."""
+ self.assertTrue(isValidInputFormat( getFileFormat("ab.fasta")) )
+ self.assertTrue(isValidInputFormat( getFileFormat("ab.fa")) )
+ self.assertTrue(isValidInputFormat( getFileFormat("ab.pls.h5")) )
+ self.assertTrue(isValidInputFormat( getFileFormat("ab.plx.h5")) )
+ self.assertTrue(isValidInputFormat( getFileFormat("ab.bas.h5")) )
+ self.assertTrue(isValidInputFormat( getFileFormat("ab.bax.h5")) )
+ self.assertTrue(isValidInputFormat( getFileFormat("ab.fofn")) )
+ self.assertFalse(isValidInputFormat( getFileFormat("ab.sam")) )
+ self.assertFalse(isValidInputFormat( getFileFormat("ab.cmp.h5")) )
+ self.assertFalse(isValidInputFormat( getFileFormat("ab.xyz")) )
+
+ def test_isValidOutputFormat(self):
+ """Test isOutputFormat()."""
+ self.assertFalse(isValidOutputFormat( getFileFormat("ab.fasta")) )
+ self.assertFalse(isValidOutputFormat( getFileFormat("ab.fa")) )
+ self.assertFalse(isValidOutputFormat( getFileFormat("ab.pls.h5")) )
+ self.assertFalse(isValidOutputFormat( getFileFormat("ab.plx.h5")) )
+ self.assertFalse(isValidOutputFormat( getFileFormat("ab.bas.h5")) )
+ self.assertFalse(isValidOutputFormat( getFileFormat("ab.bax.h5")) )
+ self.assertFalse(isValidOutputFormat( getFileFormat("ab.fofn")) )
+ self.assertTrue(isValidOutputFormat( getFileFormat("ab.sam")) )
+ self.assertTrue(isValidOutputFormat( getFileFormat("ab.cmp.h5")) )
+ self.assertFalse(isValidOutputFormat( getFileFormat("ab.xyz")) )
+
+ def test_getFilesFromFOFN(self):
+ """Test getFilesFromFOFN()."""
+ fofnFN = "{0}/data/ecoli_lp.fofn".format(self.rootDir)
+ fns = ["/home/UNIXHOME/yli/yliWorkspace/private/yli/data" + \
+ "/testLoadPulses/m121215_065521_richard_c10042571" + \
+ "0150000001823055001121371_s1_p0.pls.h5",
+ "/home/UNIXHOME/yli/yliWorkspace/private/yli/data" + \
+ "/testLoadPulses/m121215_065521_richard_c10042571" + \
+ "0150000001823055001121371_s2_p0.pls.h5"]
+ self.assertEqual(fns, getFilesFromFOFN(fofnFN))
+
+ def test_checkInputFile(self):
+ """Test checkInputFile()."""
+ fastaFN = "{0}/data/ecoli.fasta".format(self.rootDir)
+ plsFN = "/home/UNIXHOME/yli/yliWorkspace/private/yli/" + \
+ "data/testLoadPulses/m121215_065521_richard_" + \
+ "c100425710150000001823055001121371_s1_p0.pls.h5"
+ self.assertTrue(filecmp.cmp(fastaFN, checkInputFile(fastaFN)))
+ self.assertTrue(filecmp.cmp(plsFN, checkInputFile(plsFN)))
+
+ fofnFN = "{0}/data/ecoli_lp.fofn".format(self.rootDir)
+ self.assertTrue(filecmp.cmp(fofnFN, checkInputFile(fofnFN)))
+
+
+ def test_checkOutputFile(self):
+ """Test checkOutputFile()."""
+ samFN = "{0}/out/lambda_out.sam".format(self.rootDir)
+ cmpFN = "{0}/out/lambda_out.cmp.h5".format(self.rootDir)
+ self.assertTrue(filecmp.cmp(samFN, checkOutputFile(samFN)))
+ self.assertTrue(filecmp.cmp(cmpFN, checkOutputFile(cmpFN)))
+
+
+ def test_checkReferencePath(self):
+ """Test checkReferencePath()."""
+ refDir = "/mnt/secondary/Smrtanalysis/opt/smrtanalysis/common/" + \
+ "references"
+ refPath = path.join(refDir, "lambda")
+ refPath, refFastaOut, refSaOut, isWithinRepository, annotation = \
+ checkReferencePath(refPath)
+ self.assertTrue(filecmp.cmp(refFastaOut,
+ path.join(refPath,
+ "sequence/lambda.fasta")))
+ self.assertTrue(filecmp.cmp(refSaOut,
+ path.join(refPath,
+ "sequence/lambda.fasta.sa")))
+ self.assertTrue(isWithinRepository)
+
+ refpath, refFastaOut, refSaOut, isWithinRepository, annotation = \
+ checkReferencePath(refFastaOut)
+ self.assertTrue(filecmp.cmp(refFastaOut,
+ path.join(refPath,
+ "sequence/lambda.fasta")))
+ self.assertTrue(filecmp.cmp(refSaOut,
+ path.join(refPath,
+ "sequence/lambda.fasta.sa")))
+ self.assertTrue(isWithinRepository)
+
+
+ fastaFN = "{0}/data/ecoli.fasta".format(self.rootDir)
+ refpath, refFastaOut, refSaOut, isWithinRepository, annotation = \
+ checkReferencePath(fastaFN)
+ self.assertTrue(filecmp.cmp(refpath, refFastaOut))
+ self.assertIsNone(refSaOut)
+ self.assertFalse(isWithinRepository)
+
+ refPathWithAnnotation = "/mnt/secondary-siv/" + \
+ "testdata/BlasrTestData/pbalign/data/references/H1_6_Scal_6x/"
+ _refPath, _refFaOut, _refSaOut, _isWithinRepository, annotation = \
+ checkReferencePath(refPathWithAnnotation)
+ self.assertEqual(path.abspath(annotation),
+ path.abspath(path.join(refPathWithAnnotation,
+ "annotations/H1_6_Scal_6x_adapters.gff")))
+
+ def test_isExist(self):
+ """Test isExist(ff)."""
+ self.assertFalse(isExist(None))
+
+ def test_realpath(self):
+ """Test real_upath and real_ppath."""
+ print real_upath("ref with space")
+ self.assertTrue(real_upath("ref with space").endswith("ref\ with\ space"))
+ self.assertTrue(real_upath("ref\ with\ space").endswith("ref\ with\ space"))
+ self.assertTrue(real_ppath("ref with space").endswith("ref with space"))
+ self.assertTrue(real_ppath("ref\ with\ space").endswith("ref with space"))
+
+
+if __name__ == "__main__":
+ unittest.main()
+
diff --git a/tests/unit/test_filterservice.py b/tests/unit/test_filterservice.py
new file mode 100755
index 0000000..02aaca4
--- /dev/null
+++ b/tests/unit/test_filterservice.py
@@ -0,0 +1,72 @@
+"""Test pbalign.filterservice."""
+from pbalign.filterservice import FilterService
+from os import path
+import unittest
+
+class Opt(object):
+ """The Option class."""
+ def __init__(self, maxDivergence, minAccuracy, minLength,
+ seed, scoreCutoff, hitPolicy):
+ self.maxDivergence = maxDivergence
+ self.minAccuracy = minAccuracy
+ self.minLength = minLength
+ self.seed = seed
+ self.scoreCutoff = scoreCutoff
+ self.hitPolicy = hitPolicy
+ self.filterAdapterOnly = None
+
+class Test_FilterService(unittest.TestCase):
+ """Test pbalign.filterservice."""
+ def setUp(self):
+ self.testDir = path.dirname(path.dirname(path.abspath(__file__)))
+ self.alignedSam = path.join(self.testDir,
+ "data/lambda.sam")
+ self.targetFileName = "/mnt/secondary/Smrtanalysis/opt/" + \
+ "smrtanalysis/common/references/" + \
+ "lambda/sequence/lambda.fasta"
+ self.filteredSam = path.join(self.testDir,
+ "out/lambda_filtered.sam")
+
+ def test_init(self):
+ """Test FilterService.__init__()."""
+ options = Opt(30, 70, 50, 1, None, "random")
+
+ obj = FilterService(self.alignedSam, self.targetFileName,
+ self.filteredSam, "BlasrService", -1,
+ options)
+
+ self.assertTrue(obj.availability) # samFilter should be available
+ self.assertIn("-minPctSimilarity 70", obj.cmd)
+ self.assertIn("-minAccuracy 70", obj.cmd)
+ self.assertIn("-scoreSign -1", obj.cmd)
+
+ def test_run(self):
+ """Test FilterService.run()."""
+ options = Opt(30, 70, 50, 1, None, "random")
+
+ obj = FilterService(self.alignedSam, self.targetFileName,
+ self.filteredSam, "BlasrService", -1,
+ options)
+
+ _output, errCode, _errMsg = obj.run()
+
+ self.assertEqual(errCode, 0)
+
+
+ def test_run_without_scoreCutoff(self):
+ """Test FilterService.run() without score cutoff."""
+ options2 = Opt(40, 50, None, None, None, "allbest")
+ obj2 = FilterService(self.alignedSam, self.targetFileName,
+ self.filteredSam, "BowtieService", 1,
+ options2)
+
+ self.assertNotIn("-seed", obj2.cmd)
+ self.assertNotIn("-scoreCutoff", obj2.cmd)
+ self.assertIn("-scoreSign 1", obj2.cmd)
+
+ _output, errCode, _errMsg = obj2.run()
+
+ self.assertEqual(errCode, 0)
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/tests/unit/test_forquiverservice.py b/tests/unit/test_forquiverservice.py
new file mode 100755
index 0000000..ccaf9d2
--- /dev/null
+++ b/tests/unit/test_forquiverservice.py
@@ -0,0 +1,47 @@
+"""Test pbalign.forquiverservice.forquiver."""
+import unittest
+from os import path, remove
+from shutil import copyfile
+from pbalign.forquiverservice.forquiver import ForQuiverService
+from pbalign.pbalignfiles import PBAlignFiles
+from tempfile import mkstemp
+
+class Opt(object):
+ """Simulate PBAlign options."""
+ def __init__(self):
+ """Option class."""
+ self.verbosity = 2
+ self.metrics = "DeletionQV, InsertionQV"
+ self.byread = None
+
+
+class Test_ForQuiverService(unittest.TestCase):
+ """Test pbalign.forquiverservice.forquiver."""
+ def setUp(self):
+ self.rootDir = "/mnt/secondary-siv/" + \
+ "testdata/BlasrTestData/pbalign"
+ self.inCmpFile = path.join(self.rootDir, "data/testforquiver.cmp.h5")
+ #self.outCmpFile = path.join(self.rootDir, "out/testforquiver.cmp.h5")
+ self.outCmpFile = mkstemp(suffix=".cmp.h5")[1]
+
+ copyfile(self.inCmpFile, self.outCmpFile)
+ self.basFile = path.join(self.rootDir, "data/lambda_bax.fofn")
+
+ refpath = "/mnt/secondary/Smrtanalysis/opt/" + \
+ "smrtanalysis/common/references/lambda/"
+
+ self.fileNames = PBAlignFiles()
+ self.fileNames.SetInOutFiles(self.basFile, refpath,
+ self.outCmpFile, None, None)
+ self.options = Opt()
+ self.obj = ForQuiverService(self.fileNames, self.options)
+
+ def tearDown(self):
+ remove(self.outCmpFile)
+
+ def test_run(self):
+ """Test ForQuiverService.__init__()."""
+ self.obj.run()
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/tests/unit/test_gmap.py b/tests/unit/test_gmap.py
new file mode 100755
index 0000000..68c5013
--- /dev/null
+++ b/tests/unit/test_gmap.py
@@ -0,0 +1,54 @@
+"""Test pbalign.alignservices.gmap."""
+import unittest
+from os import path
+from pbalign.alignservice.gmap import GMAPService
+from pbalign.pbalignfiles import PBAlignFiles
+from pbalign.options import parseOptions
+import argparse
+
+
+class Test_GMAPService(unittest.TestCase):
+ """Test pbalign.alignservices.gmap."""
+ def setUp(self):
+ """Set up test data."""
+ self.rootDir = path.dirname(path.dirname(path.abspath(__file__)))
+ self.outDir = path.join(self.rootDir, "out/")
+ self.outSam = path.join(self.outDir, "test_gmap_01.sam")
+ self.dataDir = path.join(self.rootDir, "data/")
+ self.queryFofn = path.join(self.dataDir, "ecoli_lp.fofn")
+ self.refFa = path.join(self.dataDir, "ecoli.fasta")
+ self.repoPath = "/mnt/secondary/Smrtanalysis/opt/smrtanalysis/" + \
+ "common/references/ecoli/"
+
+ def test_gmapCreateDB_case1(self):
+ """Test _gmapCreateDB(refFile, isWithinRepository, tempRootDir).
+ Condition: the reference is not within a reference repository.
+ """
+ # Case 1: the reference is not within a reference repository
+ files = PBAlignFiles()
+ parser = argparse.ArgumentParser()
+ argumentList = [self.queryFofn, self.refFa, self.outSam,
+ '--algorithm', 'gmap']
+ parser, options, _info = parseOptions(argumentList=argumentList,
+ parser=parser)
+ service = GMAPService(options, files)
+ dbRoot, dbName = service._gmapCreateDB(self.refFa, False, self.outDir)
+ self.assertTrue(path.exists(dbRoot))
+ self.assertTrue(path.exists(path.join(dbRoot, dbName)))
+
+ def test_gmapCreateDB_case2(self):
+ """Test _gmapCreateDB(refFile, isWithinRepository, tempRootDir).
+ Condition: the reference is within a reference repository.
+ """
+ # Case 2: the reference is within a reference repository
+ files = PBAlignFiles()
+ parser = argparse.ArgumentParser()
+ argumentList = [self.queryFofn, self.repoPath, self.outSam,
+ '--algorithm', 'gmap']
+ parser, options, _info = parseOptions(argumentList=argumentList,
+ parser=parser)
+ service = GMAPService(options, files)
+ dbRoot, dbName = service._gmapCreateDB(files.targetFileName, True,
+ self.outDir)
+ self.assertEqual(path.abspath(dbRoot), path.abspath(self.repoPath))
+ self.assertEqual(dbName, "gmap_db")
diff --git a/tests/unit/test_loadpulsesservice.py b/tests/unit/test_loadpulsesservice.py
new file mode 100755
index 0000000..6a094ba
--- /dev/null
+++ b/tests/unit/test_loadpulsesservice.py
@@ -0,0 +1,35 @@
+"""Test pbalign.forquiverservice.loadpulses."""
+import unittest
+from os import path, remove
+from shutil import copyfile
+from pbalign.forquiverservice.loadpulses import LoadPulsesService
+from argparse import Namespace
+from tempfile import mkstemp
+
+
+class Test_LoadPulsesService(unittest.TestCase):
+ """Test pbalign.forquiverservice.loadpulses."""
+ def setUp(self):
+ """Set up tests."""
+ self.rootDir = "/mnt/secondary-siv/" + \
+ "testdata/BlasrTestData/pbalign"
+ self.inCmpFile = path.join(self.rootDir, "data/testloadpulses.cmp.h5")
+ #self.outCmpFile = path.join(self.rootDir, "out/testloadpulses.cmp.h5")
+ self.outCmpFile = mkstemp(suffix=".cmp.h5")[1]
+
+ self.basFile = path.join(self.rootDir, "data/lambda_bax.fofn")
+ copyfile(self.inCmpFile, self.outCmpFile)
+ self.options = Namespace(metrics="DeletionQV", byread=False)
+ self.obj = LoadPulsesService(self.basFile,
+ self.outCmpFile, self.options)
+
+ def tearDown(self):
+ remove(self.outCmpFile)
+
+ def test_run(self):
+ """Test LoadPulsesService.__init__()."""
+ _output, errCode, _errMsg = self.obj.run()
+ self.assertEqual(errCode, 0)
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/tests/unit/test_options.py b/tests/unit/test_options.py
new file mode 100755
index 0000000..6b5c8e5
--- /dev/null
+++ b/tests/unit/test_options.py
@@ -0,0 +1,136 @@
+from pbalign.options import *
+from argparse import *
+from os import path
+import filecmp
+import unittest
+
+rootDir = path.dirname(path.dirname(path.abspath(__file__)))
+configFile = path.join(rootDir, "data/2.config")
+configFile3 = path.join(rootDir, "data/3.config")
+
+def writeConfigFile(configFile, configOptions):
+ """Write configs to a file."""
+ with open (configFile, 'w') as f:
+ f.write("\n".join(configOptions))
+
+class Test_Options(unittest.TestCase):
+
+ def test_importConfigOptions(self):
+ """Test importConfigOptions()."""
+ configOptions = ("--minAccuracy = 40",
+ "--maxHits = 20")
+ writeConfigFile(configFile, configOptions)
+ options = Namespace(configFile=configFile,
+ minAccuracy=10,
+ maxHits=12)
+
+ newOptions, infoMsg = importConfigOptions(options)
+
+ self.assertEqual(int(newOptions.maxHits), 20)
+ self.assertEqual(int(newOptions.minAccuracy), 40)
+
+ def test_ConstructOptionParser(self):
+ """Test constructOptionParser()."""
+ ret = constructOptionParser()
+ self.assertEqual(type(ret), argparse.ArgumentParser)
+
+ def test_parseOptions(self):
+ """Test parseOptions()."""
+ configOptions = (
+ "--maxHits = 20",
+ "--minAnchorSize = 15",
+ "--minLength = 100",
+ "--algorithmOptions = '-noSplitSubreads " + \
+ "-maxMatch 30 -nCandidates 30'",
+ "# Some comments",
+ "--scoreFunction = blasr",
+ "--hitPolicy = random",
+ "--maxDivergence = 40",
+ "--debug")
+ writeConfigFile(configFile, configOptions)
+
+ def test_parseOptions_with_config(self):
+ """Test parseOptions with a config file."""
+ # With the above config file
+ argumentList = ['--configFile', configFile,
+ '--maxHits', '30',
+ '--minAccuracy', '50',
+ 'readfile', 'reffile', 'outfile']
+ parser, options, infoMsg = parseOptions(argumentList)
+
+ self.assertTrue(filecmp.cmp(options.configFile, configFile))
+ self.assertEqual(int(options.maxHits), 30)
+ self.assertEqual(int(options.minAccuracy), 50)
+
+ self.assertEqual("".join(options.algorithmOptions),
+ "-noSplitSubreads -maxMatch 30 -nCandidates 30")
+ self.assertEqual(options.scoreFunction, "blasr")
+ self.assertEqual(options.hitPolicy, "random")
+ self.assertEqual(int(options.maxDivergence), 40)
+
+ def test_parseOptions_without_config(self):
+ """Test parseOptions without any config file."""
+ argumentList = ['--maxHits=30',
+ '--minAccuracy=50',
+ 'readfile', 'reffile', 'outfile']
+ parser, options,infoMsg = parseOptions(argumentList)
+
+ self.assertIsNone(options.configFile)
+ self.assertEqual(int(options.maxHits), 30)
+ self.assertEqual(int(options.minAccuracy), 50)
+ self.assertIsNone(options.algorithmOptions)
+ self.assertIsNone(options.minAnchorSize)
+
+ def test_parseOptions_multi_algorithmOptions(self):
+ """Test parseOptions with multiple algorithmOptions."""
+ algo1 = " -holeNumbers 1"
+ algo2 = " -nCandidate 25"
+ algo3 = " ' -bestn 11 '"
+ argumentList = ['--algorithmOptions=%s' % algo1,
+ '--algorithmOptions=%s' % algo2,
+ 'readfile', 'reffile', 'outfile']
+
+ print argumentList
+ parser, options, infoMsg = parseOptions(argumentList)
+ # Both algo1 and algo2 should be in algorithmOptions.
+ print options.algorithmOptions
+ #self.assertTrue(algo1 in options.algorithmOptions)
+ #self.assertTrue(algo2 in options.algorithmOptions)
+
+ # Construct a config file.
+ configOptions = ("--algorithmOptions = \"%s\"" % algo3)
+ writeConfigFile(configFile3, [configOptions])
+
+ argumentList.append("--configFile={0}".format(configFile3))
+ print argumentList
+ parser, options, infoMsg = parseOptions(argumentList)
+ # Make sure algo3 have been overwritten.
+ print options.algorithmOptions
+ self.assertTrue(algo1 in options.algorithmOptions)
+ self.assertTrue(algo2 in options.algorithmOptions)
+ self.assertFalse(algo3 in options.algorithmOptions)
+
+ def test_parseOptions_without_some_options(self):
+ """Test parseOptions without specifying maxHits and minAccuracy."""
+ # Test if maxHits and minAccuracy are not set,
+ # whether both options.minAnchorSize and maxHits are None
+ argumentList = ["--minAccuracy", "50",
+ 'readfile', 'reffile', 'outfile']
+ parser, options,infoMsg = parseOptions(argumentList)
+ self.assertIsNone(options.minAnchorSize)
+ self.assertIsNone(options.maxHits)
+
+ def test_importDefaultOptions(self):
+ """Test importDefaultOptions"""
+ options = Namespace(configFile=configFile,
+ minAccuracy=10,
+ maxHits=12)
+ defaultOptions = {"minAccuracy":30, "maxHits":14}
+ newOptions, infoMsg = importDefaultOptions(options, defaultOptions)
+ self.assertEqual(newOptions.minAccuracy, 10)
+ self.assertEqual(newOptions.maxHits, 12)
+
+
+if __name__ == "__main__":
+ unittest.main()
+
diff --git a/tests/unit/test_pbalign.py b/tests/unit/test_pbalign.py
new file mode 100755
index 0000000..369ae79
--- /dev/null
+++ b/tests/unit/test_pbalign.py
@@ -0,0 +1,56 @@
+import unittest
+from os import path
+from pbalign.pbalignrunner import PBAlignRunner
+
+class Test_PBAlignRunner(unittest.TestCase):
+ def setUp(self):
+ self.rootDir = path.dirname(path.dirname(path.abspath(__file__)))
+ self.queryFile = path.join(self.rootDir, "data/lambda_query.fasta")
+ self.referenceFile = "/mnt/secondary/Smrtanalysis/opt/" + \
+ "smrtanalysis/common/references/" + \
+ "lambda/sequence/lambda.fasta"
+ self.configFile = path.join(self.rootDir, "data/1.config")
+ self.samOut = path.join(self.rootDir, "out/lambda_out.sam")
+ self.cmph5Out = path.join(self.rootDir, "out/lambda_out.cmp.h5")
+
+ def test_init(self):
+ """Test PBAlignRunner.__init__()."""
+ argumentList = ['--minAccuracy', '70', '--maxDivergence', '30',
+ self.queryFile, self.referenceFile,
+ self.samOut]
+ pbobj = PBAlignRunner(argumentList = argumentList)
+ self.assertEqual(pbobj.start(), 0)
+
+ def test_init_with_algorithmOptions(self):
+ """Test PBAlignRunner.__init__() with --algorithmOptions."""
+ argumentList = ['--algorithmOptions', '-minMatch 10 -useccsall',
+ self.queryFile, self.referenceFile,
+ self.cmph5Out]
+ pbobj = PBAlignRunner(argumentList = argumentList)
+ self.assertEqual(pbobj.start(), 0)
+
+ def test_init_with_config_algorithmOptions(self):
+ """Test PBAlignRunner.__init__() with a config file and --algorithmOptions."""
+ argumentList = ['--algorithmOptions', '-maxMatch 20 -nCandidates 30',
+ '--configFile', self.configFile,
+ self.queryFile, self.referenceFile,
+ self.cmph5Out]
+
+ pbobj = PBAlignRunner(argumentList = argumentList)
+ self.assertEqual(pbobj.start(), 0)
+
+ def test_init_expect_conflicting_options(self):
+ """Test PBAlignRunner.__init__() with a config file and --algorithmOptions
+ and expect a ValueError for conflicting options."""
+ argumentList = ['--algorithmOptions', '-minMatch 10 -useccsall',
+ '--configFile', self.configFile,
+ self.queryFile, self.referenceFile,
+ self.cmph5Out]
+ pbobj = PBAlignRunner(argumentList = argumentList)
+ with self.assertRaises(ValueError) as cm:
+ # Expect a ValueError since -minMatch and --minAnchorSize conflicts.
+ pbobj.start()
+
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/tests/unit/test_pbalignfiles.py b/tests/unit/test_pbalignfiles.py
new file mode 100755
index 0000000..30a241b
--- /dev/null
+++ b/tests/unit/test_pbalignfiles.py
@@ -0,0 +1,83 @@
+import unittest
+import filecmp
+from os import path
+from pbalign.pbalignfiles import PBAlignFiles
+
+class Test_PbAlignFiles_Ecoli(unittest.TestCase):
+ def setUp(self):
+ self.rootDir = path.dirname(path.dirname(path.abspath(__file__)))
+ self.inputFileName = path.join(self.rootDir, "data/ecoli.fasta")
+ self.referencePath = "/mnt/secondary/Smrtanalysis/opt/" + \
+ "smrtanalysis/common/references/ecoli_K12_MG1655/"
+ self.targetFileName = path.join(self.referencePath,
+ "sequence/ecoli_K12_MG1655.fasta")
+ self.sawriterFileName = self.targetFileName + ".sa"
+ self.outputFileName = path.join(self.rootDir, "out/tmp.sam")
+
+ def test_init(self):
+ """Test PBAlignFiles.__init__() with a reference repository."""
+ # Without region table
+ p = PBAlignFiles(self.inputFileName,
+ self.referencePath,
+ self.outputFileName)
+ self.assertTrue(filecmp.cmp(p.inputFileName, self.inputFileName))
+ self.assertTrue(p.referencePath, path.abspath(path.expanduser(self.referencePath)))
+ self.assertTrue(filecmp.cmp(p.targetFileName, self.targetFileName))
+ self.assertTrue(filecmp.cmp(p.outputFileName, self.outputFileName))
+ self.assertIsNone(p.regionTable)
+
+
+
+class Test_PbAlignFiles(unittest.TestCase):
+ def setUp(self):
+ self.rootDir = path.dirname(path.dirname(path.abspath(__file__)))
+ self.inputFileName = path.join(self.rootDir, "data/lambda_bax.fofn")
+ self.referenceFile = "/mnt/secondary/Smrtanalysis/opt/" + \
+ "smrtanalysis/common/references/" + \
+ "lambda/sequence/lambda.fasta"
+ self.outputFileName = path.join(self.rootDir, "out/tmp.sam")
+
+ def test_init(self):
+ """Test PBAlignFiles.__init__()."""
+ # Without region table
+ p = PBAlignFiles(self.inputFileName,
+ self.referenceFile,
+ self.outputFileName)
+ self.assertTrue(filecmp.cmp(p.inputFileName, self.inputFileName))
+ self.assertTrue(filecmp.cmp(p.referencePath, self.referenceFile))
+ self.assertTrue(filecmp.cmp(p.targetFileName, self.referenceFile))
+ self.assertTrue(filecmp.cmp(p.outputFileName, self.outputFileName))
+ self.assertIsNone(p.regionTable)
+
+ def test_init_region_table(self):
+ """Test PBAlignFiles.__init__() with a region table."""
+ # With an artifical region table
+ regionTable = path.join(self.rootDir, "data/lambda.rgn.h5")
+ p = PBAlignFiles(self.inputFileName,
+ self.referenceFile,
+ self.outputFileName,
+ regionTable)
+ self.assertTrue(filecmp.cmp(p.regionTable, regionTable))
+
+
+ def test_setInOutFiles(self):
+ """Test PBAlignFiles.SetInOutFiles()."""
+ p = PBAlignFiles()
+ self.assertIsNone(p.inputFileName)
+ self.assertIsNone(p.outputFileName)
+ self.assertIsNone(p.referencePath)
+
+ p.SetInOutFiles(self.inputFileName,
+ self.referenceFile,
+ self.outputFileName,
+ None)
+ self.assertTrue(filecmp.cmp(p.inputFileName, self.inputFileName))
+ self.assertTrue(filecmp.cmp(p.referencePath, self.referenceFile))
+ self.assertTrue(filecmp.cmp(p.targetFileName, self.referenceFile))
+ self.assertTrue(filecmp.cmp(p.outputFileName, self.outputFileName))
+ self.assertIsNone(p.regionTable)
+
+
+if __name__ == "__main__":
+ unittest.main()
+
diff --git a/tests/unit/test_progutil.py b/tests/unit/test_progutil.py
new file mode 100755
index 0000000..d96bce7
--- /dev/null
+++ b/tests/unit/test_progutil.py
@@ -0,0 +1,19 @@
+import unittest
+from os import path
+from pbalign.utils.progutil import *
+
+class Test_progutil(unittest.TestCase):
+ def setUp(self):
+ self.prog = "blasr"
+
+ def testAvailability(self):
+ self.assertTrue(Availability(self.prog))
+
+ def testCheckAvailability(self):
+ CheckAvailability(self.prog)
+
+ def testExecute(self):
+ Execute("ls", "ls")
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/tests/unit/test_referenceInfo.py b/tests/unit/test_referenceInfo.py
new file mode 100755
index 0000000..c6f7fc2
--- /dev/null
+++ b/tests/unit/test_referenceInfo.py
@@ -0,0 +1,22 @@
+from pbalign.utils.fileutil import ReferenceInfo
+import unittest
+
+class Test_ReferenceInfo(unittest.TestCase):
+
+ def test_init(self):
+ """Test ReferenceInfo.__init__() with a valid reference.info.xml."""
+ rootDir = "/mnt/secondary/Smrtanalysis/opt/" + \
+ "smrtanalysis/common/references/lambda/"
+ r = ReferenceInfo(rootDir + "reference.info.xml")
+ self.assertEqual(r.refFastaFile, rootDir + "sequence/lambda.fasta")
+ self.assertEqual(r.refSawriterFile, rootDir + "sequence/lambda.fasta.sa")
+
+ def test_init_with_errors(self):
+ with self.assertRaises(ValueError) as cm:
+ r2 = ReferenceInfo("noexist.txt")
+
+ with self.assertRaises(IOError) as cm:
+ r2 = ReferenceInfo("noexist.xml")
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/tests/unit/test_repackservice.py b/tests/unit/test_repackservice.py
new file mode 100755
index 0000000..19d9555
--- /dev/null
+++ b/tests/unit/test_repackservice.py
@@ -0,0 +1,35 @@
+"""Test pbalign.forquiverservice.repack."""
+import unittest
+from os import path, remove
+from shutil import copyfile
+from pbalign.forquiverservice.repack import RepackService
+from tempfile import mkstemp
+
+
+class Test_RepackService(unittest.TestCase):
+ """Test pbalign.forquiverservice.repack."""
+ def setUp(self):
+ """Set up the tests."""
+ self.rootDir = "/mnt/secondary-siv/" + \
+ "testdata/BlasrTestData/pbalign"
+ self.inCmpFile = path.join(self.rootDir, "data/testrepack.cmp.h5")
+ #self.outCmpFile = path.join(self.rootDir, "out/testrepack.cmp.h5")
+ self.outCmpFile = mkstemp(suffix=".cmp.h5")[1]
+ self.tmpCmpFile = self.outCmpFile + ".tmp"
+
+ #self.tmpCmpFile = path.join(self.rootDir, "out/testrepack.cmp.h5.tmp")
+ copyfile(self.inCmpFile, self.outCmpFile)
+ self.options = {}
+ self.obj = RepackService(self.outCmpFile, self.tmpCmpFile)
+
+ def tearDown(self):
+ remove(self.outCmpFile)
+
+ def test_run(self):
+ """Test LoadPulsesService.__init__()."""
+ print self.obj.cmd
+ _output, errCode, _errMsg = self.obj.run()
+ self.assertEqual(errCode, 0)
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/tests/unit/test_rgnh5io.py b/tests/unit/test_rgnh5io.py
new file mode 100755
index 0000000..6083bb2
--- /dev/null
+++ b/tests/unit/test_rgnh5io.py
@@ -0,0 +1,119 @@
+"""Test pbalign.utils.RgnH5IO.py."""
+
+import unittest
+from pbcore.io.BasH5IO import ADAPTER_REGION, INSERT_REGION, HQ_REGION
+from pbalign.utils.RgnH5IO import Region, RegionTable, RgnH5Reader, \
+ RgnH5Writer, addStrListAttr
+from os import path
+import h5py
+
+
+class Test_RgnH5IO(unittest.TestCase):
+ """Test RgnH5Reader and RgnH5Writer."""
+
+ def setUp(self):
+ """Set up test data."""
+ self.rootDir = path.dirname(path.dirname(path.abspath(__file__)))
+ self.inRgnFN = "/mnt/secondary-siv/testdata/" + \
+ "BlasrTestData/pbalign/data/test_rgnh5io.rgn.h5"
+ self.outRgnFN = path.join(self.rootDir, "out/test_rgnh5io_out.rgn.h5")
+ self.outTmpFN = path.join(self.rootDir, "out/test_rgnh5io_tmp.h5")
+ self.movieName = "m130427_152935_42178_" + \
+ "c100518602550000001823079209281316_s1_p0"
+
+ def test_Region(self):
+ """Test class Region."""
+ rtuple = (0, 2, 2, 3, 4)
+ r = Region(list(rtuple))
+ self.assertTrue(r.toTuple() == rtuple)
+ r.setStartAndEnd(10, 20)
+ self.assertTrue(r.toTuple() == (0, 2, 10, 20, 4))
+ self.assertTrue(r.isHqRegion)
+ self.assertTrue(r.holeNumber == 0)
+ self.assertTrue(r.typeIndex == HQ_REGION)
+ self.assertTrue(r.start == 10)
+ self.assertTrue(r.end == 20)
+ self.assertTrue(r.score == 4)
+
+ # Create an instance of Region with type = ADAPTER_REGION.
+ self.assertTrue(Region([11, ADAPTER_REGION, 30, 50, -1]).isAdapter)
+ # Create an instance of Region with type = INSERT_REGION.
+ self.assertTrue(Region([11, INSERT_REGION, 30, 50, -1]).isInsert)
+
+ def test_RegionTable(self):
+ """Test class RegionTable."""
+ l = [Region([11, 1, 1634, 7207, -1]), Region([11, 2, 1634, 7207, 872])]
+ rt = RegionTable(11, l)
+ self.assertEqual(rt.numRegions, 2)
+ self.assertEqual(rt.toList(), [(11, 1, 1634, 7207, -1),
+ (11, 2, 1634, 7207, 872)])
+
+ def test_reader(self):
+ """Test RgnH5Reader."""
+ reader = RgnH5Reader(self.inRgnFN)
+ for rt in reader:
+ if (rt.holeNumber in [0, 1, 81740]):
+ self.assertEqual(
+ rt.toList(),
+ [(rt.holeNumber, 2, 0, 0, 0)])
+ elif rt.holeNumber == 11:
+ self.assertEqual(
+ rt.toList(),
+ [(11, 1, 1634, 7207, -1), (11, 2, 1634, 7207, 882)])
+ elif rt.holeNumber == 30:
+ self.assertEqual(
+ rt.toList(),
+ [(30, 1, 14046, 17047, -1),
+ (30, 1, 17092, 19610, -1),
+ (30, 0, 17047, 17092, 955),
+ (30, 2, 14046, 19610, 890)])
+ # Reset HQRegion and test.
+ rt.setHQRegion(0, 0)
+ self.assertEqual(
+ rt.toList(),
+ [(30, 1, 14046, 17047, -1),
+ (30, 1, 17092, 19610, -1),
+ (30, 0, 17047, 17092, 955),
+ (30, 2, 0, 0, 890)])
+ self.assertEqual(reader.movieName, self.movieName)
+ self.assertEqual(reader.numZMWs, 81741)
+ reader.close()
+
+ def test_writer(self):
+ """Test RgnH5Writer()."""
+ reader = RgnH5Reader(self.inRgnFN)
+ writer = RgnH5Writer(self.outRgnFN)
+ writer.writeScanDataGroup(reader.scanDataGroup)
+ for rt in reader:
+ writer.addRegionTable(rt)
+ if rt.holeNumber == 1000:
+ break
+ reader.close()
+ writer.close()
+
+ reader1 = RgnH5Reader(self.inRgnFN)
+ reader2 = RgnH5Reader(self.outRgnFN)
+ self.assertTrue("PulseData" in reader2.file)
+ self.assertTrue("ScanData" in reader2.file)
+ for (rt1, rt2) in zip(reader1, reader2):
+ self.assertEqual(rt1.toList(), rt2.toList())
+ if rt1.holeNumber == 1000:
+ break
+
+ def test_addStrListAttr(self):
+ """Test function addStrListAttr(obj, name, strlist)."""
+ f = h5py.File(self.outTmpFN, 'w')
+ obj = f.create_group("PulseData")
+ addStrListAttr(obj, "addedAttr", ["val1", "val2"])
+ f.close()
+
+ f = h5py.File(self.outTmpFN, 'r')
+ self.assertTrue("addedAttr" in f["PulseData"].attrs)
+ attrList = f["PulseData"].attrs["addedAttr"]
+ self.assertEqual(attrList[0], 'val1')
+ self.assertEqual(attrList[1], 'val2')
+ f.close()
+
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/tests/unit/test_sortservice.py b/tests/unit/test_sortservice.py
new file mode 100755
index 0000000..dad10a4
--- /dev/null
+++ b/tests/unit/test_sortservice.py
@@ -0,0 +1,38 @@
+"""Test pbalign.forquiverservice.sort."""
+import unittest
+from os import path, remove
+from shutil import copyfile
+from pbalign.forquiverservice.sort import SortService
+from tempfile import mkstemp
+
+
+class Opt(object):
+ """Simulate pbalign options."""
+ def __init__(self):
+ """Option class."""
+ self.verbosity = 2
+
+class Test_SortService(unittest.TestCase):
+ """Test pbalign.forquiverservice.sort."""
+ def setUp(self):
+ """Set up tests."""
+ self.rootDir = "/mnt/secondary-siv/" + \
+ "testdata/BlasrTestData/pbalign"
+ self.inCmpFile = path.join(self.rootDir, "data/testsort.cmp.h5")
+ self.outCmpFile = mkstemp(suffix=".cmp.h5")[1]
+
+ copyfile(self.inCmpFile, self.outCmpFile)
+ self.options = Opt()
+ self.obj = SortService(self.outCmpFile, self.options)
+
+ def tearDown(self):
+ remove(self.outCmpFile)
+
+ def test_run(self):
+ """Test SortService.__init__()."""
+ print self.obj.cmd
+ _output, errCode, _errMsg = self.obj.run()
+ self.assertEqual(errCode, 0)
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/tests/unit/test_tmpfileutil.py b/tests/unit/test_tmpfileutil.py
new file mode 100755
index 0000000..67fd80b
--- /dev/null
+++ b/tests/unit/test_tmpfileutil.py
@@ -0,0 +1,91 @@
+from pbalign.utils.tempfileutil import TempFileManager
+import unittest
+from os import path
+
+def keep_writing_to_file(fn):
+ """Keep writing a to a file."""
+ f = open(fn, 'w')
+ while True:
+ # Keep writing a to a file,
+ # note that this function will never end unless
+ # being killed by the main process.
+ f.write('a')
+
+class Test_TempFileManager(unittest.TestCase):
+
+ def test_init(self):
+ """Test TempFileManager all functions."""
+ t = TempFileManager()
+ t.SetRootDir("/scratch")
+
+ newFN = t.RegisterNewTmpFile()
+ self.assertTrue(path.isfile(newFN))
+
+ existingDir = t.RegisterExistingTmpFile("/tmp", isDir=True)
+ self.assertTrue(path.isdir(existingDir))
+
+ with self.assertRaises(IOError) as cm:
+ t.RegisterExistingTmpFile("filethatdoesnotexist")
+
+ newDN = t.RegisterNewTmpFile(isDir=True)
+ self.assertTrue(path.isdir(newDN))
+ self.assertTrue(t._isRegistered(newDN))
+
+ newTxt = t.RegisterNewTmpFile(suffix=".txt")
+ self.assertTrue(newTxt.endswith(".txt"))
+
+ t.SetRootDir("~/tmp/")
+
+ t.CleanUp()
+ self.assertFalse(path.exists(newFN))
+ self.assertFalse(path.exists(newDN))
+ self.assertEqual(t.fileDB, [])
+ self.assertEqual(t.dirDB, [])
+
+# def test_CleanUp(self):
+# """Create a temp directory and register several tmp files.
+# Then, manually open another file under temp dir without
+# registering it. Finally, call CleanUp to delete temp dirs
+# and files. Note that by doing this, an nfs lock is created
+# manually, CleanUp should exit with a warning instead of an
+# error."""
+# t = TempFileManager()
+# t.SetRootDir("/scratch")
+# newFN = t.RegisterNewTmpFile()
+# with open(newFN, 'w') as writer:
+# writer.write("x")
+#
+# newFN2 = t.RegisterNewTmpFile()
+# with open(newFN2, 'w') as writer:
+# writer.write("x")
+#
+# # Manually create a temp file under temp dir without register
+# rootDir = t.defaultRootDir
+# extraFN = path.join(t.defaultRootDir, 'extra_file.txt')
+# # Keep the file open while trying to Clean up temp dir.
+# from multiprocessing import Process
+# p = Process(target=keep_writing_to_file, args=(extraFN, ))
+# p.start()
+# self.assertTrue(p.is_alive())
+#
+# t.CleanUp()
+#
+# self.assertFalse(path.exists(newFN))
+# self.assertFalse(path.exists(newFN2))
+#
+# self.assertTrue(p.is_alive())
+# self.assertTrue(path.exists(extraFN))
+# self.assertEqual(t.fileDB, [])
+# self.assertEqual(t.dirDB, [])
+#
+# p.terminate()
+#
+# import time
+# time.sleep(1)
+# import shutil
+# shutil.rmtree(rootDir)
+#
+
+if __name__ == "__main__":
+ unittest.main()
+
--
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