[med-svn] [Git][med-team/pbalign][master] 3 commits: New upstream version 0.3.2
Steffen Möller
gitlab at salsa.debian.org
Sat Jan 26 12:33:59 GMT 2019
Steffen Möller pushed to branch master at Debian Med / pbalign
Commits:
0aaa1cbf by Steffen Moeller at 2019-01-26T12:20:00Z
New upstream version 0.3.2
- - - - -
f3f6a18b by Steffen Moeller at 2019-01-26T12:20:01Z
Update upstream source from tag 'upstream/0.3.2'
Update to upstream version '0.3.2'
with Debian dir 2dfd358013305fb97a55632e92a34f761429e23e
- - - - -
24eaf3e7 by Steffen Moeller at 2019-01-26T12:32:31Z
Preparing for 0.3.2
- - - - -
18 changed files:
- LICENSES.txt → LICENSE
- MANIFEST.in
- README.md
- + debian/README.Debian
- debian/changelog
- debian/control
- debian/docs → debian/pbalign.docs
- debian/rules
- pbalign/__init__.py
- pbalign/bampostservice.py
- − pbalign/tasks/consolidate_alignments.py
- − pbalign/tasks/consolidate_alignments_ccs.py
- pbalign/tools/extractUnmappedSubreads.py
- pbalign/tools/mask_aligned_reads.py
- pbalign/utils/progutil.py
- scripts/ci/build.sh
- setup.py
- tests/unit/test_tool_contract.py
Changes:
=====================================
LICENSES.txt → LICENSE
=====================================
@@ -1,4 +1,4 @@
-Copyright (c) 2016, Pacific Biosciences of California, Inc.
+Copyright (c) 2016-2018, Pacific Biosciences of California, Inc.
All rights reserved.
=====================================
MANIFEST.in
=====================================
@@ -1 +1 @@
-include LICENSES.txt
+include LICENSE
=====================================
README.md
=====================================
@@ -1,6 +1,18 @@
-pbalign maps PacBio reads to reference sequences.
+<h1 align="center"><img src="http://www.pacb.com/wp-content/themes/pacific-biosciences/img/pacific-biosciences-logo-mobile.svg"/></h1>
+<h1 align="center">pbalign</h1>
+<p align="center">A python wrapper to easily align PacBio reads to reference sequences</p>
-Want to know how to install and run pbalign?
+***
+
+## Availability
+Latest version can be installed via bioconda package `pbalign`.
+
+Please refer to our [official pbbioconda page](https://github.com/PacificBiosciences/pbbioconda)
+for information on Installation, Support, License, Copyright, and Disclaimer.
+
+
+## How To?
+Want to know how to manually install or run pbalign?
Please refer to https://github.com/PacificBiosciences/pbalign/blob/master/doc/howto.rst
=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,4 @@
+pbalign
+=======
+
+Some good soul needs to add a Python3 package.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+pbalign (0.3.2-1) unstable; urgency=medium
+
+ * Team upload
+
+ * Standards-Version: 4.2.1
+ * d/rules: clean up all build remnants
+
+ * TODO: Python3-version, added README.Debian as a reminder
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 26 Jan 2019 13:20:46 +0100
+
pbalign (0.3.1-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper (>= 11~),
python-pbcommand,
python3-sphinx,
python-nose
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/pbalign
Vcs-Git: https://salsa.debian.org/med-team/pbalign.git
Homepage: https://github.com/PacificBiosciences/pbalign
=====================================
debian/docs → debian/pbalign.docs
=====================================
@@ -1 +1,2 @@
README.md
+debian/README.Debian
=====================================
debian/rules
=====================================
@@ -58,3 +58,10 @@ no_override_dh_installmanpages:
$(HELP2MAN) --name="$${description[`basename $$executable`]}" \
$$executable > $(MANDIR)/`basename $$executable.1`; \
done
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -rf doc/_build/
+ rm -f doc/pbalign.alignservice.rst doc/pbalign.rst doc/pbalign.tasks.rst doc/pbalign.tools.rst doc/pbalign.utils.rst
+ rm -rf pbalign.egg-info
+
=====================================
pbalign/__init__.py
=====================================
@@ -57,7 +57,7 @@ def get_changelist():
return _get_changelist(_changelist)
-VERSION = (0, 3, 1)
+VERSION = (0, 4, 1)
def get_version():
=====================================
pbalign/bampostservice.py
=====================================
@@ -37,7 +37,7 @@
# Author: Yuan Li
-from __future__ import absolute_import
+from __future__ import absolute_import, division, print_function
import logging
from pbalign.service import Service
from pbalign.utils.progutil import Execute
@@ -92,12 +92,13 @@ class BamPostService(Service):
except Exception:
pass
_stvmajor = int(_samtoolsversion[0])
+ sort_nproc = max(1, nproc//4)
if _stvmajor >= 1:
- cmd = 'samtools sort --threads {t} -m 4G -o {sortedBamFile} {unsortedBamFile}'.format(
- t=nproc, sortedBamFile=sortedBamFile, unsortedBamFile=unsortedBamFile)
+ cmd = 'samtools sort --threads {t} -m 768M -o {sortedBamFile} {unsortedBamFile}'.format(
+ t=sort_nproc, sortedBamFile=sortedBamFile, unsortedBamFile=unsortedBamFile)
else:
- cmd = 'samtools sort --threads {t} -m 4G {unsortedBamFile} {prefix}'.format(
- t=nproc, unsortedBamFile=unsortedBamFile, prefix=sortedPrefix)
+ cmd = 'samtools sort --threads {t} -m 768M {unsortedBamFile} {prefix}'.format(
+ t=sort_nproc, unsortedBamFile=unsortedBamFile, prefix=sortedPrefix)
Execute(self.name, cmd)
def _makebai(self, sortedBamFile, outBaiFile):
=====================================
pbalign/tasks/consolidate_alignments.py deleted
=====================================
@@ -1,140 +0,0 @@
-
-# FIXME this should probably live somewhere more general, e.g. pbdataset?
-
-"""
-Consolidate AlignmentSet .bam files
-"""
-
-import functools
-import tempfile
-import logging
-import os.path as op
-import os
-import sys
-
-from pbcommand.models import get_pbparser, FileTypes, ResourceTypes, DataStore, DataStoreFile
-from pbcommand.cli import pbparser_runner
-from pbcommand.utils import setup_log
-from pbcore.io import openDataSet
-
-
-class Constants(object):
- TOOL_ID = "pbalign.tasks.consolidate_alignments"
- VERSION = "0.2.0"
- DRIVER = "python -m pbalign.tasks.consolidate_alignments --resolved-tool-contract "
- CONSOLIDATE_ID = "pbalign.task_options.consolidate_aligned_bam"
- N_FILES_ID = "pbalign.task_options.consolidate_n_files"
- BAI_FILE_TYPES = {
- FileTypes.BAMBAI.file_type_id,
- FileTypes.I_BAI.file_type_id
- }
-
-
-def get_parser(tool_id=Constants.TOOL_ID,
- file_type=FileTypes.DS_ALIGN,
- driver_exe=Constants.DRIVER,
- version=Constants.VERSION,
- description=__doc__):
- ds_type = file_type.file_type_id.split(".")[-1]
- p = get_pbparser(tool_id,
- version,
- "{t} consolidate".format(t=ds_type),
- description,
- driver_exe,
- is_distributed=True,
- resource_types=(ResourceTypes.TMP_DIR,))
-
- p.add_input_file_type(file_type,
- "align_in",
- "Input {t}".format(t=ds_type),
- "Gathered {t} to consolidate".format(t=ds_type))
- p.add_output_file_type(file_type,
- "ds_out",
- "Alignments",
- description="Alignment results dataset",
- default_name="combined")
- p.add_output_file_type(FileTypes.DATASTORE,
- "datastore",
- "JSON Datastore",
- description="Datastore containing BAM resource",
- default_name="resources")
- p.add_boolean(Constants.CONSOLIDATE_ID, "consolidate",
- default=False,
- name="Consolidate .bam",
- description="Merge chunked/gathered .bam files")
- p.add_int(Constants.N_FILES_ID, "consolidate_n_files",
- default=1,
- name="Number of .bam files",
- description="Number of .bam files to create in consolidate mode")
- return p
-
-
-def run_consolidate(dataset_file, output_file, datastore_file,
- consolidate, n_files, task_id=Constants.TOOL_ID):
- datastore_files = []
- with openDataSet(dataset_file) as ds_in:
- if consolidate:
- if len(ds_in.toExternalFiles()) != 1:
- new_resource_file = op.splitext(output_file)[0] + ".bam"
- ds_in.consolidate(new_resource_file, numFiles=n_files)
- # always display the BAM/BAI if consolidation is enabled
- # XXX there is no uniqueness constraint on the sourceId, but this
- # seems sloppy nonetheless - unfortunately I don't know how else to
- # make view rule whitelisting work
- for ext_res in ds_in.externalResources:
- if ext_res.resourceId.endswith(".bam"):
- ds_file = DataStoreFile(
- ext_res.uniqueId,
- task_id + "-out-2",
- ext_res.metaType,
- ext_res.bam)
- datastore_files.append(ds_file)
- for index in ext_res.indices:
- if index.metaType in Constants.BAI_FILE_TYPES:
- ds_file = DataStoreFile(
- index.uniqueId,
- task_id + "-out-3",
- index.metaType,
- index.resourceId)
- datastore_files.append(ds_file)
- ds_in.newUuid()
- ds_in.write(output_file)
- datastore = DataStore(datastore_files)
- datastore.write_json(datastore_file)
- return 0
-
-
-def args_runner(args, task_id=Constants.TOOL_ID):
- return run_consolidate(
- dataset_file=args.align_in,
- output_file=args.ds_out,
- datastore_file=args.datastore,
- consolidate=args.consolidate,
- n_files=args.consolidate_n_files,
- task_id=task_id)
-
-
-def rtc_runner(rtc, task_id=Constants.TOOL_ID):
- tempfile.tempdir = rtc.task.tmpdir_resources[0].path
- return run_consolidate(
- dataset_file=rtc.task.input_files[0],
- output_file=rtc.task.output_files[0],
- datastore_file=rtc.task.output_files[1],
- consolidate=rtc.task.options[Constants.CONSOLIDATE_ID],
- n_files=rtc.task.options[Constants.N_FILES_ID],
- task_id=task_id)
-
-
-def main(argv=sys.argv):
- logging.basicConfig(level=logging.DEBUG)
- log = logging.getLogger()
- return pbparser_runner(argv[1:],
- get_parser(),
- args_runner,
- rtc_runner,
- log,
- setup_log)
-
-
-if __name__ == '__main__':
- sys.exit(main())
=====================================
pbalign/tasks/consolidate_alignments_ccs.py deleted
=====================================
@@ -1,40 +0,0 @@
-
-"""
-Consolidate ConsensusAlignmentSet .bam files
-"""
-
-import logging
-import sys
-
-from pbcommand.models import FileTypes
-from pbcommand.cli import pbparser_runner
-from pbcommand.utils import setup_log
-
-from pbalign.tasks.consolidate_alignments import Constants as BaseConstants, get_parser, args_runner, rtc_runner
-
-
-class Constants(BaseConstants):
- TOOL_ID = "pbalign.tasks.consolidate_alignments_ccs"
- VERSION = "0.1.0"
- DRIVER = "python -m pbalign.tasks.consolidate_alignments_ccs --resolved-tool-contract "
-
-
-def main(argv=sys.argv):
- logging.basicConfig(level=logging.DEBUG)
- log = logging.getLogger()
- p = get_parser(
- tool_id=Constants.TOOL_ID,
- file_type=FileTypes.DS_ALIGN_CCS,
- driver_exe=Constants.DRIVER,
- version=Constants.VERSION,
- description=__doc__)
- return pbparser_runner(argv[1:],
- p,
- lambda rtc: args_runner(rtc, Constants.TOOL_ID),
- lambda rtc: rtc_runner(rtc, Constants.TOOL_ID),
- log,
- setup_log)
-
-
-if __name__ == '__main__':
- sys.exit(main())
=====================================
pbalign/tools/extractUnmappedSubreads.py
=====================================
@@ -111,7 +111,7 @@ class ExtractRunner(PBToolRunner):
def run(self):
"""Executes the body of the script."""
- logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
+ logging.info("Running {f} v{v}.".format(f="extractUnmappedSubreads.py",
v=self.getVersion))
args = self.args
logging.info("Extracting unmapped reads from a fasta file.")
=====================================
pbalign/tools/mask_aligned_reads.py
=====================================
@@ -13,7 +13,7 @@ from pbcore.io import CmpH5Reader, EmptyCmpH5Error
import traceback
from pbalign.utils.RgnH5IO import RgnH5Reader, RgnH5Writer
-__VERSION__ = "0.3"
+__VERSION__ = "0.3.2"
class AlignedReadsMasker(object):
@@ -187,7 +187,7 @@ def main():
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__))
+ r=rcode, f="mask_aligned_reads.py", v=__VERSION__))
return rcode
if __name__ == "__main__":
=====================================
pbalign/utils/progutil.py
=====================================
@@ -61,10 +61,10 @@ def Execute(name, cmd):
errMsg : the error message
"""
logging.info(name + ": Call \"{0}\"".format(cmd))
- output, errCode, errMsg = backticks(cmd, merge_stderr=True)
+ output, errCode, errMsg = backticks(cmd, merge_stderr=False)
if errCode != 0:
- errMsg = "%s returned a non-zero exit status %s. CMD: '%s'\nERROR: %s\nOutput:%r" % \
- (name, cmd, errCode, errMsg, output)
+ errMsg = "%s returned a non-zero exit status %d\nCMD: '%s'\nERROR: %s\nOutput:%r" % \
+ (name, errCode, cmd, errMsg, output)
logging.error(errMsg)
raise RuntimeError(errMsg)
return output, errCode, errMsg
=====================================
scripts/ci/build.sh
=====================================
@@ -6,7 +6,6 @@ set -vex
#########
${PIP} install --user \
- $NX3PBASEURL/pythonpkgs/pysam-0.13-cp27-cp27mu-linux_x86_64.whl \
$NX3PBASEURL/pythonpkgs/xmlbuilder-1.0-cp27-none-any.whl \
$NX3PBASEURL/pythonpkgs/avro-1.7.7-cp27-none-any.whl \
iso8601 \
@@ -14,6 +13,7 @@ ${PIP} install --user \
cram \
nose
+${PIP} install --user pysam==0.15.1
${PIP} install --user pylint
${PIP} install --user -e repos/PacBioTestData
${PIP} install --user -e repos/pbcore
=====================================
setup.py
=====================================
@@ -1,20 +1,19 @@
-from setuptools import setup, Extension, find_packages
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
-import os
-import sys
+from setuptools import setup, find_packages
setup(
name='pbalign',
- version='0.3.1',
+ version='0.3.2',
author='Pacific Biosciences',
author_email='devnet at pacificbiosciences.com',
- license='LICENSE.txt',
+ license='BSD-3-Clause-Clear',
packages=find_packages(),
- zip_safe=False,
install_requires=[
'pbcore >= 0.8.5',
'pbcommand >= 0.2.0',
- 'pysam',
+ 'pysam >= 0.15.1',
],
test_requires=[
'nose',
@@ -22,7 +21,7 @@ setup(
],
test_suite='nose.collector',
entry_points={'console_scripts': [
- 'pbalign=pbalign.pbalignrunner:main',
+ 'pbalign = pbalign.pbalignrunner:main',
'maskAlignedReads.py = pbalign.tools.mask_aligned_reads:main',
'loadChemistry.py = pbalign.tools.loadChemistry:main',
'extractUnmappedSubreads.py = pbalign.tools.extractUnmappedSubreads:main',
=====================================
tests/unit/test_tool_contract.py
=====================================
@@ -59,55 +59,5 @@ class TestPbalignMinorVariants(pbcommand.testkit.PbTestApp):
type(ds_out).__name__)
-HAVE_PBMERGE = False
-try:
- with tempfile.TemporaryFile() as O, \
- tempfile.TemporaryFile() as E:
- assert subprocess.call(["pbmerge", "--help"], stdout=O, stderr=E) == 0
-except Exception as e:
- sys.stderr.write(str(e)+"\n")
- sys.stderr.write("pbmerge missing, skipping test\n")
-else:
- HAVE_PBMERGE = True
-
-
- at unittest.skipUnless(HAVE_PBMERGE, "pbmerge not installed")
-class TestConsolidateBam(pbcommand.testkit.PbTestApp):
- DRIVER_BASE = "python -m pbalign.tasks.consolidate_alignments"
- INPUT_FILES = [pbtestdata.get_file("aligned-ds-2")]
- TASK_OPTIONS = {
- "pbalign.task_options.consolidate_aligned_bam": True,
- }
-
- def run_after(self, rtc, output_dir):
- with openDataSet(rtc.task.output_files[0]) as f:
- f.assertIndexed()
- self.assertEqual(len(f.toExternalFiles()), 1)
- # test for bug 33778
- qnames = set()
- for rec in f:
- qnames.add(rec.qName)
- self.assertEqual(len(qnames), len(f))
- ds = DataStore.load_from_json(rtc.task.output_files[1])
- self.assertEqual(len(ds.files), 2)
-
-
- at unittest.skipUnless(HAVE_PBMERGE, "pbmerge not installed")
-class TestConsolidateBamDisabled(TestConsolidateBam):
- TASK_OPTIONS = {
- "pbalign.task_options.consolidate_aligned_bam": False,
- }
-
- def run_after(self, rtc, output_dir):
- with AlignmentSet(rtc.task.output_files[0]) as f:
- self.assertEqual(len(f.toExternalFiles()), 2)
-
-
- at unittest.skipUnless(HAVE_PBMERGE, "pbmerge not installed")
-class TestConsolidateBamCCS(TestConsolidateBam):
- DRIVER_BASE = "python -m pbalign.tasks.consolidate_alignments_ccs"
- INPUT_FILES = [pbtestdata.get_file("rsii-ccs-aligned")]
-
-
if __name__ == "__main__":
unittest.main()
View it on GitLab: https://salsa.debian.org/med-team/pbalign/compare/f863211eee11a39f6d95a64b0c1c03c5c5caf66b...24eaf3e73fd2684f2a9c9975f7332c38168ab247
--
View it on GitLab: https://salsa.debian.org/med-team/pbalign/compare/f863211eee11a39f6d95a64b0c1c03c5c5caf66b...24eaf3e73fd2684f2a9c9975f7332c38168ab247
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