[med-svn] [Git][med-team/nanoplot][master] 4 commits: New upstream version 1.30.1
Steffen Möller
gitlab at salsa.debian.org
Sun Jul 5 21:14:29 BST 2020
Steffen Möller pushed to branch master at Debian Med / nanoplot
Commits:
a5721728 by Steffen Moeller at 2020-07-05T22:14:55+02:00
New upstream version 1.30.1
- - - - -
a7584c56 by Steffen Moeller at 2020-07-05T22:14:55+02:00
routine-update: New upstream version
- - - - -
20e98f2a by Steffen Moeller at 2020-07-05T22:14:55+02:00
Update upstream source from tag 'upstream/1.30.1'
Update to upstream version '1.30.1'
with Debian dir 1090cfcdbb28d865f76faaded79b72db5e73dbe4
- - - - -
612411d7 by Steffen Moeller at 2020-07-05T22:14:55+02:00
routine-update: debhelper-compat 13
- - - - -
14 changed files:
- + LICENSE
- NanoPlot.egg-info/PKG-INFO
- NanoPlot.egg-info/SOURCES.txt
- NanoPlot.egg-info/requires.txt
- PKG-INFO
- README.md
- + README.rst
- debian/changelog
- debian/control
- nanoplot/NanoPlot.py
- nanoplot/utils.py
- nanoplot/version.py
- scripts/test.sh
- setup.py
Changes:
=====================================
LICENSE
=====================================
@@ -0,0 +1,674 @@
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+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>..
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
=====================================
NanoPlot.egg-info/PKG-INFO
=====================================
@@ -1,11 +1,11 @@
Metadata-Version: 2.1
Name: NanoPlot
-Version: 1.29.0
+Version: 1.30.1
Summary: Plotting suite for Oxford Nanopore sequencing data and alignments
Home-page: https://github.com/wdecoster/NanoPlot
Author: Wouter De Coster
Author-email: decosterwouter at gmail.com
-License: MIT
+License: GPLv3
Description: # NanoPlot
Plotting tool for long read sequencing data and alignments.
@@ -175,6 +175,8 @@ Description: # NanoPlot
## CITATION
If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
+ Copyright: 2016-2020 Wouter De Coster <decosterwouter at gmail.com>
+
Keywords: nanopore sequencing plotting quality control
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
=====================================
NanoPlot.egg-info/SOURCES.txt
=====================================
@@ -1,5 +1,7 @@
+LICENSE
MANIFEST.in
README.md
+README.rst
setup.py
NanoPlot.egg-info/PKG-INFO
NanoPlot.egg-info/SOURCES.txt
=====================================
NanoPlot.egg-info/requires.txt
=====================================
@@ -4,10 +4,9 @@ pandas>=0.22.0
numpy
scipy
python-dateutil
-seaborn>=0.9.0
+seaborn>=0.10.1
matplotlib>=3.1.3
-nanoget>=1.9.0
+nanoget>=1.13.0
nanomath>=0.23.1
-pauvre==0.1.86
-statsmodels==0.10.1
+pauvre==0.2.0
plotly>=4.1.0
=====================================
PKG-INFO
=====================================
@@ -1,11 +1,11 @@
Metadata-Version: 2.1
Name: NanoPlot
-Version: 1.29.0
+Version: 1.30.1
Summary: Plotting suite for Oxford Nanopore sequencing data and alignments
Home-page: https://github.com/wdecoster/NanoPlot
Author: Wouter De Coster
Author-email: decosterwouter at gmail.com
-License: MIT
+License: GPLv3
Description: # NanoPlot
Plotting tool for long read sequencing data and alignments.
@@ -175,6 +175,8 @@ Description: # NanoPlot
## CITATION
If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
+ Copyright: 2016-2020 Wouter De Coster <decosterwouter at gmail.com>
+
Keywords: nanopore sequencing plotting quality control
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
=====================================
README.md
=====================================
@@ -166,3 +166,5 @@ Bivariate plot of mapping quality against basecall quality||||x|||dot, hex, kde
## CITATION
If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
+
+Copyright: 2016-2020 Wouter De Coster <decosterwouter at gmail.com>
=====================================
README.rst
=====================================
@@ -0,0 +1,346 @@
+NanoPlot
+========
+
+Plotting tool for long read sequencing data and alignments.
+
+|Twitter URL| |conda badge| |Build Status|
+
+NanoPlot is also available as a `web service <http://nanoplot.bioinf.be>`__.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. figure:: https://github.com/wdecoster/NanoPlot/blob/master/examples/scaled_Log_Downsampled_LengthvsQualityScatterPlot_kde.png
+ :alt: Example plot
+
+ Example plot
+
+The example plot above shows a bivariate plot comparing log transformed
+read length with average basecall Phred quality score. More examples can
+be found in the `gallery on my blog ‘Gigabase Or
+Gigabyte’. <https://gigabaseorgigabyte.wordpress.com/2017/06/01/example-gallery-of-nanoplot/>`__
+
+In addition to various plots also a NanoStats file is created
+summarizing key features of the dataset.
+
+| This script performs data extraction from Oxford Nanopore sequencing
+ data in the following formats:
+| - fastq files
+| (can be bgzip, bzip2 or gzip compressed)
+| - fastq files generated by albacore, guppy or MinKNOW containing
+ additional information
+| (can be bgzip, bzip2 or gzip compressed)
+| - sorted bam files
+| - sequencing_summary.txt output table generated by albacore, guppy or
+ MinKnow basecalling (can be gzip, bz2, zip and xz compressed) - fasta
+ files (can be bgzip, bzip2 or gzip compressed)
+| Multiple files of the same type can be offered simultaneously
+
+INSTALLATION
+~~~~~~~~~~~~
+
+``pip install NanoPlot``
+
+| Upgrade to a newer version using:
+| ``pip install NanoPlot --upgrade``
+
+or
+
+| |conda badge|
+| ``conda install -c bioconda nanoplot``
+
+The script is written for python3.
+
+OUTPUT
+~~~~~~
+
+NanoPlot creates: - a statistical summary - a number of plots - a html
+summary file
+
+USAGE
+~~~~~
+
+::
+
+ NanoPlot [-h] [-v] [-t THREADS] [--verbose] [--store] [--raw]
+ [-o OUTDIR] [-p PREFIX] [--maxlength N] [--minlength N]
+ [--drop_outliers] [--downsample N] [--loglength]
+ [--percentqual] [--alength] [--minqual N]
+ [--readtype {1D,2D,1D2}] [--barcoded] [--runtime_until N]
+ [-c COLOR]
+ [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
+ [--plots [{kde,hex,dot,pauvre} [{kde,hex,dot,pauvre} ...]]]
+ [--listcolors] [--no-N50] [--N50] [--title TITLE]
+ (--fastq file [file ...] | --fasta file [file ...] | --fastq_rich file [file ...] | --fastq_minimal file [file ...] | --summary file [file ...] | --bam file [file ...] | --cram file [file ...] | --pickle pickle)
+
+
+ General options:
+ -h, --help show the help and exit
+ -v, --version Print version and exit.
+ -t, --threads THREADS Set the allowed number of threads to be used by the script
+ --verbose Write log messages also to terminal.
+ --store Store the extracted data in a pickle file for future plotting.
+ --raw Store the extracted data in tab separated file.
+ -o, --outdir OUTDIR Specify directory in which output has to be created.
+ -p, --prefix PREFIX Specify an optional prefix to be used for the output files.
+
+ Options for filtering or transforming input prior to plotting:
+ --maxlength N Hide reads longer than length specified.
+ --minlength N Hide reads shorter than length specified.
+ --drop_outliers Drop outlier reads with extreme long length.
+ --downsample N Reduce dataset to N reads by random sampling.
+ --loglength Logarithmic scaling of lengths in plots.
+ --percentqual Use qualities as theoretical percent identities.
+ --alength Use aligned read lengths rather than sequenced length (bam mode)
+ --minqual N Drop reads with an average quality lower than specified.
+ --runtime_until N Only take the N first hours of a run
+ --readtype Which read type to extract information about from a summary file.
+ One of 1D (default), 2D, 1D2
+ --barcoded Use if you want to split the summary file by barcode
+
+ Options for customizing the plots created:
+ -c, --color COLOR Specify a color for the plots, must be a valid matplotlib color
+ -f, --format Specify the output format of the plots.
+ One of png [default], eps,jpeg,jpg,pdf,pgf,ps,raw,rgba,svg,svgz,tif,tiff
+ --plots Specify which bivariate plots have to be made..
+ One or more of 'dot' (default), 'kde' (default), 'hex' and 'pauvre'
+ --listcolors List the colors which are available for plotting and exit.
+ --no-N50 Hide the N50 mark in the read length histogram
+ --N50 Show the N50 mark in the read length histogram
+ --title TITLE Add a title to all plots, requires quoting if using spaces
+
+ Input data sources, one of these is required.:
+ --fastq file [file ...]
+ Data is in one or more default fastq file(s).
+ --fasta file [file ...]
+ Data is in one or more default fasta file(s).
+ --fastq_rich file [file ...]
+ Data is in one or more fastq file(s) generated by albacore or MinKNOW with
+ additional information concerning channel and time.
+ --fastq_minimal file [file ...]
+ Data is in one or more fastq file(s) generated by albacore or MinKNOW with
+ additional information concerning channel and time. Minimal data is extracted
+ swiftly without elaborate checks.
+ --summary file [file ...]
+ Data is in one or more summary file(s) generated by albacore or guppy.
+ --bam file [file ...]
+ Data is in one or more sorted bam file(s).
+ --cram file [file ...]
+ Data is in one or more sorted cram file(s).
+ --pickle pickle Data is a pickle file stored earlier.
+
+NOTES
+~~~~~
+
+- ``--downsample`` won’t save you tons of time, as down sampling is
+ only done after collecting all data and probably would only make a
+ difference for a huge amount of data. If you want to save time you
+ could down sample your data upfront. Note also that extracting
+ information from a summary file is faster than other formats, and
+ that you can extract from multiple files simultaneously (which will
+ happen in parallel then). Some plot types (especially kde) are slower
+ than others and you can take a look at the input for ``--plots`` to
+ speed things up (default is to make both kde and dot plot). If you
+ are only interested in say the read length histogram it is possible
+ to write a script to just get you that and avoid wasting time on the
+ rest. Let me know if you need any help here.
+
+EXAMPLE USAGE
+~~~~~~~~~~~~~
+
+.. code:: bash
+
+ Nanoplot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed
+ NanoPlot -t 2 --fastq reads1.fastq.gz reads2.fastq.gz --maxlength 40000 --plots hex dot
+ NanoPlot -t 12 --color yellow --bam alignment1.bam alignment2.bam alignment3.bam --downsample 10000 -o bamplots_downsampled
+
+This script now also provides read length vs mean quality plots in the
+‘`pauvre <https://github.com/conchoecia/pauvre>`__’-style from
+[@conchoecia](https://github.com/conchoecia).
+
+ACKNOWLEDGMENTS/CONTRIBUTORS
+----------------------------
+
+- Andreas Sjödin for building and maintaining conda recipes
+- Darrin Schultz [@conchoecia](https://github.com/conchoecia) for
+ Pauvre code
+- [@alexomics](https://github.com/alexomics) for fixing the indentation
+ of the printed stats
+- Botond Sipos [@bsipos](https://github.com/bsipos) for speeding up the
+ calculation of average quality scores
+
+CONTRIBUTING
+------------
+
+I welcome all suggestions, bug reports, feature requests and
+contributions. Please leave an
+`issue <https://github.com/wdecoster/NanoPlot/issues>`__ or open a pull
+request. I will usually respond within a day, or rarely within a few
+days.
+
+PLOTS GENERATED
+---------------
+
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Plot | Fastq | Fast | F | Bam | S | O | Style |
+| | | q_rich | astq_m | | ummary | ptions | |
+| | | | inimal | | | | |
++========+========+========+========+========+========+========+========+
+| His | x | x | x | x | x | N50 | |
+| togram | | | | | | | |
+| of | | | | | | | |
+| read | | | | | | | |
+| length | | | | | | | |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| His | x | x | x | x | x | N50 | |
+| togram | | | | | | | |
+| of | | | | | | | |
+| (log | | | | | | | |
+| transf | | | | | | | |
+| ormed) | | | | | | | |
+| read | | | | | | | |
+| length | | | | | | | |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Biv | x | x | | x | x | log | dot, |
+| ariate | | | | | | tr | hex, |
+| plot | | | | | | ansfor | kde, |
+| of | | | | | | mation | pauvre |
+| length | | | | | | | |
+| a | | | | | | | |
+| gainst | | | | | | | |
+| base | | | | | | | |
+| call | | | | | | | |
+| q | | | | | | | |
+| uality | | | | | | | |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| H | | x | | | x | | |
+| eatmap | | | | | | | |
+| of | | | | | | | |
+| reads | | | | | | | |
+| per | | | | | | | |
+| c | | | | | | | |
+| hannel | | | | | | | |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Cumu | | x | x | | x | | |
+| lative | | | | | | | |
+| yield | | | | | | | |
+| plot | | | | | | | |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Violin | | x | x | | x | | |
+| plot | | | | | | | |
+| of | | | | | | | |
+| read | | | | | | | |
+| length | | | | | | | |
+| over | | | | | | | |
+| time | | | | | | | |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Violin | | x | | | x | | |
+| plot | | | | | | | |
+| of | | | | | | | |
+| base | | | | | | | |
+| call | | | | | | | |
+| q | | | | | | | |
+| uality | | | | | | | |
+| over | | | | | | | |
+| time | | | | | | | |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Biv | | | | x | | | dot, |
+| ariate | | | | | | | hex, |
+| plot | | | | | | | kde |
+| of | | | | | | | |
+| a | | | | | | | |
+| ligned | | | | | | | |
+| read | | | | | | | |
+| length | | | | | | | |
+| a | | | | | | | |
+| gainst | | | | | | | |
+| seq | | | | | | | |
+| uenced | | | | | | | |
+| read | | | | | | | |
+| length | | | | | | | |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Biv | | | | x | | log | dot, |
+| ariate | | | | | | tr | hex, |
+| plot | | | | | | ansfor | kde |
+| of | | | | | | mation | |
+| p | | | | | | | |
+| ercent | | | | | | | |
+| ref | | | | | | | |
+| erence | | | | | | | |
+| id | | | | | | | |
+| entity | | | | | | | |
+| a | | | | | | | |
+| gainst | | | | | | | |
+| read | | | | | | | |
+| length | | | | | | | |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Biv | | | | x | | | dot, |
+| ariate | | | | | | | hex, |
+| plot | | | | | | | kde |
+| of | | | | | | | |
+| p | | | | | | | |
+| ercent | | | | | | | |
+| ref | | | | | | | |
+| erence | | | | | | | |
+| id | | | | | | | |
+| entity | | | | | | | |
+| a | | | | | | | |
+| gainst | | | | | | | |
+| base | | | | | | | |
+| call | | | | | | | |
+| q | | | | | | | |
+| uality | | | | | | | |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Biv | | | | x | | log | dot, |
+| ariate | | | | | | tr | hex, |
+| plot | | | | | | ansfor | kde |
+| of | | | | | | mation | |
+| m | | | | | | | |
+| apping | | | | | | | |
+| q | | | | | | | |
+| uality | | | | | | | |
+| a | | | | | | | |
+| gainst | | | | | | | |
+| read | | | | | | | |
+| length | | | | | | | |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Biv | | | | x | | | dot, |
+| ariate | | | | | | | hex, |
+| plot | | | | | | | kde |
+| of | | | | | | | |
+| m | | | | | | | |
+| apping | | | | | | | |
+| q | | | | | | | |
+| uality | | | | | | | |
+| a | | | | | | | |
+| gainst | | | | | | | |
+| ba | | | | | | | |
+| secall | | | | | | | |
+| q | | | | | | | |
+| uality | | | | | | | |
++--------+--------+--------+--------+--------+--------+--------+--------+
+
+COMPANION SCRIPTS
+-----------------
+
+- `NanoComp <https://github.com/wdecoster/nanocomp>`__: comparing
+ multiple runs
+- `NanoStat <https://github.com/wdecoster/nanostat>`__: statistic
+ summary report of reads or alignments
+- `NanoFilt <https://github.com/wdecoster/nanofilt>`__: filtering and
+ trimming of reads
+- `NanoLyse <https://github.com/wdecoster/nanolyse>`__: removing
+ contaminant reads (e.g. lambda control DNA) from fastq
+
+CITATION
+--------
+
+If you use this tool, please consider citing our
+`publication <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939>`__.
+
+Copyright: 2016-2020 Wouter De Coster decosterwouter at gmail.com
+
+.. |Twitter URL| image:: https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster
+ :target: https://twitter.com/wouter_decoster
+.. |conda badge| image:: https://anaconda.org/bioconda/nanoplot/badges/installer/conda.svg
+ :target: https://anaconda.org/bioconda/nanoplot
+.. |Build Status| image:: https://travis-ci.org/wdecoster/NanoPlot.svg?branch=master
+ :target: https://travis-ci.org/wdecoster/NanoPlot
=====================================
debian/changelog
=====================================
@@ -1,5 +1,9 @@
-nanoplot (1.29.0-1) UNRELEASED; urgency=medium
+nanoplot (1.30.1-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Initial release (Closes: #<bug>)
+ [ Steffen Moeller ]
+ * debhelper-compat 13 (routine-update)
+
-- Andreas Tille <tille at debian.org> Wed, 22 Apr 2020 16:40:23 +0200
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
dh-python,
python3,
python3-setuptools,
=====================================
nanoplot/NanoPlot.py
=====================================
@@ -59,7 +59,8 @@ def main():
readtype=args.readtype,
combine="simple",
barcoded=args.barcoded,
- huge=args.huge)
+ huge=args.huge,
+ keep_supp=not(args.no_supplementary))
if args.store:
pickle.dump(
obj=datadf,
=====================================
nanoplot/utils.py
=====================================
@@ -139,6 +139,10 @@ def get_args():
filtering.add_argument("--barcoded",
help="Use if you want to split the summary file by barcode",
action="store_true")
+ filtering.add_argument("--no_supplementary",
+ help="Use if you want to remove supplementary alignments",
+ action="store_true",
+ default=False)
visual = parser.add_argument_group(
title='Options for customizing the plots created')
visual.add_argument("-c", "--color",
=====================================
nanoplot/version.py
=====================================
@@ -1 +1 @@
-__version__ = "1.29.0"
+__version__ = "1.30.1"
=====================================
scripts/test.sh
=====================================
@@ -12,6 +12,11 @@ NanoPlot --bam nanotest/alignment.bam --verbose
echo ""
echo ""
echo ""
+echo "testing bam without supplementary alignments:"
+NanoPlot --bam nanotest/alignment.bam --verbose --no_supplementary
+echo ""
+echo ""
+echo ""
echo "testing summary:"
NanoPlot --summary nanotest/sequencing_summary.txt --loglength --verbose
echo ""
=====================================
setup.py
=====================================
@@ -16,7 +16,7 @@ setup(
url='https://github.com/wdecoster/NanoPlot',
author='Wouter De Coster',
author_email='decosterwouter at gmail.com',
- license='MIT',
+ license='GPLv3',
classifiers=[
'Development Status :: 4 - Beta',
'Intended Audience :: Science/Research',
@@ -36,12 +36,11 @@ setup(
'numpy',
'scipy',
'python-dateutil',
- 'seaborn>=0.9.0',
+ 'seaborn>=0.10.1',
'matplotlib>=3.1.3',
- 'nanoget>=1.9.0',
+ 'nanoget>=1.13.0',
'nanomath>=0.23.1',
- "pauvre==0.1.86",
- "statsmodels==0.10.1",
+ "pauvre==0.2.0",
'plotly>=4.1.0',
],
package_data={'NanoPlot': []},
@@ -52,4 +51,5 @@ setup(
'NanoPlot=nanoplot.NanoPlot:main',
],
},
+ data_files=[("", ["LICENSE"])]
)
View it on GitLab: https://salsa.debian.org/med-team/nanoplot/-/compare/d815968f256a70ca8065efcfc8fb2a83900bceee...612411d72b7ea940566fc853bb5cd47b3f85e374
--
View it on GitLab: https://salsa.debian.org/med-team/nanoplot/-/compare/d815968f256a70ca8065efcfc8fb2a83900bceee...612411d72b7ea940566fc853bb5cd47b3f85e374
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