pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

https://github.com/pysam-developers/pysam

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
Links to: ncbi.nlm.nih.gov
✓
Committers with academic emails
23 of 120 committers (19.2%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (11.6%) to scientific vocabulary

Keywords

bioinformatics htslib ngs python

Keywords from Contributors

genomics dna sequence-alignment phylogenetics protein protein-structure biopython sequencing workflow-management reproducibility

Last synced: 6 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: pysam-developers
License: mit
Language: Cython
Default Branch: master
Homepage: https://pysam.readthedocs.io/en/latest/
Size: 21.3 MB

Statistics

Stars: 843
Watchers: 46
Forks: 289
Open Issues: 255
Releases: 39

Topics

bioinformatics htslib ngs python

Created about 12 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog License Authors

README.rst

=====
Pysam
=====

|build-status| |docs|

Pysam is a python module for reading and manipulating files in the
SAM/BAM format. The SAM/BAM format is a way to store efficiently large
numbers of alignments (`Li 2009`_), such as those routinely created by
next-generation sequencing methods.

Pysam is a lightweight wrapper of the samtools_ C-API. Pysam also
includes an interface for tabix_.

If you are using the conda packaging manager (e.g. miniconda or anaconda),
you can install pysam from the `bioconda channel `_::

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
conda install pysam

Installation through bioconda is the recommended way to install pysam
as it resolves non-python dependencies and uses pre-configured
compilation options. Especially for OS X this will potentially save a
lot of trouble.

The current version of pysam wraps 3rd-party code from htslib-1.21, samtools-1.21, and bcftools-1.21.

Pysam is available through `PyPI `_.
To install, type::

pip install pysam

Pysam documentation is available
`here `_

Questions and comments are very welcome and should be sent to the
`pysam user group `_

.. _samtools: http://samtools.sourceforge.net/
.. _tabix: http://samtools.sourceforge.net/tabix.shtml
.. _Li 2009: http://www.ncbi.nlm.nih.gov/pubmed/19505943

.. |build-status| image:: https://github.com/pysam-developers/pysam/actions/workflows/ci.yaml/badge.svg
:alt: build status
:scale: 100%
:target: https://github.com/pysam-developers/pysam/actions/workflows/ci.yaml

.. |docs| image:: https://readthedocs.org/projects/pysam/badge/?version=latest
:alt: Documentation Status
:scale: 100%
:target: https://pysam.readthedocs.org/en/latest/?badge=latest

Owner

Name: pysam-developers
Login: pysam-developers
Kind: organization

Repositories: 3
Profile: https://github.com/pysam-developers

GitHub Events

Total

Issues event: 74
Watch event: 71
Delete event: 4
Issue comment event: 167
Push event: 46
Pull request review comment event: 1
Pull request review event: 4
Pull request event: 18
Fork event: 17
Create event: 10

Last Year

Issues event: 74
Watch event: 71
Delete event: 4
Issue comment event: 167
Push event: 46
Pull request review comment event: 1
Pull request review event: 4
Pull request event: 18
Fork event: 17
Create event: 10

Committers

Last synced: over 2 years ago

All Time

Total Commits: 1,840
Total Committers: 120
Avg Commits per committer: 15.333
Development Distribution Score (DDS): 0.447

Past Year

Commits: 98
Committers: 11
Avg Commits per committer: 8.909
Development Distribution Score (DDS): 0.367

Top Committers

Name	Email	Commits
Andreas Heger	a**r@g**m	1,017
John Marshall	j**l@h**m	149
Kevin Jacobs	j**s@b**m	98
Kyle Beauchamp	k**p@g**m	82
Marcel Martin	m**n@s**e	57
John Marshall	J**l@g**k	50
Kevin Jacobs	j**s@b**m	34
andreas@fgu210.anat.ox.ac.uk	a**s@f**k	31
Marcel Martin	m**n@t**e	21
Douglas Wu	w**s@g**m	20
Andreas Heger	a**r@g**m	15
marting@fgu210.anat.ox.ac.uk	m**g@f**k	12
dnephi	d**r@a**m	11
Devon Ryan	d**9@g**m	10
Grant Belgard	b**t@m**v	10
andreas@localhost.localdomain	a**s@l**n	10
Florian Finkernagel	f**l@i**e	10
mvdbeek	m**k@g**m	9
Nils Homer	n****3	8
Matthew Pearson	m**n@g**m	8
Nicola Soranzo	n**o@e**k	7
Marcus Kinsella	m**a@g**m	7
lg@fgu029	lg@f****9	7
Matt Stone	m**e@c**u	6
ben.j.schiller@gmail.com	b**r@g**m	6
tfwillems	t****s	4
Dannon Baker	d**r@g**m	4
Amber Wright	a**t@n**m	4
bunbun68	n**e@n**e	3
Julian Gehring	j****g	3
and 90 more...

Committer Domains (Top 20 + Academic)

nanoporetech.com: 3 fgu210.anat.ox.ac.uk: 2 invitae.com: 2 btinternet.com: 1 genome.wustl.edu: 1 google.com: 1 illumina.com: 1 genestack.com: 1 nxn.se: 1 ghraoui.name: 1 puresoftware.com: 1 helsinki.fi: 1 jon.es: 1 well.ox.ac.uk: 1 debian.org: 1 abjonnes.com: 1 chgr.mgh.harvard.edu: 1 earlham.ac.uk: 1 imt.uni-marburg.de: 1 localhost.localdomain: 1 mail.nih.gov: 1 tu-dortmund.de: 1 glasgow.ac.uk: 1 dartmouth.edu: 1 sanger.ac.uk: 1 fgu053.anat.ox.ac.uk: 1 broadinstitute.org: 1 env.ethz.ch: 1 u.washington.edu: 1 ucsc.edu: 1 stanford.edu: 1 embl.de: 1 fgu204.anat.ox.ac.uk: 1 alum.mit.edu: 1 mamt229.imt.uni-marburg.de: 1 ebi.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 253
Total pull requests: 89
Average time to close issues: almost 2 years
Average time to close pull requests: 2 months
Total issue authors: 210
Total pull request authors: 36
Average comments per issue: 2.29
Average comments per pull request: 1.73
Merged pull requests: 47
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 38
Pull requests: 25
Average time to close issues: 15 days
Average time to close pull requests: 13 days
Issue authors: 33
Pull request authors: 8
Average comments per issue: 1.63
Average comments per pull request: 0.76
Merged pull requests: 12
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

nh13 (6)
awgymer (6)
lwtan90 (4)
arpanda (3)
tedil (3)
yurivict (3)
blex-max (3)
emollier (3)
SoapGentoo (3)
jmarshall (3)
kyleabeauchamp (3)
PikalaxALT (2)
ddubocan (2)
msto (2)
AndreasHeger (2)

Pull Request Authors

jmarshall (17)
nh13 (7)
AndreasHeger (7)
msto (6)
DrYak (4)
althonos (3)
nsoranzo (3)
marcelm (3)
ilia-kats (2)
tfwillems (2)
gshiba (2)
Fan-iX (2)
mshunjan (2)
limwz01 (2)
gtamazian (2)

Top Labels

Issue Labels

INSTALL (7) SAM/BAM/CRAM (6) question (2) VCF/BCF (2) bug (1) enhancement (1)

Pull Request Labels

Packages

Total packages: 6
Total downloads:
- pypi 791,631 last-month
Total docker downloads: 33,632,904

Total dependent packages: 404
(may contain duplicates)
Total dependent repositories: 1,384
(may contain duplicates)
Total versions: 100
Total maintainers: 5

pypi.org: pysam

Package for reading, manipulating, and writing genomic data

Homepage: https://github.com/pysam-developers/pysam
Documentation: https://pysam.readthedocs.io/
License: MIT License
Latest release: 0.23.3
published 9 months ago

Versions: 56
Dependent Packages: 370
Dependent Repositories: 1,381
Downloads: 791,612 Last month
Docker Downloads: 33,632,904

Rankings

Dependent packages count: 0.1%

Dependent repos count: 0.3%

Docker downloads count: 0.5%

Downloads: 0.6%

Average: 1.2%

Stargazers count: 2.4%

Forks count: 3.2%

Maintainers (2)

grepall johnm

Last synced: 6 months ago

spack.io: py-pysam

A python module for reading, manipulating and writing genomic data sets.

Homepage: https://github.com/pysam-developers/pysam
License: []
Latest release: 0.21.0
published almost 3 years ago

Versions: 8
Dependent Packages: 34
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Dependent packages count: 2.3%

Average: 4.4%

Forks count: 6.3%

Stargazers count: 9.1%

Maintainers (1)

adamjstewart

Last synced: 6 months ago

proxy.golang.org: github.com/pysam-developers/pysam

Documentation: https://pkg.go.dev/github.com/pysam-developers/pysam#section-documentation
License: mit
Latest release: v0.23.3
published 9 months ago

Versions: 33
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 1.7%

Stargazers count: 2.3%

Average: 6.1%

Dependent packages count: 9.6%

Dependent repos count: 10.8%

Last synced: 6 months ago

pypi.org: pysam-cabbage

pysam

Homepage: https://github.com/pysam-developers/pysam
Documentation: https://pysam-cabbage.readthedocs.io/
License: MIT
Latest release: 0.15.3
published about 6 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 4 Last month

Rankings

Stargazers count: 2.4%

Forks count: 3.2%

Dependent packages count: 7.3%

Average: 14.8%

Dependent repos count: 22.1%

Downloads: 39.2%

Maintainers (1)

ExplodingCabbage

Last synced: 6 months ago

pypi.org: pysam-arm-linux

pysam for ARM (armv7l) Linux GNUroot Debian on Nvidia Shield Tablet [Tegra K1]

Homepage: https://github.com/pysam-developers/pysam
Documentation: https://pysam-arm-linux.readthedocs.io/
License: MIT
Latest release: 0.8.3
published over 10 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 2
Downloads: 15 Last month

Rankings

Stargazers count: 2.4%

Forks count: 3.2%

Dependent packages count: 7.3%

Dependent repos count: 11.8%

Average: 22.0%

Downloads: 85.5%

Maintainers (1)

AntonWutz

Last synced: 6 months ago

anaconda.org: pysam

Pysam is a python module for reading and manipulating files in the SAM/BAM format. The SAM/BAM format is a way to store efficiently large numbers of alignments (Li 2009), such as those routinely created by next-generation sequencing methods.

Homepage: https://github.com/pysam-developers/pysam
License: MIT
Latest release: 0.23.3
published 6 months ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Forks count: 20.7%

Stargazers count: 26.0%

Average: 33.9%

Dependent packages count: 42.4%

Dependent repos count: 46.6%

Last synced: 6 months ago

Dependencies

requirements.txt pypi

cython >=0.29.12

.github/workflows/ci.yaml actions

actions/checkout v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/release.yaml actions

actions/checkout v3 composite
actions/download-artifact v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
docker/setup-qemu-action v1 composite
pypa/cibuildwheel v2.4.0 composite
pypa/gh-action-pypi-publish master composite