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alignparse

alignparse: A Python package for parsing complex features from high-throughput long-read sequencing - Published in JOSS (2019)

https://github.com/jbloomlab/alignparse

Science Score: 95.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    1 of 8 committers (12.5%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Mathematics Computer Science - 84% confidence
Biology Life Sciences - 63% confidence
Last synced: 4 months ago · JSON representation

Repository

Align sequences and then parse features.

Basic Info
  • Host: GitHub
  • Owner: jbloomlab
  • License: other
  • Language: Jupyter Notebook
  • Default Branch: master
  • Size: 8.21 MB
Statistics
  • Stars: 18
  • Watchers: 5
  • Forks: 10
  • Open Issues: 1
  • Releases: 4
Created over 6 years ago · Last pushed 9 months ago
Metadata Files
Readme Changelog Contributing License

README.rst 

===============================
alignparse
===============================

.. image:: https://img.shields.io/pypi/v/alignparse.svg
        :target: https://pypi.python.org/pypi/alignparse

.. image:: https://github.com/jbloomlab/alignparse/actions/workflows/test.yml/badge.svg
        :target: https://github.com/jbloomlab/alignparse/actions/workflows/test.yml

.. image:: https://zenodo.org/badge/194140958.svg
   :target: https://zenodo.org/badge/latestdoi/194140958

.. image:: https://joss.theoj.org/papers/10.21105/joss.01915/status.svg
   :target: https://doi.org/10.21105/joss.01915

.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/psf/black

.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json
    :target: https://github.com/astral-sh/ruff

``alignparse`` is a Python package written by `the Bloom lab `_. 
It is designed to align long sequencing reads (such as those from PacBio circular consensus sequencing) to targets, filter these alignments based on user-provided specifications, and parse out user-defined sequence features.
For each read that passes the filters, information about the features (e.g. accuracy, sequence, mutations) is retained for further analyses. 

See the `alignparse documentation `_ for details on how to install and use ``alignparse``.

Please `cite alignparse `_ if you use it in your work.

The source code is `on GitHub `_.

To contribute to this package, read the instructions in `CONTRIBUTING.rst `_.

To report issues or seek support, please use the `GitHub issue tracker `_.

Owner

  • Name: jbloomlab
  • Login: jbloomlab
  • Kind: organization
  • Email: jbloom@fredhutch.org
  • Location: Seattle, WA, USA

Jesse Bloom's lab GitHub account

JOSS Publication

alignparse: A Python package for parsing complex features from high-throughput long-read sequencing
Published
December 11, 2019
DOI
Volume 4, Issue 44, Page 1915
Authors
Katharine H.d. Crawford ORCID
Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA, Department of Genome Sciences and Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
Jesse D. Bloom ORCID
Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA, Howard Hughes Medical Institute, Seattle, Washington, USA
Editor
Will Rowe ORCID
Tags
PacBio deep mutational scanning single-cell virus sequencing genomics sequencing
View PDF Review Thread Software Archive

Papers & Mentions

Total mentions: 3

Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding
Last synced: 3 months ago
Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding
Last synced: 3 months ago
alignparse: A Python package for parsing complex features from high-throughput long-read sequencing
Last synced: 3 months ago

GitHub Events

Total
  • Create event: 3
  • Release event: 2
  • Issues event: 1
  • Delete event: 1
  • Issue comment event: 2
  • Push event: 4
  • Pull request event: 2
  • Fork event: 1
Last Year
  • Create event: 3
  • Release event: 2
  • Issues event: 1
  • Delete event: 1
  • Issue comment event: 2
  • Push event: 4
  • Pull request event: 2
  • Fork event: 1

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 297
  • Total Committers: 8
  • Avg Commits per committer: 37.125
  • Development Distribution Score (DDS): 0.461
Past Year
  • Commits: 4
  • Committers: 1
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
jbloom j****m@f****g 160
Kate Dusenbury k****y@g****m 114
Alan Rubin a****n@w****u 11
Bernadeta Dadonaite b****e@g****m 8
jianfcpku 4****u 1
Kate Dusenbury k****y 1
Arfon Smith a****n 1
Andrew Butler a****r 1
Committer Domains (Top 20 + Academic)
wehi.edu.au: 1 fredhutch.org: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 36
  • Total pull requests: 68
  • Average time to close issues: 28 days
  • Average time to close pull requests: 11 days
  • Total issue authors: 11
  • Total pull request authors: 8
  • Average comments per issue: 1.81
  • Average comments per pull request: 0.9
  • Merged pull requests: 67
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 3 minutes
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jbloom (17)
  • afrubin (5)
  • khdcrawford (4)
  • greenkidneybean (2)
  • xguse (2)
  • jianfcpku (1)
  • krdav (1)
  • Jayaos (1)
  • bede (1)
  • Bernadetadad (1)
  • cdebuck (1)
Pull Request Authors
  • jbloom (50)
  • khdcrawford (14)
  • cdebuck (2)
  • jianfcpku (2)
  • andrewwbutler (1)
  • arfon (1)
  • Bernadetadad (1)
  • afrubin (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 230 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 24
  • Total maintainers: 1
pypi.org: alignparse

Align sequences and then parse features.

  • Versions: 24
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 230 Last month
Rankings
Dependent repos count: 9.0%
Dependent packages count: 10.0%
Forks count: 11.4%
Average: 14.4%
Stargazers count: 14.8%
Downloads: 26.8%
Maintainers (1)
jbloom
Last synced: 4 months ago

Dependencies

docs/doc_requirements.txt pypi
  • ipykernel >=5.1.0
  • matplotlib >=3.0.2
  • nbsphinx >=0.4.2
  • nbsphinx-link >=1.2.0
  • pandoc >=2.7.3
  • sphinx >=2.0
  • sphinx-argparse >=0.2.5
  • sphinx_gallery >=0.3.1
environment.yml pypi
  • dms_variants >=0.8.6
setup.py pypi
  • biopython >=1.73
  • dna_features_viewer >=1.0.0
  • matplotlib >=3.0.0
  • numpy >=1.17
  • packaging *
  • pandas >=0.25.1
  • pathos >=0.2.4
  • plotnine >=0.6
  • pysam >=0.14
  • pyyaml >=5.1.1
  • regex >=2.5.33
  • scipy >=1.2
test_requirements.txt pypi
  • black * test
  • dms_variants * test
  • flake8 * test
  • flake8-bugbear * test
  • flake8-builtins * test
  • flake8-comprehensions * test
  • flake8-docstrings * test
  • flake8-import-order * test
  • flake8-print * test
  • flake8-rst-docstrings * test
  • nbval * test
  • pytest * test