Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 17 committers (5.9%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.3%) to scientific vocabulary
Keywords from Contributors
genomics
dna
phylogenetics
bioinformatics
biopython
protein
protein-structure
sequence-alignment
sequences
Last synced: 11 months ago
·
JSON representation
Repository
An imagemagick-like frontend to Biopython SeqIO
Basic Info
- Host: GitHub
- Owner: fhcrc
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Homepage: http://seqmagick.readthedocs.org
- Size: 2.25 MB
Statistics
- Stars: 115
- Watchers: 11
- Forks: 22
- Open Issues: 16
- Releases: 0
Created over 15 years ago
· Last pushed over 2 years ago
Metadata Files
Readme
Changelog
License
README.rst
=========
seqmagick
=========
.. image:: https://travis-ci.org/fhcrc/seqmagick.svg?branch=master
:target: https://travis-ci.org/fhcrc/seqmagick
We often have to convert sequence files between formats and do little
manipulations on them, and it's not worth writing scripts for that.
``seqmagick`` is a kickass little utility to expose the file format conversion
in BioPython in a convenient way. Instead of having a big mess of scripts,
there is one that takes arguments::
seqmagick convert a.fasta b.phy # convert from fasta to phylip
seqmagick mogrify --ungap a.fasta # remove all gaps from a.fasta, in place
seqmagick info *.{fasta,sto} # describe all FASTA and Stockholm
# files in the current directory
Requirements
============
* Python >= 3.5
* biopython >= 1.78
Installation
============
Use pip::
pip install seqmagick
Note that as of version 0.8.0, this package requires Python 3.5+. If
you want to use the most recent version compatible with Python 2.7::
pip install seqmagick==0.6.2
Features
========
* Modifying sequences: Remove gaps, reverse complement, reverse, change case,
- Remove gaps
- Reverse & reverse complement
- Trim to a range of residues
- Change case
- Sort by length or ID
- `more`_
* Displaying `information `_ about
sequence files
* Subsetting sequence files by:
- Position
- ID
- Deduplication
- `more`_
* Filtering sequences by `quality score
`_
* Trimming alignments to a `region of interest
`_ defined by the
forward and reverse primers
Want to learn more? Head to the `Documentation`_.
``seqmagick`` is free software under the GPL v3.
.. _`Documentation`: http://seqmagick.readthedocs.org/en/latest/
.. _`more`: http://seqmagick.readthedocs.org/en/latest/convert_mogrify.html
Owner
- Name: FHCRC Computational Biology
- Login: fhcrc
- Kind: organization
- Location: Seattle, Washington
- Website: http://compbio.fhcrc.org/
- Repositories: 12
- Profile: https://github.com/fhcrc
GitHub Events
Total
- Watch event: 5
- Issue comment event: 1
Last Year
- Watch event: 5
- Issue comment event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Connor McCoy | c****y@f****g | 249 |
| Brian Hodges | b****s@f****g | 55 |
| Noah Hoffman | n****n@g****m | 47 |
| Connor McCoy | c****m@g****m | 27 |
| Chris Rosenthal | c****h@u****u | 15 |
| Jared Galloway | j****7@g****m | 7 |
| Erick Matsen | m****n@f****g | 7 |
| eharkins | e****s@g****m | 7 |
| Erick Matsen | e****n@g****m | 6 |
| Brian Claywell | b****l@f****g | 6 |
| Aaron Gallagher | h****t@g****m | 4 |
| Nilesh Patra | n****4@g****m | 3 |
| Peter Cock | p****k@g****m | 2 |
| Christopher Small | c****l@f****g | 1 |
| Bela Hausmann | p****t@b****e | 1 |
| Étienne Mollier | 6****r | 1 |
| mbooo666 | 2****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: almost 2 years ago
All Time
- Total issues: 76
- Total pull requests: 25
- Average time to close issues: 5 months
- Average time to close pull requests: 3 months
- Total issue authors: 29
- Total pull request authors: 15
- Average comments per issue: 1.55
- Average comments per pull request: 2.16
- Merged pull requests: 17
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: about 23 hours
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- cmccoy (16)
- matsen (7)
- metasoarous (6)
- nhoffman (6)
- wwood (5)
- sjackman (4)
- jgallowa07 (3)
- crosenth (3)
- tillea (2)
- fungs (2)
- bowmanjeffs (2)
- tseemann (2)
- dunleavy005 (1)
- ressy (1)
- galud27 (1)
Pull Request Authors
- jgallowa07 (4)
- crosenth (4)
- emollier (3)
- nhoffman (2)
- nileshpatra (2)
- peterjc (2)
- omgwtfgames (1)
- cmccoy (1)
- bcclaywell (1)
- asellappen (1)
- hawkrives (1)
- wangmengbo (1)
- matsen (1)
- eharkins (1)
- nr0cinu (1)
Top Labels
Issue Labels
feature (5)
Pull Request Labels
feature (1)
Packages
- Total packages: 1
-
Total downloads:
- pypi 169 last-month
- Total docker downloads: 10
- Total dependent packages: 0
- Total dependent repositories: 10
- Total versions: 12
- Total maintainers: 6
pypi.org: seqmagick
Tools for converting and modifying sequence files from the command-line
- Homepage: http://github.com/fhcrc/seqmagick
- Documentation: https://seqmagick.readthedocs.io/
- License: GPL V3
-
Latest release: 0.8.6
published over 3 years ago
Rankings
Docker downloads count: 1.5%
Dependent repos count: 4.6%
Stargazers count: 7.0%
Average: 7.9%
Forks count: 8.1%
Dependent packages count: 10.0%
Downloads: 16.0%
Maintainers (6)
Last synced:
11 months ago
Dependencies
requirements-rtd.txt
pypi
- biopython >=1.78
- pygtrie >=2.1
- sphinx *
requirements.txt
pypi
- biopython >=1.78
- ghp-import *
- nose *
- pygtrie >=2.1
- sphinx *
- twine *
- wheel *
setup.py
pypi
- biopython >=1.78
- pygtrie >=2.1