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genomediff-write

GenomeDiff (*.gd) file parser for Python

https://github.com/biosustain/genomediff-python

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.1%) to scientific vocabulary

Keywords

breseq genomediff genomics parser
Last synced: 6 months ago · JSON representation

Repository

GenomeDiff (*.gd) file parser for Python

Basic Info
  • Host: GitHub
  • Owner: biosustain
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 15.6 KB
Statistics
  • Stars: 2
  • Watchers: 6
  • Forks: 7
  • Open Issues: 3
  • Releases: 0
Topics
breseq genomediff genomics parser
Created almost 12 years ago · Last pushed over 6 years ago
Metadata Files
Readme License

README.rst 

genomediff-python
=================

**genomediff-python** parses files in the
`GenomeDiff format `_
generated by the `breseq `_
variant caller for haploid microbial organisms.


Installation
------------

::
    
    pip3 install genomediff


Only Python 3.x is tested.

Usage
-----

GenomeDiff files are read using ``GenomeDiff.read(file)``. The ``GenomeDiff`` object contains a ``metadata`` dict with
the meta data, as well as ``mutations``, ``evidence`` and ``validation`` lists—each containing records of that type.
Records can be accessed through this list or by id. ``GenomeDiff`` is iterable and iterating will return all records of all types.

::

    >>> from genomediff import *
    >>> document = GenomeDiff.read(open('MyDiff.gd', 'r', encoding='utf-8'))
    >>> document.metadata
    {'GENOME_DIFF': '1.0', 'AUTHOR': ''}
    >>> document.mutations[0]
    Record('SNP', 1, [191], new_seq='A', seq_id='NC_000913', snp_type='intergenic',  position=12346)
    >>> document.mutations[0].parent_ids
    [191]
    >>> document[191]         
    Record('RA', 191, None, tot_cov='46/42', new_base='A', insert_position=0, ref_base='G', seq_id='NC_000913', quality=252.9, position=12345)
    >>> document.mutations[0].parents
    [Record('RA', 191, None, tot_cov='46/42', new_base='A', insert_position=0, ref_base='G', seq_id='NC_000913', quality=252.9, position=12345)]

Contribution
------------

Contribution to this project is welcomed. Wishlist:

- Writing GD files
- Python 2.x support

Owner

  • Name: DTU Biosustain
  • Login: biosustain
  • Kind: organization
  • Location: Denmark

The Novo Nordisk Foundation Center for Biosustainability

GitHub Events

Total
  • Fork event: 1
Last Year
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 20
  • Total Committers: 4
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.4
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Lars Schöning l****s@l****e 12
Joao Cardoso j****a@b****k 4
meono e****z@b****k 3
Roland Andrei Groza r****u@g****m 1
Committer Domains (Top 20 + Academic)
biosustain.dtu.dk: 2 lyschoening.de: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 4
  • Total pull requests: 2
  • Average time to close issues: about 23 hours
  • Average time to close pull requests: 5 minutes
  • Total issue authors: 4
  • Total pull request authors: 2
  • Average comments per issue: 1.75
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jeffreybarrick (1)
  • lyschoening (1)
  • antanij (1)
  • pvphaneuf (1)
Pull Request Authors
  • rohanmaddamsetti (1)
  • the-code-magician (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • pypi 18 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 11
  • Total maintainers: 1
pypi.org: genomediff-write

GenomeDiff (*.gd) file reader

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 0
Rankings
Dependent packages count: 4.8%
Dependent repos count: 6.3%
Forks count: 13.4%
Average: 20.5%
Stargazers count: 27.5%
Downloads: 50.6%
Last synced: about 1 year ago
pypi.org: genomediff3

GenomeDiff (*.gd) file reader

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 0
Rankings
Dependent packages count: 4.8%
Dependent repos count: 6.3%
Forks count: 13.4%
Average: 20.5%
Stargazers count: 27.5%
Downloads: 50.6%
Last synced: about 1 year ago
pypi.org: genomediff2

GenomeDiff (*.gd) file reader

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 18 Last month
Rankings
Dependent packages count: 6.6%
Forks count: 14.5%
Average: 21.0%
Dependent repos count: 30.6%
Stargazers count: 32.3%
Maintainers (1)
rujinlong
Last synced: 6 months ago