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crops

Cropping and Renumbering Operations for PDB structure and Sequence files

https://github.com/rigdenlab/crops

Science Score: 13.0%

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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    .zenodo.json file
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    DOI references
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    Scientific vocabulary similarity
    Low similarity (14.5%) to scientific vocabulary

Keywords

bioinformatics fasta pdb
Last synced: 6 months ago · JSON representation

Repository

Cropping and Renumbering Operations for PDB structure and Sequence files

Basic Info
  • Host: GitHub
  • Owner: rigdenlab
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 2.7 MB
Statistics
  • Stars: 1
  • Watchers: 3
  • Forks: 2
  • Open Issues: 1
  • Releases: 0
Topics
bioinformatics fasta pdb
Created over 5 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.rst 

.. image:: docs/_static/logo_crops_clipart.svg
   :width: 100%
   :align: center

************************************************************************
Cropping and Renumbering Operations for PDB structure and Sequence files
************************************************************************

.. image:: https://img.shields.io/pypi/v/crops
   :target: https://pypi.org/project/CROPS/
   :alt: Latest PyPi release
.. image:: https://img.shields.io/github/license/rigdenlab/crops
   :target: https://github.com/rigdenlab/crops/blob/master/LICENSE
   :alt: License
.. image::https://img.shields.io/pypi/pyversions/crops
   :target: https://pypi.org/project/CROPS/
   :alt: PyPI - Python Version
.. image:: https://readthedocs.org/projects/crops/badge/?version=latest
   :target: http://crops.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status

About CROPS
+++++++++++

CROPS is a useful toolkit developed by the `Rigden group `_ at the University of Liverpool, England, that allows to perform a number of customisations on structure and sequence files, aimed at improving the outcomes of a variety of processes. CROPS allows to renumber the index of residues in a PDB structure file in order to match the positional index in the complete sequence and extract specific sequences from a large sequence file. It can also make use of a number of databases to find those residues in the sequence that are either artificially inserted or belong in different biological sequences (e.g. Uniprot sequences), in order to remove artificial insertions that can hamper the search for homologues or decrease the score in a molecular replacement operation.

This toolkit has been developed to perform three specific tasks:

* renumber residue indices in structure files to make them match residue position in the sequence (provided by a sequence file from the same source);
* crop insertions off sequences in sequence files;
* crop insertions off structures in structure files;
* split large sequence files to extract specific sequences from them.

CROPS makes use of a number of databases in order to collect information about segments, insertions, sources, etc. In particular, it is built around the following databases:

* PDB-to-Uniprot `SIFTS database `_,
* `Uniclust `_ databases,
* custom user-defined interval files.

If your software has any dependencies to versions older than CROPS v0.5.0, please update your software. These versions are now deprecated.

Supported Formats
+++++++++++++++++

* **Sequences:**  *FASTA* --several header formats recognised.
* **Structures:** *PDB*. *mmCIF* to be implemented.
* **Databases:**  *CSV* (interval information), *FASTA* (UniProt).

Requirements
++++++++++++

* **Gemmi:** `gemmi.readthedocs.io `_,
* **BioPython:** `biopython.org `_.

Read the Docs !!
++++++++++++++++

You can find all the documentation including installation instructions and practical examples at `crops.readthedocs.io `_.

Owner

  • Name: Rigden Lab
  • Login: rigdenlab
  • Kind: organization
  • Location: Liverpool, UK

Post-Genome Bioinformatics

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 282
  • Total Committers: 3
  • Avg Commits per committer: 94.0
  • Development Distribution Score (DDS): 0.043
Past Year
  • Commits: 10
  • Committers: 1
  • Avg Commits per committer: 10.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
jjavier-bm j****h@g****m 270
FilomenoSanchez f****d@h****m 9
jjavier-bm 5****m 3

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 103
  • Average time to close issues: about 1 year
  • Average time to close pull requests: about 13 hours
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.02
  • Merged pull requests: 101
  • 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: N/A
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jjavier-bm (4)
Pull Request Authors
  • jjavier-bm (105)
  • FilomenoSanchez (3)
Top Labels
Issue Labels
enhancement (4) testing (1)
Pull Request Labels
documentation (21) bug (8) enhancement (7) testing (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 21 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 2
  • Total maintainers: 1
pypi.org: crops

Cropping and Renumbering Operations for PDB structure and Sequence files

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 21 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 19.1%
Dependent repos count: 21.5%
Average: 30.9%
Stargazers count: 31.9%
Downloads: 71.5%
Maintainers (1)
jjavier-bm
Last synced: 6 months ago

Dependencies

.github/workflows/main.yml actions
  • actions/checkout v1 composite
  • actions/setup-python v1 composite
docs/doc-requirements.txt pypi
  • biopython *
  • gemmi *
  • sphinx-argparse *
  • sphinx_bootstrap_theme *
requirements.txt pypi
  • biopython ==1.79
  • gemmi *
setup.py pypi