https://github.com/kronopt/uniprotidretrieval
Downloads protein sequences from Uniprot, in the desired output format, based on the given ids (either passed as arguments or identified in a file)
https://github.com/kronopt/uniprotidretrieval
python python-2 uniprot uniprot-ids
Last synced: about 2 months ago
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Downloads protein sequences from Uniprot, in the desired output format, based on the given ids (either passed as arguments or identified in a file)
- Host: GitHub
- URL: https://github.com/kronopt/uniprotidretrieval
- Owner: Kronopt
- License: gpl-3.0
- Created: 2016-06-22T14:59:01.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2021-07-27T21:04:07.000Z (almost 5 years ago)
- Last Synced: 2025-03-27T19:24:38.117Z (about 1 year ago)
- Topics: python, python-2, uniprot, uniprot-ids
- Language: Python
- Homepage:
- Size: 26.4 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# UniprotIdRetrieval
Downloads protein sequences from Uniprot, in the desired output format, based on the given ids (either passed as arguments or identified in a file)
#### Dependencies
* Python 2.7
* Module dependencies (run `pip install -r requirements.txt` to install):
* requests
#### How to run
Runs through the command line, like so:
`UniprotIdRetrieval.py [-h] (-f | -i ) [-fo {fasta, gff, tab, txt, rdf, xml}]`
* `-h, --help` shows the help text
* `-f, --file` takes a file path to search for ids
* `-i, --ids` takes 1 or more ids
* `-fo, --format` defines the output format of downloaded files (fasta, gff, tab, txt, rdf or xml), defaults to 'fasta'