Simple interface for uniprot.org
Project description
uniprot provides a command-line and python interface to access the uniprot database
available services: map, retrieve
mapping
map a string of whitespace seperated entries from one format onto another using uniprots mapping api
map(...) Args: query: to be mapped f: from ACC | P_ENTREZGENEID | ... t: to ... format: tab by default Help: for a list of all possible mappings visit 'http://www.uniprot.org/faq/28'
retrieval
retrieve uniprot entries from a string of whitespace seperated uniprot ids
retrieve(...) Args: query: to be mapped format: txt by default Help: possible formats: txt, xml, rdf, fasta, gff
Installation
From pypi (recommended)
pip install uniprot_tools
From source (UNIX) as standalone only
Clone the git repository
git clone https://github.com/jdrudolph/uniprot.git
Use distutils to install the package
cd uniprot sudo python setup.py install
Example
standalone
uniprot map ACC P_ENTREZGENEID acc_file map_file
This will read UniprotIDs seperated by whitespaces from acc_file and store them to map_file.
uniprot retrieve acc_file entries.txt
Retrieve textual etries for all uniprot ids in acc_file and save to entries.txt
Using a pipe:
echo P31749 | uniprot map ACC P_ENTREZGENEID
will print the result to stdout which can be redirected further
echo P31749 | uniprot retrieve
will print the result to stdout which can be redirected further
inside a python script
import uniprot as uni print uni.map('P31749', f='ACC', t='P_ENTREZGENEID') print uni.retrieve('P31749')
Project details
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