Simple interface for uniprot.org/mapping
Project description
map a string of whitespace seperated entries from one format onto another using uniprots mapping api
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'
Installation
From pypi (recommended)
pip install uniprot_mapper
From source (UNIX) as standalone
Clone the git repository
git clone https://github.com/jdrudolph/uniprot_mapper.git
Make the script executable and add it to your PATH:
chmod +x uniprot_mapper/uniprot_mapper/uniprot_mapper.py cd /usr/local/bin sudo ln -s /path/to/uniprot_mapper.py .
Example
standalone
uniprot_mapper.py ACC P_ENTREZGENEID acc_file map_file
This will read UniprotIDs seperated by whitespaces from acc_file and store them to map_file.
Using a pipe:
echo P31749 | uniprot_mapper.py ACC P_ENTREZGENEID
will print the result to stdout which can be redirected further
inside a python script
import uniprot_mapper as mapper print mapper.map('P31749')
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uniprot_mapper-0.6.tar.gz
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