Simple interface for uniprot.org
Project description
uniprot_tools
=============
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')
=============
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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