semvec/pypi-packages huggingface dataset:
gene-map 0.4.4
Map gene ids using UniProt.
License: MIT
Keywords: uniprot genes mapping

gene_map
========

|PyPI| |Build Status| |codecov|

Tool for converting between various gene ids.

Installation
------------

.. code:: bash

   $ pip install gene_map

Usage
-----

.. code:: bash

   $ gene_map --help
   Usage: gene_map [OPTIONS]

     Map gene ids between various formats.

   Options:
     -i, --input TEXT                If it exists, treated as file with
                                     whitespace-separated gene ids. Otherwise
                                     treated as a gene id itself.  [required]
     --from TEXT                     Source ID type.  [required]
     --to TEXT                       Target ID type.  [required]
     -o, --output FILENAME           CSV-file to save result to.
     --organism [ARATH_3702|CAEEL_6239|CHICK_9031|DANRE_7955|DICDI_44689|DROME_7227|ECOLI_83333|HUMAN_9606|MOUSE_10090|RAT_10116|SCHPO_284812|YEAST_559292]
                                     Organism to convert IDs in.
     --cache-dir DIRECTORY           Folder to store ID-databases in.
     -q, --quiet                     Suppress logging of mapping-statistics.
     --force-download                Force download of mapping-database.
     --help                          Show this message and exit.

Getting started
---------------

Commandline usage
~~~~~~~~~~~~~~~~~

Inputs can be either gene ids or files containing whitespace-separated
gene ids:

.. code:: bash

   $ cat mygenes.txt
   P63244 P08246
   P68871
   $ gene_map \
       -i P35222 -i InvalidID -i mygenes.txt -i P04637 \
       --from ACC --to Gene_Name \
       -o gene_mapping.csv
   Mapped 5/6 genes.
   $ cat gene_mapping.csv
   ID_from,ID_to
   P04637,TP53
   P08246,ELANE
   P35222,CTNNB1
   P63244,RACK1
   P68871,HBB

It is also possible to simply try to convert all given inputs without
knowing their ID type, by using ``--from auto``:

.. code:: bash

   $ gene_map \
       -i P35222 \
       -i TP53 \
       -i '9606.ENSP00000306407' \
       --from auto \
       --to GeneID
   Mapped 3/3 genes.
   ID_from,ID_to
   9606.ENSP00000306407,79007
   P35222,1499
   TP53,7157

Attention: if an ID is valid for multiple types, unintended side-effects
may occur. Furthermore, all IDs are treated as strings.

API usage
~~~~~~~~~

.. code:: python

   >>> from gene_map import GeneMapper

   >>> stringdb_ids = ['9606.ENSP00000306407', '9606.ENSP00000337461']
   >>> gm = GeneMapper()  # defaults to HUMAN_9606
   >>> gm.query(stringdb_ids, source_id_type='STRING', target_id_type='GeneID')
   #                ID_from  ID_to
   #0  9606.ENSP00000306407  79007
   #1  9606.ENSP00000337461  90529

.. |PyPI| image:: https://img.shields.io/pypi/v/gene_map.svg?style=flat
   :target: https://pypi.python.org/pypi/gene_map
.. |Build Status| image:: https://img.shields.io/travis/kpj/gene_map.svg?style=flat
   :target: https://travis-ci.org/kpj/gene_map
.. |codecov| image:: https://codecov.io/gh/kpj/gene_map/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/kpj/gene_map