Metadata-Version: 1.1
Name: gene_map
Version: 0.4.2
Summary: Map gene ids using UniProt.
Home-page: https://github.com/kpj/gene_map
Author: kpj
Author-email: kpjkpjkpjkpjkpjkpj@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Description: gene_map
        ========
        
        |PyPI| |Build Status|
        
        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.
              --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
        
Keywords: vydia video playback
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: End Users/Desktop
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3 :: Only
