Metadata-Version: 1.1
Name: revmut
Version: 0.1
Summary: REVertant MUTation finder
Home-page: https://github.com/inodb/revmut
Author: Ino de Bruijn
Author-email: ino@ino.pm
License: MIT
Description: REVertant MUTation finder (REVMUT)
        ==================================
        
        You have (a) some transcript mutations in HGVS format that change the reading
        frame. You want to see if (b) some other transcript mutations in HGVS format
        revert the mutations in (a).  This script applies the mutations in (a) followed
        by the mutations in (b) and shows how the resulting protein changes in length. 
        
        Current workflow of finding revertant mutations is:
        
        1. Find putative revertant mutations (SNVs at the same location as original
           SNV, indels that restore the reading frame)
        2. Run those mutations through Oncotator to get transcript change of putative
           revertant mutations in HGVS format 
        3. Check if one of the transcript change in HGVS format is revertant by looking
           how the length of the protein changes
        
        This script helps you to do 3. Steps 1 and 2 might be added at a later stage in
        development.
        
        Installation
        ------------
        ::
        
            pip install revmut
        
        Run
        ---
        ::
            usage: revmut [-h] [--version] vcf oncotator_file fasta
        
            Check if a mutation is reverted
        
            positional arguments:
            vcf             VCF with mutation to be reverted
            oncotator_file  MAF to find mutations in
            fasta           Fasta file with transcripts
        
            optional arguments:
            -h, --help      show this help message and exit
            --version       show program's version number and exit
        
        Example
        -------
        To be reverted mutations like:
        
        - `tests/test_data/to_be_reverted_mutations.txt <tests/test_data/to_be_reverted_mutations.txt>`
        
        Oncotator MAF Putative revertant mutations like:
        
        - `tests/test_data/oncotator.del.maf.txt <tests/test_data/oncotator.del.maf.txt>`
        
        Check if given mutations are in a bam file::
        
            revmut tests/test_data/to_be_reverted_mutations.txt \
                   tests/test_data/oncotator.del.maf.txt \
                   tests/test_data/BRCA_transcripts.fa \
                   2> example/revmut.log
        
        Output:
        
        - `example/revmut.log <example/revmut.log>`_
         
        Developers
        ----------
        Tests
        ~~~~~
        In root dir run::
        
            nosetests
        
Keywords: Python revertant mutation finder HGVS
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Software Development :: Libraries :: Python Modules
