Metadata-Version: 1.1
Name: revmut
Version: 0.3.0
Summary: REVertant MUTation finder
Home-page: https://github.com/inodb/revmut
Author: Ino de Bruijn
Author-email: ino@ino.pm
License: MIT
Description: .. image:: https://travis-ci.org/inodb/revmut.svg?branch=master 
          :target: https://travis-ci.org/inodb/revmut
        REVertant MUTation find & verify (REVMUT)
        =========================================
        REVMUT can help to **find** and **verify** putative revertant mutations (PRMs). Common workflow is:
        
        1. **Find** PRMs (deletions of given mutation, indels that restore the reading frame)
        2. **Annotatote** PRMs with Oncotator to get transcript change of putative
           revertant mutations in HGVS format 
        3. **Verify** if one of the transcript change in HGVS format is revertant by looking
           how the length of the protein changes
        
        There are scripts to do 1 and 3. Steps 2 might be added at a later stage in
        development.
        
        .. image:: img/revmut_overview.png
        
        Installation
        ------------
        ::
        
            pip install revmut
        
        Find
        ----
        The finding module takes a mutation and finds
        PRMs that:
        
        - Delete the entire given mutation
        - Restore the reading frame in case the given mutation (GM) is an indel. The criterium is::
          
            length(PRM) +/- length(GM) % 3 == 0
          
        Run with::
        
          revmut-find tests/test_data/human_g1k_v37_chr17.fa \
                      tests/test_data/germline_mutations/T1_test_mutation.tsv \
                      tests/test_data/T1.bam \
                      tests/test_data/N1.bam > tests/test_data/output/T1_test.tsv
          
        View input/output files:
        
        - `tests/test_data/germline_mutations/T1_test_mutation.tsv <tests/test_data/germline_mutations/T1_test_mutation.tsv>`_
        - `tests/test_data/output/T1_test.tsv <tests/test_data/output/T1_test.tsv>`_
        
        
        Annotate
        --------
        Annotation of the PRMs is currently done semi-manually with `Oncotator webserice <http://www.broadinstitute.org/oncotator/>`_. Perhaps at a later stage in development this will be done automatically. Missing is a VCF to Oncotator format converter.
        
        Verify
        ------
        Applies a given mutation in cDNA format to a transcript followed by the cDNA change of the PRM as predicted by Oncotator. Output gives a prediction of how the protein changes.
        
        Run with::
        
          revmut-verify tests/test_data/to_be_reverted_mutations.txt \
                        tests/test_data/oncotator.ins.txt \
                        tests/test_data/BRCA_transcripts.fa > tests/test_data/oncotator.ins.maf.out.tsv
          
        View input/output files:
          
        - `tests/test_data/to_be_reverted_mutations.txt <tests/test_data/to_be_reverted_mutations.txt>`_
        - `tests/test_data/oncotator.ins.txt <tests/test_data/oncotator.ins.txt>`_
        - `tests/test_data/oncotator.ins.maf.out.tsv <tests/test_data/oncotator.ins.maf.out.tsv>`_
        
        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
