revmut 0.3.0

REVertant MUTation finder

.. 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