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revmut 0.3.0

.. image:: https://travis-ci.org/inodb/revmut.svg?branch=master :target: https://travis-ci.org/inodb/revmutREVertant 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 changesThere are scripts to do 1 and 3. Steps 2 might be added at a later stage indevelopment... image:: img/revmut_overview.pngInstallation------------:: pip install revmutFind----The finding module takes a mutation and findsPRMs 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