{ "info": { "author": "Ino de Bruijn", "author_email": "ino@ino.pm", "bugtrack_url": null, "classifiers": [ "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Natural Language :: English", "Operating System :: OS Independent", "Programming Language :: Python", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.6", "Programming Language :: Python :: 2.7", "Topic :: Software Development :: Libraries :: Python Modules" ], "description": ".. image:: https://travis-ci.org/inodb/revmut.svg?branch=master \n :target: https://travis-ci.org/inodb/revmut\nREVertant MUTation find & verify (REVMUT)\n=========================================\nREVMUT can help to **find** and **verify** putative revertant mutations (PRMs). Common workflow is:\n\n1. **Find** PRMs (deletions of given mutation, indels that restore the reading frame)\n2. **Annotatote** PRMs with Oncotator to get transcript change of putative\n revertant mutations in HGVS format \n3. **Verify** if one of the transcript change in HGVS format is revertant by looking\n how the length of the protein changes\n\nThere are scripts to do 1 and 3. Steps 2 might be added at a later stage in\ndevelopment.\n\n.. image:: img/revmut_overview.png\n\nInstallation\n------------\n::\n\n pip install revmut\n\nFind\n----\nThe finding module takes a mutation and finds\nPRMs that:\n\n- Delete the entire given mutation\n- Restore the reading frame in case the given mutation (GM) is an indel. The criterium is::\n \n length(PRM) +/- length(GM) % 3 == 0\n \nRun with::\n\n revmut-find tests/test_data/human_g1k_v37_chr17.fa \\\n tests/test_data/germline_mutations/T1_test_mutation.tsv \\\n tests/test_data/T1.bam \\\n tests/test_data/N1.bam > tests/test_data/output/T1_test.tsv\n \nView input/output files:\n\n- `tests/test_data/germline_mutations/T1_test_mutation.tsv `_\n- `tests/test_data/output/T1_test.tsv `_\n\n\nAnnotate\n--------\nAnnotation of the PRMs is currently done semi-manually with `Oncotator webserice `_. Perhaps at a later stage in development this will be done automatically. Missing is a VCF to Oncotator format converter.\n\nVerify\n------\nApplies 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.\n\nRun with::\n\n revmut-verify tests/test_data/to_be_reverted_mutations.txt \\\n tests/test_data/oncotator.ins.txt \\\n tests/test_data/BRCA_transcripts.fa > tests/test_data/oncotator.ins.maf.out.tsv\n \nView input/output files:\n \n- `tests/test_data/to_be_reverted_mutations.txt `_\n- `tests/test_data/oncotator.ins.txt `_\n- `tests/test_data/oncotator.ins.maf.out.tsv `_\n\nDevelopers\n----------\nTests\n~~~~~\nIn root dir run::\n\n nosetests", "description_content_type": null, "docs_url": null, "download_url": "UNKNOWN", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/inodb/revmut", "keywords": "Python revertant mutation finder HGVS", "license": "MIT", "maintainer": null, "maintainer_email": null, "name": "revmut", "package_url": "https://pypi.org/project/revmut/", "platform": "UNKNOWN", "project_url": "https://pypi.org/project/revmut/", "project_urls": { "Download": "UNKNOWN", 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