Name: snv-processing
Owner: raphael-group
Description: A script for converting MAF files for use with MAGI, CoMEt, and HotNet2.
Created: 2016-05-24 18:33:49.0
Updated: 2016-05-26 03:39:16.0
Pushed: 2016-07-11 13:32:53.0
Homepage: null
Size: 870
Language: Python
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Proces SNV data (.maf files) for use in CoMEt, MAGI, and HotNet2.
python MAFprocessing.py -f <path to MAF file> -d <path to transcripts database>
A tab separated file, each row is a sample and associated gene mutations. The first column is the sample name, each entry after is a gene. The name is {prefix}_hotnet2.tsv. The prefix is a optional argument. If no prefix is supplied, the default is 'output'.
The same as HotNet2, named {prefix}_comet.tsv.
A eight column, tab separated file with a header. Each row (in order) consists of a gene, a sample, the transcript ID, the transcript length, the locus of the mutation, the mutation type, the original amino acid, and the new amino acid.
All options can be set by command line or via a configuration file. The command line will override configuration file settings, and the names and usage for command line and configuration file options are the same.
The following options must be specified by the user either at the command line or in the config file, and cannot be left to defaults:
Config/long argument | Short argument | Input type | Description :————————————-| :—– |:—– |:—– database | -d | Path to transcript database |Path to the transcript database, a json file with a key/value pair of { 'database' : {'transcript' : length (integer)} }. See example in this repository (transcript-lenghts.json). file | -f | Path to MAF file | Path to the maf file to be processed.