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        "author": "Aditi Gupta",
        "author_email": "aditi9783@gmail.com",
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        "description": "# ScarTrek\nPython package for identifying gene disrupting and restoring indels in whole-genome sequencing data of Mycobacterium tuberculosis samples\n\n\n-----------------------------------------------------------------------------------------\n### Description\n\n\"Insertion\" or \"deletions\" (affectionly called \"indels\") of nucleotides are two types of genetic changes besides \nsingle nucleotide polymorphims (SNPs) that can be detected by analyzing sequencing data. ScarTrek is an application\nwritten in python to detect indels in whole-genome sequencing data mapped to a reference genome, and if gene information\nfor the referece organism is provided, then determine the genes that have the indels and if the indels influence the \ntranslated product of the gene. This analyses is useful to detect gene inactivations due to indels.\n\n### Installation\n\n##### Using pip\n`$ pip install scartrek`\n\n##### From GitHub\n\nScarTrek project can be downloaded directly from GitHub and python scripts can be run directly from the command line as shown in usage.\n\n### Usage\n\nIf installed using pip, ScarTrek can be run as:\n\n`$ find-scars [-h] -i INPUT [-m MAPRATE] [-c COVTHRES] [-g GENESEQ]\n                     [-p PROTSEQ]`\n\nIf downloaded from GitHub, ScarTrek can be run in the directory ScarTrek/scartrek/ as:\n\n`$ python find_scars.py [-h] -i INPUT [-m MAPRATE] [-c COVTHRES] [-g GENESEQ]\n                     [-p PROTSEQ]`\n\nwhere the arguments are:\n```\n  -h, --help            show this help message and exit\n  -i INPUT, --input INPUT\n                        Input directory that has mpileup files for each\n                        sample. See tests/test1 for example (default: None)\n  -m MAPRATE, --maprate MAPRATE\n                        Minimum read mapping rate required to consider a\n                        sample (default: 20.0)\n  -c COVTHRES, --covthres COVTHRES\n                        Minimum read coverage required at a position to detect\n                        an indel (default: 20)\n  -g GENESEQ, --geneseq GENESEQ\n                        Gene sequences in the reference genome, default\n                        reference: M. tuberculosis (default:\n                        ../reference/H37Rv_genes.txt)\n  -p PROTSEQ, --protseq PROTSEQ\n                        Protein sequences for the reference organism, default:\n                        M. tuberculosis (default:\n                        ../reference/H37Rv_proteins_from_genbank.txt)\n```\n\n\n",
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