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geneparse - Module to parse genetics data file\n\n`geneparse` is a module that helps developers to parse multiple genetics file\nformat (*e.g.* Plink binary files, IMPUTE2 files, BGEN and VCF).\n\n\n## Dependencies\n\nThe tool requires a standard [Python](http://python.org/) installation (3.6 or\nhigher are supported) with the following modules:\n\n1. [numpy](http://www.numpy.org/)\n2. [pandas](http://pandas.pydata.org/)\n3. [pyplink](https://github.com/lemieuxl/pyplink)\n4. [pybgen](https://github.com/lemieuxl/pybgen)\n5. [cyvcf2](https://github.com/brentp/cyvcf2)\n6. [biopython](https://github.com/biopython/biopython)\n\nThe tool has been tested on *Linux* only, but should work on *MacOS* operating\nsystems as well.\n\n\n## Installation\n\nYou can install or update `geneparse` using `pip`:\n\n```bash\npip install -U geneparse\n```\n\n\n## Testing\n\nTo test the module, just perform the following command:\n\n```console\n$ python -m geneparse.tests\n..sssss.........s..sssss.........ssssssss...ss.ss...s.................\n.......................................................s....ss.....\n----------------------------------------------------------------------\nRan 137 tests in 1.549s\n\nOK (skipped=27)\n```\n\n\n## Indexing\n\nSome genotype data require indexing for fast access. This can be done using\ngeneparse.\n\n```console\n$ python -m geneparse.index --help\nusage: geneparse-indexer [-h] [--impute2 IMPUTE2 [IMPUTE2 ...]]\n                         [--bgen BGEN [BGEN ...]] [--legacy]\n\nGenotype file indexer.\n\noptional arguments:\n  -h, --help            show this help message and exit\n\nIMPUTE2 index:\n  --impute2 IMPUTE2 [IMPUTE2 ...]\n                        Index an IMPUTE2 genotype file format. The file can be\n                        plain text or bgzipped.\n\nBGEN index:\n  --bgen BGEN [BGEN ...]\n                        Index a BGEN genotype file. This requires 'bgenix' to\n                        be in the PATH.\n  --legacy              Index the file using the '-with-rowid' option. This\n                        flag enables compatibility with SQLITE prior to\n                        version 3.8.2. See\n                        https://bitbucket.org/gavinband/bgen/wiki/bgenix for\n                        more information.\n```\n\n\n## Extraction\n\nWe provide a simple tool to extract genotypes from different format to either\nVCF or Binary plink files.\n\n\n```console\n$ python -m geneparse.extract --help\nusage: geneparse-extractor [-h] -f FORMAT [-e FILE] [-k FILE] [--maf] -o FILE\n                           [--output-format FORMAT]\n                           PARSER_ARGS [PARSER_ARGS ...]\n\nGenotype file extractor. This tool will extract markers according to names or\nto genomic locations.\n\noptional arguments:\n  -h, --help            show this help message and exit\n\nInput Options:\n  -f FORMAT, --format FORMAT\n                        The input file format.\n  PARSER_ARGS           The arguments that will be passed to the genotype\n                        parsers.\n\nExtract Options:\n  -e FILE, --extract FILE\n                        The list of markers to extract (one per line, no\n                        header).\n  -k FILE, --keep FILE  The list of samples to keep (one per line, no header).\n  --maf                 Check MAF and flip the allele coding if the MAF is\n                        higher than 50%.\n\nOutput Options:\n  -o FILE, --output FILE\n                        The output file (can be '-' for STDOUT when using VCF\n                        or CSV as output format).\n  --output-format FORMAT\n                        The output file format. Note that the extension will\n                        be added if absent. Note that CSV is a long format\n                        (hence it might take more disk space).\n\nThe parser arguments (PARSER_ARGS) are the same as the one in the API. For\nexample, the arguments for the Plink parser is 'prefix:PREFIX' (where PREFIX\nis the prefix of the BED/BIM/FAM files).\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpgxcentre%2Fgeneparse","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpgxcentre%2Fgeneparse","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpgxcentre%2Fgeneparse/lists"}