{ "info": { "author": "Ram Krishna Shrestha", "author_email": "ram_krishna.shrestha@tsl.ac.uk", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: OSI Approved :: Python Software Foundation License", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.0", "Programming Language :: Python :: 3.1", "Programming Language :: Python :: 3.2", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "[![Build Status](https://travis-ci.com/TeamMacLean/snpFC.svg?branch=master)](https://travis-ci.com/TeamMacLean/snpFC)\n\n![GitHub All Releases](https://img.shields.io/github/downloads/tsl-ramkrishna/https://github.com/TeamMacLean/snpFC/total.svg)\n\n![PyPI - Python Version](https://img.shields.io/pypi/pyversions/3.svg)\n\n## Introduction\n\nsnpFC - a python tool for filtering and comparing SNPs from multiple VCF files\n\n## Requirement\n\n1) python v3.0+\n2) pyvcf\n\nCommand line Usage\n\n1) snpfc.py --help\n\n```\n\tusage: snpfc.py [-h] [--vcf VCF [VCF ...]] [--filter] [--compare]\n\t [--frequency FREQUENCY] [--pvalue PVALUE]\n\t [--genotype GENOTYPE] [--quality GENOTYPE_QUALITY]\n\t [--rawreaddepth RAW_READ_DEPTH]\n\t [--qualityreaddepth QUALITY_READ_DEPTH]\n\t [--depthreference DEPTH_IN_REFERENCE]\n\t [--depthvariant DEPTH_IN_VARIANT] [--show] [--outdir OUTDIR]\n\n\tScript to filter the SNPs using user threshold values and compare the SNPs\n\tfrom multiple VCF files\n\n\toptional arguments:\n\t -h, --help show this help message and exit\n\t --vcf VCF [VCF ...] Space separated vcf input files\n\t --filter Filter the SNPs\n\t --compare Compare the SNPs\n\t --frequency FREQUENCY\n\t Frequency of SNP call. Default: 70 [int]\n\t --pvalue PVALUE Pvalue of the SNP call. Default: 0.05 [float]\n\t --genotype GENOTYPE Genotype of the SNP call -\n\t heterozygous/homozygous/both. Default: heterozygous\n\t --quality GENOTYPE_QUALITY\n\t Genotype quality of the SNP call. Default: 10\n\t --rawreaddepth RAW_READ_DEPTH\n\t Raw read depth of the SNP call. Default: 5\n\t --qualityreaddepth QUALITY_READ_DEPTH\n\t Quality read depth of the SNP call. Default: 5\n\t --depthreference DEPTH_IN_REFERENCE\n\t Depth in reference of the SNP call. Default: 5\n\t --depthvariant DEPTH_IN_VARIANT\n\t Depth in variant of the SNP call. Default: 5\n\t --show Display the results on the screen\n\t --outdir OUTDIR Path to the output folder. Default: Current working\n directory\n```\n2) python3 scripts/snpfc.py --vcf testfiles/test1.vcf testfiles/test2.vcf testfiles/test3.vcf --filter --outdir ./\n3) python3 scripts/snpfc.py --vcf testfiles/test1.vcf testfiles/test2.vcf testfiles/test3.vcf --filter --compare --outdir ./\n4) python3 scripts/snpfc.py --vcf testfiles/test1.vcf testfiles/test2.vcf testfiles/test3.vcf --filter --outdir ./ --genotype homozygous --frequency 80\n5) python3 scripts/snpfc.py --vcf testfiles/test1.vcf testfiles/test2.vcf testfiles/test3.vcf --filter --outdir ./ --genotype_quality 20\n\n## Usage as python module\n### usage of filter module\n```\nimport snpfc\nfrom snpfc.snpFilter import snpfilter\ndofilter = snpfilter(input.vcf, output.vcf, frequency=70, pvalue=0.05, genotype='any', genotype_quality=20, raw_read_depth=5, quality_read_depth=5, depth_in_reference=5, depth_in_variant=5)\ndofilter.filter()\n```\nThis will filter the SNPs and save in output.vcf file.\n\n### usage of compare module\n\n```\nfrom snpCompare import snpcompare\ndocompare = snpcompare([input1.vcf, input2.vcf, input3.vcf])\t# takes array of input files\ndocompare.compare()\n\n```\n\nThis will compare the SNPs in the input files and save the output in the files - input1_snpcompare.txt, input2_snpcompare.txt and input3_snpcompare.txt in the current working directory.\n\n```\ndocompare.compare(output_directory)\n```\n\nThis will save the output files in the output directory specified.\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/TeamMacLean/snpFC", "keywords": "snp,filter,compare,vcf", "license": "Open Software License", "maintainer": "", "maintainer_email": "", "name": "snpfc", "package_url": "https://pypi.org/project/snpfc/", "platform": "", "project_url": "https://pypi.org/project/snpfc/", "project_urls": { "Homepage": "https://github.com/TeamMacLean/snpFC" }, "release_url": "https://pypi.org/project/snpfc/1.0.0/", "requires_dist": [ "pyvcf" ], "requires_python": ">=3", "summary": "", "version": "1.0.0" }, "last_serial": 5018908, "releases": { "1.0.0": [ { "comment_text": "", "digests": { "md5": "282428f065b985a1adc9873e55fa9428", "sha256": "7beb606f0ab970191da0b08ae9109b7d4598f7adf12d613166c1fc14b4b82ea2" }, "downloads": -1, "filename": "snpfc-1.0.0-py3-none-any.whl", "has_sig": false, "md5_digest": "282428f065b985a1adc9873e55fa9428", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3", "size": 8163, "upload_time": "2019-04-01T13:42:40", "url": "https://files.pythonhosted.org/packages/d1/7d/87de44c39781f11b003f9a18f394dbe56dc08fb38507a1e8c2b5e1edb39f/snpfc-1.0.0-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "2349a1596f48c700857019641a637147", "sha256": "dc8e7c9243e91a1f1d6aeb8949e62a9365a0752e60bdb1b683663e15911246aa" }, "downloads": -1, "filename": "snpfc-1.0.0.tar.gz", "has_sig": false, "md5_digest": "2349a1596f48c700857019641a637147", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3", "size": 8053, "upload_time": "2019-04-01T13:42:42", "url": "https://files.pythonhosted.org/packages/5d/a7/64f8075aa5d7abea19f27502ab1e3a777ebf107ce7a2ffc003b2d63eb695/snpfc-1.0.0.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "282428f065b985a1adc9873e55fa9428", "sha256": "7beb606f0ab970191da0b08ae9109b7d4598f7adf12d613166c1fc14b4b82ea2" }, "downloads": -1, "filename": "snpfc-1.0.0-py3-none-any.whl", "has_sig": false, "md5_digest": "282428f065b985a1adc9873e55fa9428", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": ">=3", "size": 8163, "upload_time": "2019-04-01T13:42:40", "url": "https://files.pythonhosted.org/packages/d1/7d/87de44c39781f11b003f9a18f394dbe56dc08fb38507a1e8c2b5e1edb39f/snpfc-1.0.0-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "2349a1596f48c700857019641a637147", "sha256": "dc8e7c9243e91a1f1d6aeb8949e62a9365a0752e60bdb1b683663e15911246aa" }, "downloads": -1, "filename": "snpfc-1.0.0.tar.gz", "has_sig": false, "md5_digest": "2349a1596f48c700857019641a637147", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3", "size": 8053, "upload_time": "2019-04-01T13:42:42", "url": "https://files.pythonhosted.org/packages/5d/a7/64f8075aa5d7abea19f27502ab1e3a777ebf107ce7a2ffc003b2d63eb695/snpfc-1.0.0.tar.gz" } ] }