{ "info": { "author": "Kiran Bishwa", "author_email": "everestial007@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Natural Language :: English", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "=========\nvcfparser\n=========\n\n.. image:: https://img.shields.io/pypi/v/vcfparser.svg\n :target: https://pypi.python.org/pypi/vcfparser\n\n.. image:: https://img.shields.io/travis/everestial/vcfparser.svg\n :target: https://travis-ci.org/everestial/vcfparser\n\n.. image:: https://readthedocs.org/projects/vcfparser/badge/?version=latest\n :target: https://vcfparser.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n\n\nPython parser for parsing the genomics and transcriptomics VCF data.\n\n\n* Free software: MIT license\n* Documentation: https://vcfparser.readthedocs.io.\n\n\nFeatures\n--------\n- No external dependency except python\n- Minimalistic in nature\n- With lots of control to api users\n\n\nInstallation\n------------\nTo install vcfparser, run this command in your terminal:\n\n.. code-block:: console\n\n $ pip install vcfparser\n\nIn order to build from source, you can follow :doc:_`installation guide <./docs/installation.rst>`\n\n\nUsage\n-----\n\n>>> from vcfparser import VcfParser\n>>> vcf_obj = VcfParser('input_test.vcf')\n\nGet meta information about the vcf file\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n>>> metainfo = vcf_obj.parse_metadata()\n>>> metainfo.fileformat\n'VCFv4.2'\n>>> metainfo.filters_\n[{'ID': 'LowQual', 'Description': 'Low quality'}, {'ID': 'my_indel_filter', 'Description': 'QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0'}, {'ID': 'my_snp_filter', 'Description': 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0'}]\n\n>>> metainfo.alt_\n[{'ID': 'NON_REF', 'Description': 'Represents any possible alternative allele at this location'}]\n>>> metainfo.sample_names\n['ms01e', 'ms02g', 'ms03g', 'ms04h', 'MA611', 'MA605', 'MA622']\n>>> metainfo.record_keys\n['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT', 'ms01e', 'ms02g', 'ms03g', 'ms04h', 'MA611', 'MA605', 'MA622']\n\n\n\n\nGet Records from vcf file\n^^^^^^^^^^^^^^^^^^^^^^^^^\n>>> records = vcf_obj.parse_records() \nHere records is an generator.\n>>> first_record = next(records)\n>>> first_record.CHROM\n'2'\n>>> first_record.POS\n'15881018'\n>>> first_record.REF\n'G'\n>>> first_record.ALT\n'A,C'\n>>> first_record.QUAL\n'5082.45'\n>>> first_record.FILTER\n['PASS']\n>>> first_record.get_mapped_samples()\n{'ms01e': {'GT': './.', 'PI': '.', 'GQ': '.', 'PG': './.', 'PM': '.', 'PW': './.', 'AD': '0,0', 'PL': '0,0,0,.,.,.', 'DP': '0', 'PB': '.', 'PC': '.'}, 'ms02g': {'GT': './.', 'PI': '.', 'GQ': '.', 'PG': './.', 'PM': '.', 'PW': './.', 'AD': '0,0', 'PL': '0,0,0,.,.,.', 'DP': '0', 'PB': '.', 'PC': '.'}, 'ms03g': {'GT': './.', 'PI': '.', 'GQ': '.', 'PG': './.', 'PM': '.', 'PW': './.', 'AD': '0,0', 'PL': '0,0,0,.,.,.', 'DP': '0', 'PB': '.', 'PC': '.'}, 'ms04h': {'GT': '1/1', 'PI': '.', 'GQ': '6', 'PG': '1/1', 'PM': '.', 'PW': '1/1', 'AD': '0,2', 'PL': '49,6,0,.,.,.', 'DP': '2', 'PB': '.', 'PC': '.'}, 'MA611': {'GT': '0/0', 'PI': '.', 'GQ': '78', 'PG': '0/0', 'PM': '.', 'PW': '0/0', 'AD': '29,0,0', 'PL': '0,78,1170,78,1170,1170', 'DP': '29', 'PB': '.', 'PC': '.'}, 'MA605': {'GT': '0/0', 'PI': '.', 'GQ': '9', 'PG': '0/0', 'PM': '.', 'PW': '0/0', 'AD': '3,0,0', 'PL': '0,9,112,9,112,112', 'DP': '3', 'PB': '.', 'PC': '.'}, 'MA622': {'GT': '0/0', 'PI': '.', 'GQ': '99', 'PG': '0/0', 'PM': '.', 'PW': '0/0', 'AD': '40,0,0', 'PL': '0,105,1575,105,1575,1575', 'DP': '40', 'PB': '.', 'PC': '.\\n'}}\n\n\nSimilarly, we can loop over rest of the records by following for loop:\n\n.. code-block:: bash\n\n for record in records:\n chrom = record.CHROM\n pos = record.POS\n id = record.ID\n ref = record.REF\n alt = record.ALT\n qual = record.QUAL\n filter = record.FILTER\n format_ = record.format_\n infos = record.get_info_dict()\n mapped_sample = record.get_mapped_samples()\n\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/everestial/vcfparser", "keywords": "vcfparser", "license": "MIT license", "maintainer": "", "maintainer_email": "", "name": "vcfparser", "package_url": "https://pypi.org/project/vcfparser/", "platform": "", "project_url": "https://pypi.org/project/vcfparser/", "project_urls": { "Homepage": "https://github.com/everestial/vcfparser" }, "release_url": "https://pypi.org/project/vcfparser/0.1.9/", "requires_dist": null, "requires_python": "", "summary": "Minimaistic VCf parser in python", "version": "0.1.9" }, "last_serial": 5872285, "releases": { "0.1.6": [ { "comment_text": "", "digests": { "md5": "67f6ff979c608d805d9000af3eaaf460", "sha256": "1b46a7d5e4acf3f4d7adf1a404b66ccaa750c76b236c0a28a68097f4b8a22690" }, "downloads": -1, "filename": "vcfparser-0.1.6-py3-none-any.whl", "has_sig": false, "md5_digest": "67f6ff979c608d805d9000af3eaaf460", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 8380, "upload_time": "2019-09-21T15:29:16", "url": "https://files.pythonhosted.org/packages/66/44/ad87cd08c2b286f141201dfe12c8f0177aa507bba8634a64ce79097b4f80/vcfparser-0.1.6-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "594f7dcb00007e55d3f738d5835d86a9", "sha256": "cb92e4892e28eea9b52617f645d77d6b6ab9d85a498478929acf524b90ef8901" }, "downloads": -1, "filename": "vcfparser-0.1.6.tar.gz", "has_sig": false, "md5_digest": "594f7dcb00007e55d3f738d5835d86a9", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 7840, "upload_time": "2019-09-21T15:29:18", "url": "https://files.pythonhosted.org/packages/99/9c/68fda5b0a6c657b2f0a3d9d47efdafc30b5d7a2c3cd9201b934c5f6550a3/vcfparser-0.1.6.tar.gz" } ], "0.1.7": [ { "comment_text": "", "digests": { "md5": "14237682853e71f1dc8f3513df5b3a39", "sha256": "b15ecaa5e77cb8b8fa78ae74f069750f4519cdc5a70df93beab44f68e739be75" }, "downloads": -1, "filename": "vcfparser-0.1.7-py3-none-any.whl", "has_sig": false, "md5_digest": "14237682853e71f1dc8f3513df5b3a39", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 9995, "upload_time": "2019-09-22T13:12:37", "url": "https://files.pythonhosted.org/packages/5a/b1/5e9e35c328cd6d6396d9d06af3188a7679927ac9a33191dc74e4a4a06010/vcfparser-0.1.7-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "d30e8b0e3f1742cd0ee76ea463343449", "sha256": "2d7d1178091addd7b47669e4ba5e81c6120c9b4b2d1e8793287dbd223a4ad5fd" }, "downloads": -1, "filename": "vcfparser-0.1.7.tar.gz", "has_sig": false, "md5_digest": "d30e8b0e3f1742cd0ee76ea463343449", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 9436, "upload_time": "2019-09-22T13:12:39", "url": "https://files.pythonhosted.org/packages/fe/ea/f738ccf7545d2ed4ef9a58512b115d242a44e8ea2be67a43b0f8d091b63f/vcfparser-0.1.7.tar.gz" } ], "0.1.8": [ { "comment_text": "", "digests": { "md5": "e0b4afe2cdc7641650d311c6c3199105", "sha256": "c2634e66e76e6b7e66f964e88fcb4f6ca2ff0d62399213fb21f05bec53c9cca8" }, "downloads": -1, "filename": "vcfparser-0.1.8-py3-none-any.whl", "has_sig": false, "md5_digest": "e0b4afe2cdc7641650d311c6c3199105", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 9995, "upload_time": "2019-09-23T05:51:28", "url": "https://files.pythonhosted.org/packages/d1/ee/f7e7e691c79ee22a4df50fc3cf8d0fe7e1f05c7068151607abad24a09764/vcfparser-0.1.8-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "9404bd817a9ea9d52efc908d6961defb", "sha256": "923b859b93c66503ee2c55294620ecc9c6b5c87e94b2b72c78e9b5f5e743240f" }, "downloads": -1, "filename": "vcfparser-0.1.8.tar.gz", "has_sig": false, "md5_digest": "9404bd817a9ea9d52efc908d6961defb", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 9437, "upload_time": "2019-09-23T05:51:30", "url": "https://files.pythonhosted.org/packages/93/78/651a96e56b093f627eb88f7e78a8f2d3b9a786ec627c343239d16bfb3000/vcfparser-0.1.8.tar.gz" } ], "0.1.9": [ { "comment_text": "", "digests": { "md5": "1af77aaf4d5a2233eff7d85f7bf2eb80", "sha256": "d16cbbe9b0afcbe645b81cebb9a259f6bf759b89785c1e529ebde909602a1554" }, "downloads": -1, "filename": "vcfparser-0.1.9-py3-none-any.whl", "has_sig": false, "md5_digest": "1af77aaf4d5a2233eff7d85f7bf2eb80", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 10018, "upload_time": "2019-09-23T08:53:37", "url": "https://files.pythonhosted.org/packages/ca/b7/1b46ebad8739495f318a08cfbcfa5d54aed3409191686269ab075328cf2b/vcfparser-0.1.9-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "3e93d52b2c6cfdcfab8bcc77eaef486b", "sha256": "12354ed602f7cdacd72e3b972d0338d79b5c1fba926a24ec58ad46658a3135bd" }, "downloads": -1, "filename": "vcfparser-0.1.9.tar.gz", "has_sig": false, "md5_digest": "3e93d52b2c6cfdcfab8bcc77eaef486b", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 9450, "upload_time": "2019-09-23T08:53:39", "url": "https://files.pythonhosted.org/packages/11/b7/5a5ebde681d15436f6d83f99905112ab74564a2ba13b8a9759e57066efb9/vcfparser-0.1.9.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "1af77aaf4d5a2233eff7d85f7bf2eb80", "sha256": "d16cbbe9b0afcbe645b81cebb9a259f6bf759b89785c1e529ebde909602a1554" }, "downloads": -1, "filename": "vcfparser-0.1.9-py3-none-any.whl", "has_sig": false, "md5_digest": "1af77aaf4d5a2233eff7d85f7bf2eb80", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 10018, "upload_time": "2019-09-23T08:53:37", "url": "https://files.pythonhosted.org/packages/ca/b7/1b46ebad8739495f318a08cfbcfa5d54aed3409191686269ab075328cf2b/vcfparser-0.1.9-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "3e93d52b2c6cfdcfab8bcc77eaef486b", "sha256": "12354ed602f7cdacd72e3b972d0338d79b5c1fba926a24ec58ad46658a3135bd" }, "downloads": -1, "filename": "vcfparser-0.1.9.tar.gz", "has_sig": false, "md5_digest": "3e93d52b2c6cfdcfab8bcc77eaef486b", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 9450, "upload_time": "2019-09-23T08:53:39", "url": "https://files.pythonhosted.org/packages/11/b7/5a5ebde681d15436f6d83f99905112ab74564a2ba13b8a9759e57066efb9/vcfparser-0.1.9.tar.gz" } ] }