{ "info": { "author": "Tariq Daouda", "author_email": "tariq.daouda@umontreal.ca", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Healthcare Industry", "Intended Audience :: Science/Research", "License :: OSI Approved :: Apache Software License", "Programming Language :: Python :: 2.7", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries", "Topic :: Software Development :: Libraries :: Application Frameworks" ], "description": "pyGeno: A python package for Precision Medicine, Personalized Genomics and Proteomics\n=====================================================================================\n\nShort description:\n------------------\n\npyGeno is developed by `Tariq Daouda`_ at the *Institute for Research in Immunology and Cancer* (IRIC_).\n\n.. _Tariq Daouda: http://www.tariqdaouda.com\n.. _IRIC: http://www.iric.ca\n\nWith pyGeno you can do that:\n\n.. code:: python\n\n from pyGeno.Genome import *\n \n #load a genome \n ref = Genome(name = 'GRCh37.75')\n #load a gene\n gene = ref.get(Gene, name = 'TPST2')[0]\n #print the sequences of all the isoforms\n for prot in gene.get(Protein) :\n print prot.sequence\n\nYou can also do it for the **specific genomes** of your subjects:\n\n.. code:: python\n\n pers = Genome(name = 'GRCh37.75', SNPs = [\"RNA_S1\"], SNPFilter = myFilter())\n\nAnd much more: https://github.com/tariqdaouda/pyGeno\n\nVerbose Description\n--------------------\n\npyGeno is a personal bioinformatic database that runs directly into python, on your laptop and does not depend\nupon any REST API. pyGeno is here to make extracting data such as gene sequences a breeze, and is designed to\nbe able cope with huge queries. The most exciting feature of pyGeno, is that it allows to work with seamlessly with both reference and **Presonalized Genomes**.\n\nPersonalized Genomes, are custom genomes that you create by combining a reference genome, sets of polymorphims and an optional filter.\npyGeno will take care of applying the filter and inserting the polymorphisms at their right place, so you get\ndirect access to the DNA and Protein sequences of your patients.\n\nMultiple sets of of polymorphisms can also be combined together to leverage their independent benefits ex: \n\nRNA-seq and DNA-seq for the same individual to improve the coverage\nRNA-seq of an individual + dbSNP for validation\nCombine the results of RNA-seq of several individual to create a genome only containing the common polymorphisms\npyGeno is also a personal database that give you access to all the information provided by Ensembl (for both Reference and Personalized Genomes) without the need of queries to distant HTTP APIs. Allowing for much faster and reliable genome wide study pipelines.\n\nIt also comes with parsers for several file types and various other useful tools.\n\nFull Documentation\n------------------\n\nThe full documentation is available here_\n\n.. _here: http://pygeno.iric.ca/\n\nIf you like pyGeno, please let me know.\nFor the latest news, you can follow me on twitter `@tariqdaouda`_.\n\n.. _@tariqdaouda: https://www.twitter.com/tariqdaouda", "description_content_type": null, "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "http://pyGeno.iric.ca", "keywords": "proteogenomics genomics proteomics annotations medicine research personalized gene sequence protein", "license": "ApacheV2.0", "maintainer": "", "maintainer_email": "", "name": "pyGeno", "package_url": "https://pypi.org/project/pyGeno/", "platform": "", "project_url": "https://pypi.org/project/pyGeno/", "project_urls": { "Homepage": "http://pyGeno.iric.ca" }, "release_url": "https://pypi.org/project/pyGeno/1.3.1/", "requires_dist": null, "requires_python": "", "summary": "Personalized Genomics and Proteomics. 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