{ "info": { "author": "Michael Imelfort", "author_email": "mike@mikeimelfort.com", "bugtrack_url": null, "classifiers": [], "description": ". \n. .d8888b. d8b 888 \n. d88P Y88b Y8P 888 \n. Y88b. 888 \n. \"Y888b. 888 88888b.d88b. 88888b. 888 .d88b. \n. \"Y88b. 888 888 \"888 \"88b 888 \"88b 888 d8P Y8b \n. \"888 888 888 888 888 888 888 888 88888888 \n. Y88b d88P 888 888 888 888 888 d88P 888 Y8b. \n. \"Y8888P\" 888 888 888 888 88888P\" 888 \"Y8888 \n. 888 \n. 888 \n. 888 \n. \n. 888 888 888b d888 888b d888 8888888888 8888888b. \n. 888 888 8888b d8888 8888b d8888 888 888 Y88b \n. 888 888 88888b.d88888 88888b.d88888 888 888 888 \n. 8888888888 888Y88888P888 888Y88888P888 8888888 888 d88P \n. 888 888 888 Y888P 888 888 Y888P 888 888 8888888P\" \n. 888 888 888 Y8P 888 888 Y8P 888 888 888 T88b \n. 888 888 888 \" 888 888 \" 888 888 888 T88b \n. 888 888 888 888 888 888 8888888888 888 T88b \n.\n\nOverview\n=========\n\nSimpleHMMER is just that, a super simple way to run HMMER3 and parse the\noutput. No biopython, no frills, just parse\n\nInstallation\n=========\n\nShould be as simple as\n\n pip install SimpleHMMER\n\nUsing MetaChecka2000\n=========\n\nRunning hmmer\n\n from simplehmmer.simplehmmer import HMMERRunner\n HR=HMMERRunner(prefix='frode')\n HR.search('/path/to/some.hmm', '/path/to/some.fasta', '/path/to/save/to/')\n \nParsing results\n\n from simplehmmer.simplehmmer import HMMERParser\n with open('/path/to/save/to/frode_out.txt', 'r') as fh:\n HP = HMMERParser(fh)\n while True:\n result = HP.next()\n if result:\n print result\n else:\n break\n\nSuper simple!\n\nLicence and referencing\n=========\n\nProject home page, info on the source tree, documentation, issues and how to contribute, see http://github.com/minillinim/SimpleHMMER\n\nThis software is currently unpublished. Please contact me at m_dot_imelfort_at_uq_dot_edu_dot_au for more information about referencing this software.\n\nCopyright \u00a9 2012 Michael Imelfort. 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