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        "author": "Janina Mass",
        "author_email": "janina.mass@hhu.de",
        "bugtrack_url": null,
        "classifiers": [
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "=======\nScythe\n=======\n\n*Scythe*, Selection of Conserved Transcript by Homology Evaluation, tries to find the best matching set of transcripts for each one-to-one orthologous gene from two or more species.\n\n\nUsage (GUI): ::\n\t\n\tscythe-gui.py\n\n\nUsage (command line): ::\n    \n    ######################################\n    # scythe.py v0.1a1                   #\n    ######################################\n  usage:\n     scythe.py -i DIR -g .grpFILE -d DELIMITER --cleanup\n\n  usage with configuration file:\n     scythe.py --config configuration.scy\n\n  general options:\n    -C, --config                     use configuration file instead of\n                                     command line parameters\n    -c, --cleanup                    remove temporary files when done\n    -h, --help                       prints this\n    -i, --in_dir=DIR                 folder w/ subfolders \"fa\" and \"loc\"\n\n    -o, --out_dir=DIR                output directory [default:./]\n    -N, --num_cores=NUM              number of processors to use [default 1]\n\n algorithm options:\n    -R, --sl_ref                     find best matches to reference\n    -G, --sl_glob                    best scoring pair as seed\n    -M, --mx_sum                     optimize sum of pairwise scores\n\n\n  alignment options:\n     -O, --gap_open=FLOAT           needleall gap opening cost [default 10]\n     -E, --gap_extend=FLOAT         needleall gap extension cost\n\n  fasta options:\n    -d, --delim=STRING               split fasta headers at STRING\n    -a, --asID=INT                   use INTth part of fasta header as transcript-ID\n                                     (default:0)\n\n  further help:\n    Please see documentation.\n    \n\nInstallation\n============\nScythe needs Python 3. You might want to set up a virtual environment with Python 3 for easier package management. \nPlease see the documentation for more details.\n(In your virtual environment) install Scythe via ::\n\n    pip install scythe\n\n\nRequirements\n============\n\nPython modules\n~~~~~~~~~~~~~~~\n* configparser\n* mysql-connector-python\n\n ::\n\n    pip install configparser\n    pip install --allow-external mysql-connector-python mysql-connector-python \n\nExternal programs\n------------------\n* needleall (version 6.3.1; EMBOSS package, http://emboss.sourceforge.net/)",
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        "license": "GPLv3",
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        "name": "scythe",
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        "summary": "Find best matching set of transcripts for one-to-one orthologous genes from two or more species",
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