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        "description": "# `pepsyn`\nPeptide library design\n\n\n**Installation**\n\n`pepsyn` is developed for Python 3 and requires `biopython`.  The CLI uses\n`click`.\n\n```bash\npip install pepsyn\n```\n\nor for the latest development version\n\n```bash\ngit clone https://github.com/lasersonlab/pepsyn.git\ncd pepsyn\npython setup.py install\n```\n\nTo run the tests\n\n```bash\npy.test\n```\n\n**Usage**\n\n`pepsyn` can be used as a library, but also comes with a CLI.\n\nThe main CLI command is `pepsyn` and it can read from `stdin` and `stdout` by\nspecifying `-` as the input or output.  Input and output files are FASTA\nformatted.\n\n```bash\n$ pepsyn -h\nUsage: pepsyn [OPTIONS] COMMAND [ARGS]...\n\n  pepsyn -- peptide synthesis design\n\nOptions:\n  -h, --help  Show this message and exit.\n\nCommands:\n  prefix      add a prefix to each sequence\n  recodesite  remove site from each sequence's CDS by...\n  revtrans    reverse translate amino acid sequences into...\n  stats       compute some sequence statistics\n  suffix      add a suffix to each sequence\n  tile        tile a set of sequences\n\n```\n\nFor example, to tile a set of sequences, use the `pepsyn tile` command.  Each\nsubcommand has its own help message with relevant options.\n\n```bash\n$ pepsyn tile -h\nUsage: pepsyn tile [OPTIONS] INPUT OUTPUT\n\n  tile a set of sequences\n\nOptions:\n  -l, --length INTEGER   Length of output oligos\n  -p, --overlap INTEGER  Overlap of oligos\n  -h, --help             Show this message and exit.\n```\n\nCommands can be piped into each other.  (Note: `stdin` and `stdout` are\nsignified with `-`.)\n\n```bash\ncat pepsyn/tests/proteins.fasta \\\n    | pepsyn tile -l 10 -p 3 - - \\\n    | pepsyn revtrans - - \\\n    | pepsyn prefix -p ACGGG - - \\\n    | pepsyn suffix -s TGCTG - - \\\n    | pepsyn recodesite --site EcoRI --clip-left 5 --clip-right 5 - -\n```\n\n\n",
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        "license": "Apache License, Version 2.0",
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