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        "author": "Anni Zhang",
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        "description": "# buty_full\n## Introduction\n* buty_full infers traits by 16S\n* input: otu table (-t) and otu sequences (-s)\n* requirement: mafft\n* Optional: fasttree\n![alt text](https://raw.githubusercontent.com/caozhichongchong/buty_full/master/Methodology.png)\n\n## Install\n`pip install buty_full`\\\nin preparation: `anaconda download caozhichongchong/buty_full`\n\n## Availability\nin preparation: https://anaconda.org/caozhichongchong/buty_full\n\nhttps://pypi.org/project/buty_full\n\n## How to use it\n1. test the buty_full\\\n`buty_full --test`\n\n2. try your data\\\n`buty_full -t your.otu.table -s your.otu.seqs`\\\n`buty_full -t your.otu.table -s your.otu.seqs -top 2000`\n\n3. try different traits (default is butyrate production)\\\npredicting butyrate production\\\n`buty_full -t your.otu.table -s your.otu.seqs --rs your.own.reference.16s`\\\nor\\\n`buty_full -t your.otu.table -s your.otu.seqs --rs your.own.reference.16s --rt b`\\\npredicting sulfate reduction (in preparation, not yet)\\\n`buty_full -t your.otu.table -s your.otu.seqs --rs your.own.reference.16s --rt s`\\\npredicting nitrate reduction (in preparation, not yet)\\\n`buty_full -t your.otu.table -s your.otu.seqs --rs your.own.reference.16s --rt n`\n\n4. use your own traits\\\n`buty_full -t your.otu.table -s your.otu.seqs --rs your.own.reference.16s --rt your.own.reference.traits`\n\n* your.own.reference.16s is a fasta file containing the 16S sequences of your genomes\\\n\\>Genome_ID1\\\nATGC...\\\n\\>Genome_ID2\\\nATGC...\n\n* your.own.reference.traits is a metadata of whether there's trait in your genomes (0 for no and 1 for yes)\\\nGenome_ID1   0\\\nGenome_ID1   1\n\n## Results\nThe result dir of \"Bayers_model\":\n* `filename.infertraits.txt`: the OTUs inferring as butyrate-producing bacteria (1.0, 0.5) \nand non-butyrate-producing bacteria (0.0).\n* `filename.infertraits.abu`: the total abundance of butyrate-producing bacteria in all samples.\n* `filename.infertraits.otu_table`: the otu_table of butyrate-producing bacteria in all samples.\n\nThe result dir of \"Filtered_OTU\":\n* Some temp files of filtered OTUs, alignment, and tree.\n\n## Copyright\nCopyright: An Ni Zhang, Prof. Eric Alm, Alm Lab in MIT\\\nCitation: Not yet, coming soon!\\\nContact: anniz44@mit.edu\n",
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