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        "description": "# traits_finder\n## Introduction\n* traits_finder searches and summarizes traits in genomes and metagenomes\n* input: reference database and folder of genomes/metagenomes\n* requirement: python >= 3.0, blast or hmm\n* requirement: for hmm, you need to prepare the hmm database\n* optional: diamond, bwa, hs-blastn, usearch, mafft, fasttree\n\n## Install\n`pip install traits_finder`\\\nin preparation: `anaconda download caozhichongchong/traits_finder`\n### latest version (unstable though)\n`git clone https://github.com/caozhichongchong/traits_finder.git `\\\n`cd traits_finder`\\\n`python setup.py build`\\\n`python setup.py install`\n\n## Availability\n\nhttps://pypi.org/project/traits_finder\n\n## What do you need to prepare\n1. your reference database (-db your.db), protein sequences (-dbf 1) or dna sequences (-dbf 2)\n2. a mapping file of functions to each reference sequence (sequence\tfunction)\n3. all genomes/metagenomes in a folder (-i your.input.folder)\n4. suffix or file extension of your genomes/metagenomes, such as .fasta or .fastq (-fa your.input.genome/metagenome.format)\n5. programs to run: blast for similarity search (-s 1 )or hmm for domain search (-s 2)\n6. optional programs to speedup! diamond, hs-blastn (or usearch for 16S extracting), usearch (necessary for HGT and HGT_sum)\n7. optional programs to look at sequence variants! bwa, mafft, fasttree\n\n## How to use it\n### Search traits: boring and slow...\n#### Database installed in traits_finder: antibiotic resistant genes (-db ARG), butyrate producing genes (-db but)\n1. search protein reference sequences in genomes (traits_finder genome) or mobile genetic elements (traits_finder mge) by similarity search\\\n`traits_finder genome -db your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s --u diamond --bp blastp -dbf 1 -s 1`\\\n\n2. search protein reference sequences in metagenomes by similarity search\\\n`traits_finder meta -db your.db -i your.input.folder -fa your.input.metagenomes.format --r your.output.folder --r16 your.output.folder.for.16s --u diamond --bp blastp -dbf 1 -s 1`\\\n\n3. search dna reference sequences in genomes by similarity search\\\n`traits_finder genome -db your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s --u usearch.or.hs-blastn --bp blastn -dbf 2 -s 1`\\\n\n4. search dba reference sequences in metagenomes by similarity search\\\n`traits_finder meta -db your.db -i your.input.folder -fa your.input.metagenomes.format --r your.output.folder --r16 your.output.folder.for.16s --u usearch.or.hs-blastn --bp blastn -dbf 2 -s 1`\\\n\n5. search protein reference sequences in genomes by hmm\\\n`traits_finder genome -db your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s --hmm hmmscan -dbf 1 -s 2`\\\n\n6. search dna reference sequences in genomes by alignment\\\n`traits_finder genome -db your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s --u usearch.or.hs-blastn --bp blastn --bwa bwa -dbf 2 -s 1`\\\n\n7. search dna reference sequences in metagenomes by alignment\\\n`traits_finder meta -db your.db -i your.input.folder -fa your.input.metagenomes.format --r your.output.folder --r16 your.output.folder.for.16s --u usearch.or.hs-blastn --bp blastn --bwa bwa -dbf 2 -s 1`\\\n\n### Summarize results: cool and fast!\n1. summarize traits in genome\\\n`traits_finder sum_genome -db your.db -m function.mapping.your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s`\\\n\n2. summarize traits in metagenomes\\\n`traits_finder sum_meta -db your.db -m function.mapping.your.db -i your.input.folder -fa your.input.metagenomes.format --r your.output.folder --r16 your.output.folder.for.16s --meta metadata.txt`\\\n\n### HGT finder and summarizing: cool and fast! (still-testing)\n\n## Results\n\n## Copyright\nCopyright: An Ni Zhang, Prof. Eric Alm, Alm Lab in MIT\\\nCitation: Not yet, coming soon!\\\nContact: anniz44@mit.edu",
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