Metadata-Version: 2.1
Name: traits-finder
Version: 1.3
Summary: search and summarize traits in genomes and metagenomes
Home-page: https://github.com/caozhichongchong/traits_finder
Author: Anni Zhang
Author-email: anniz44@mit.edu
License: MIT
Description: # traits_finder
        ## Introduction
        * traits_finder searches and summarizes traits in genomes and metagenomes
        * input: reference database and folder of genomes/metagenomes
        * requirement: blast or hmm
        * requirement: for hmm, you need to prepare the hmm database
        * optional: diamond, bwa, hs-blastn, usearch
        
        ## Install
        `pip install traits_finder`\
        in preparation: `anaconda download caozhichongchong/traits_finder`
        
        ## Availability
        
        https://pypi.org/project/traits_finder
        
        ## How to use it
        ### Search traits: boring and slow...
        1. search protein reference sequences in genomes by similarity search\
        `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`\
        
        2. search protein reference sequences in metagenomes by similarity search\
        `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`\
        
        3. search dna reference sequences in genomes by similarity search\
        `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`\
        
        4. search dba reference sequences in metagenomes by similarity search\
        `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`\
        
        5. search protein reference sequences in genomes by hmm\
        `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`\
        
        6. search dna reference sequences in genomes by alignment\
        `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`\
        
        7. search dna reference sequences in metagenomes by alignment\
        `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`\
        
        ### Summarize results: cool and fast!
        1. summarize traits in genome\
        `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`\
        
        2. summarize traits in metagenomes\
        `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 -s 1`\
        
        ## Results
        
        ## Copyright
        Copyright: An Ni Zhang, Prof. Eric Alm, Alm Lab in MIT\
        Citation: Not yet, coming soon!\
        Contact: anniz44@mit.edu
        
Keywords: metagenomes,genomes,function,traits
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/markdown
