Metadata-Version: 1.1
Name: blastbesties
Version: 1.1.1
Summary: Rapid discovery of reciprocal best blast pairs from BLAST output files.
Home-page: https://github.com/Adamtaranto/blast-besties
Author: Adam Taranto
Author-email: adam.taranto@anu.edu.au
License: MIT
Description: # Blast-Besties
        
        Rapid discovery of reciprocal best blast pairs from BLAST output files.  
        
        
        # Table of contents
        
        * [Example usage](#example-usage)
          * [Input requirements](#input-requirements)
        * [Standard options](#standard-options)
        * [License](#license) 
        
        # Example usage
        
        Run BLASTp for each protein set AvsB and BvsA.
        Require vaild alignments to cover 95% of the query sequence and with an e-value of < 0.001.
        
        ```bash
        blastp -qcov_hsp_perc 95 -query A_prot.fa -subject B_prot.fa -out AvB.tab -evalue 0.001 -outfmt 6 -use_sw_tback
        blastp -qcov_hsp_perc 95 -query B_prot.fa -subject A_prot.fa -out BVA.tab -evalue 0.001 -outfmt 6 -use_sw_tback
        ```
        
        Report reciprocal best match pairs where each hit meets criteria e-value 
        <= 0.001, hit-length >= 100, bitscore >= 100.  
        
        ```bash
        ./blastBesties.py -e 0.001 -l 100 -s 100 -a *blastAvB.tab* -b *blastBvA.tab
        ```
        
        ## Input requirements
        
          - Takes two BLAST output files as input. SetA vs SetB, and SetB vs SetA.
          - BLAST output format 6 (tabular)
          - Hits must be sorted by query name then descending match quality - this is default BLAST behaviour.
        
        # Standard options
        
        ```
        Usage: BLAST-Besties [-h] [-v] -a BLASTAVB -b BLASTBVA [-l MINLEN] [-e EVAL]
                             [-s BITSCORE] [-o OUTFILE] [-d OUTDIR]
        
        Options:
        
          # Info
          -h, --help        Show this help message and exit.
          -v, --version     Show program's version number and exit.
          
          # Input 
          -a, --blastAvB    Blast tab result file for fastaA query against fastaB
                            subject.
          -b, --blastBvA    Blast tab result file for fastaB query against fastaA
                            subject.
          
          # Settings
          -l, --minLen      Minimum length of hit to consider valid.
          -e, --eVal        Maximum e-value to consider valid pair.
          -s, --bitScore    Minimum bitscore to consider valid pair.
        
          # Output
          -o, --outFile     Write reciprocal blast pairs to this file.
          -d, --outDir      Directory for new sequence files to be written to.
        ```
        
        # License
        
        Software provided under MIT license.
        
        
Keywords: Orthologues,Reciprocal best BLAST
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: License :: OSI Approved :: MIT License
