Christopher Fields > BioPerl-1.6.924 > bp_search2tribe


Annotate this POD


New  3
Open  3
View/Report Bugs
Source   Latest Release: BioPerl-1.007001


bp_search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix


Usage: bp_search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1 file2 ..


This script is probably too slow for most people's uses. It is better to use something like scripts/searchio/fastam9_to_table, -m 9 output from BLAST, or the blast2table from the BLAST O'Reilly book to get a tabular output from these programs and then feed the table into MCL with the mcxdeblast script and the --m9 option.

This script will turn a protein Search report (BLASTP, FASTP, SSEARCH) into a Markov Matrix for TribeMCL clustering.

The options are:

   -o filename          - the output filename [default STDOUT]
   -f format            - search result format (blast, fasta)
                          (ssearch is fasta format). default is blast.
   -w or --weight VALUE - Change the default weight for E(0.0) hits
                          to VALUE (default=200 (i.e. 1e-200) )
   -h                   - this help menu

Additionally specify the filenames you want to process on the command-line. If no files are specified then STDIN input is assumed. You specify this by doing: bp_search2tribe < file1 file2 file3


Jason Stajich, jason-at-bioperl-dot-org

syntax highlighting: