BP_SEARCH2TRIBE(1) User Contributed Perl Documentation BP_SEARCH2TRIBE(1)NAME
search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix
SYNOPSIS
Usage:
search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1
file2 ..
DESCRIPTION
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: search2tribe < file1 file2 file3
AUTHOR
Jason Stajich, jason-at-bioperl-dot-org
perl v5.14.1 2011-07-22 BP_SEARCH2TRIBE(1)