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.IX Title "BP_SEARCH2TRIBE 1p"
.TH BP_SEARCH2TRIBE 1p "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
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.SH "NAME"
bp_search2tribe \- Turn SearchIO parseable reports(s) into TRIBE matrix
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Usage:
  bp_search2tribe [\-o outputfile] [\-f reportformat] [\-w/\-\-weight] file1 file2 ..
.SH "DESCRIPTION"
.IX Header "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 \s-1BLAST,\s0 or the blast2table from the \s-1BLAST O\s0'Reilly book to get a
tabular output from these programs and then feed the table into \s-1MCL\s0
with the mcxdeblast script and the \-\-m9 option.
.PP
This script will turn a protein Search report (\s-1BLASTP, FASTP, SSEARCH\s0)
into a Markov Matrix for TribeMCL clustering.
.PP
The options are:
.PP
.Vb 6
\&   \-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
.Ve
.PP
Additionally specify the filenames you want to process on the
command-line.  If no files are specified then \s-1STDIN\s0 input is assumed.
You specify this by doing: bp_search2tribe < file1 file2 file3
.SH "AUTHOR"
.IX Header "AUTHOR"
Jason Stajich, jason-at-bioperl-dot-org