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Shell Programming and Scripting
Editing headers
Post 302476802 by Lucky Ali on Thursday 2nd of December 2010 03:42:49 PM
12-02-2010
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LEARN ABOUT DEBIAN
bp_search2tribe
BP_SEARCH2TRIBE(1p) User Contributed Perl Documentation BP_SEARCH2TRIBE(1p) 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 v5.14.2 2012-03-02 BP_SEARCH2TRIBE(1p)