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bp_search2tribe.pl
Langue: en
Version: 2009-02-27 (fedora - 04/07/09)
Section: 1 (Commandes utilisateur)
Sommaire
NAME
search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrixSYNOPSIS
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-orgContenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre