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bp_search2tribe.pl

Langue: en

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Version: 2009-02-27 (fedora - 04/07/09)

Section: 1 (Commandes utilisateur)

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
Rien n'est sérieux pour l'esprit ; tout peut le devenir pour le coeur.
-+- Jean Rostand (1894-1977) -+-