GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BP_SEARCH2TRIBE.PL (1)

.ds Aq ’

NAME

bp_search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix

CONTENTS

SYNOPSIS

Usage:
bp_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: bp_search2tribe < file1 file2 file3

AUTHOR

Jason Stajich, jason-at-bioperl-dot-org
Search for    or go to Top of page |  Section 1 |  Main Index


perl v5.20.3 BP_SEARCH2TRIBE (1) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.