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bp_search2alnblocks.1p
Langue: en
Version: 2009-03-10 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
NAME
search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocksSYNOPSIS
search2alnblocks --minid PERCENTID --minlen LEN --minevalue EVALUE file1. blast file2.blast ...> out.fas
DESCRIPTION
This script will parse and filter BLAST (or other formats Bio::SearchIO can parse) output and format the alignment as blocks of alignments based on the HSPs. Note this can only work if the input file parsed contains the necessary.Typically this can be used to turn BLAST output into a FASTA alignment format for input into the QRNA comparative gene finder for RNA genes (E.Rivas).
OPTIONS
--maxevalue Maximum E-value for an HSP --minevalue Minimum E-value for an HSP --minlen Minimum length of an HSP [default 0] --maxid Maximum Percent Id [default 100] (to help remove sequences which are really close) --minid Minimum Percent Identity for an HSP [default 0] -i/--input An optional input filename (expects input on STDIN by default) -o/--output An optional output filename (exports to STDOUT by default) -f/--format Specify a different Search Alignment format- {fasta, axt, waba, blast, blastxml} are all permitted although the format must have actual alignment sequence for this script to work See L<Bio::SearchIO> for more information. -of/--outformat Output format for the alignment blocks, anything L<Bio::AlignIO> supports. -v/--verbose Turn on debugging
AUTHOR - Jason Stajich
Jason Stajich, jason-at-bioperl-dot-org.Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre