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bp_search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks


bp_search2alnblocks --minid PERCENTID --minlen LEN --minevalue EVALUE file1.
blast file2.blast ...> out.fas


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).


--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.

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