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BP_SEARCH2ALNBLOCKS(1p) 				User Contributed Perl Documentation				   BP_SEARCH2ALNBLOCKS(1p)

NAME
search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks SYNOPSIS
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. perl v5.14.2 2012-03-02 BP_SEARCH2ALNBLOCKS(1p)

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Bio::Search::HSP::FastaHSP(3pm) 			User Contributed Perl Documentation			   Bio::Search::HSP::FastaHSP(3pm)

NAME
Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data SYNOPSIS
# get a FastaHSP from a SearchIO stream my $in = Bio::SearchIO->new(-format => 'fasta', -file => 'filename.fasta'); while( my $r = $in->next_result) { while( my $hit = $r->next_result ) { while( my $hsp = $hit->next_hsp ) { print "smith-waterman score (if available): ", $hsp->sw_score()," "; } } } DESCRIPTION
Describe the object here FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich Email jason-at-bioperl.org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $obj = Bio::Search::HSP::FastaHSP->new(); Function: Builds a new Bio::Search::HSP::FastaHSP object Returns : Bio::Search::HSP::FastaHSP Args : -swscore => smith-waterman score sw_score Title : sw_score Usage : $obj->sw_score($newval) Function: Get/Set Smith-Waterman score Returns : value of sw_score Args : newvalue (optional) evalue2 Title : evalue2 Usage : $obj->evalue2($newval) Function: Get/Set E2() expectation value Returns : value of evalue2 Args : newvalue (optional) perl v5.14.2 2012-03-02 Bio::Search::HSP::FastaHSP(3pm)
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