bp_search2gff(1p) [debian man page]
BP_SEARCH2GFF(1p) User Contributed Perl Documentation BP_SEARCH2GFF(1p) NAME
search2gff - Turn SearchIO parseable reports(s) into a GFF report SYNOPSIS
Usage: search2gff [-o outputfile] [-f reportformat] [-i inputfilename] OR file1 file2 .. DESCRIPTION
This script will turn a protein Search report (BLASTP, FASTP, SSEARCH, AXT, WABA) into a GFF File. The options are: -i infilename - (optional) inputfilename, will read either ARGV files or from STDIN -o filename - the output filename [default STDOUT] -f format - search result format (blast, fasta,waba,axt) (ssearch is fasta format). default is blast. -t/--type seqtype - if you want to see query or hit information in the GFF report -s/--source - specify the source (will be algorithm name otherwise like BLASTN) --method - the method tag (primary_tag) of the features (default is similarity) --scorefunc - a string or a file that when parsed evaluates to a closure which will be passed a feature object and that returns the score to be printed --locfunc - a string or a file that when parsed evaluates to a closure which will be passed two features, query and hit, and returns the location (Bio::LocationI compliant) for the GFF3 feature created for each HSP; the closure may use the clone_loc() and create_loc() functions for convenience, see their PODs --onehsp - only print the first HSP feature for each hit -p/--parent - the parent to which HSP features should refer if not the name of the hit or query (depending on --type) --target/--notarget - whether to always add the Target tag or not -h - this help menu --version - GFF version to use (put a 3 here to use gff 3) --component - generate GFF component fields (chromosome) -m/--match - generate a 'match' line which is a container of all the similarity HSPs --addid - add ID tag in the absence of --match -c/--cutoff - specify an evalue cutoff 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: search2gff < file1 file2 file3 AUTHOR
Jason Stajich, jason-at-bioperl-dot-org Contributors Hilmar Lapp, hlapp-at-gmx-dot-net clone_loc Title : clone_loc Usage : my $l = clone_loc($feature->location); Function: Helper function to simplify the task of cloning locations for --locfunc closures. Presently simply implemented using Storable::dclone(). Example : Returns : A L<Bio::LocationI> object of the same type and with the same properties as the argument, but physically different. All structured properties will be cloned as well. Args : A L<Bio::LocationI> compliant object create_loc Title : create_loc Usage : my $l = create_loc("10..12"); Function: Helper function to simplify the task of creating locations for --locfunc closures. Creates a location from a feature- table formatted string. Example : Returns : A L<Bio::LocationI> object representing the location given as formatted string. Args : A GenBank feature-table formatted string. perl v5.14.2 2012-03-02 BP_SEARCH2GFF(1p)
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Bio::Search::HSP::BlastPullHSP(3pm) User Contributed Perl Documentation Bio::Search::HSP::BlastPullHSP(3pm) NAME
Bio::Search::HSP::BlastPullHSP - A parser and HSP object for BlastN hsps SYNOPSIS
# generally we use Bio::SearchIO to build these objects use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 'result.blast'); while (my $result = $in->next_result) { while (my $hit = $result->next_hit) { print $hit->name, " "; print $hit->score, " "; print $hit->significance, " "; while (my $hsp = $hit->next_hsp) { # process HSPI objects } } } DESCRIPTION
This object implements a parser for BlastN hsp output. 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 - Sendu Bala Email bix@sendu.me.uk 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::BlastNHSP->new(); Function: Builds a new Bio::Search::HSP::BlastNHSP object. Returns : Bio::Search::HSP::BlastNHSP Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent) -parent => Bio::PullParserI object (required if no -chunk) where the array ref provided to -chunk contains an IO object for a filehandle to something representing the raw data of the hsp, and $start and $end define the tell() position within the filehandle that the hsp data starts and ends (optional; defaults to start and end of the entire thing described by the filehandle) query Title : query Usage : my $query = $hsp->query Function: Returns a SeqFeature representing the query in the HSP Returns : L<Bio::SeqFeature::Similarity> Args : none hit Title : hit Usage : my $hit = $hsp->hit Function: Returns a SeqFeature representing the hit in the HSP Returns : L<Bio::SeqFeature::Similarity> Args : [optional] new value to set gaps Title : gaps Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] ); Function : Get the number of gap characters in the query, hit, or total alignment. Returns : Integer, number of gap characters or 0 if none Args : 'query' = num conserved / length of query seq (without gaps) 'hit' = num conserved / length of hit seq (without gaps) 'total' = num conserved / length of alignment (with gaps) default = 'total' strand Title : strand Usage : $hsp->strand('query') Function: Retrieves the strand for the HSP component requested Returns : +1 or -1 (0 if unknown) Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject 'query' to retrieve the query strand (default) 'list' or 'array' to retreive both query and hit together start Title : start Usage : $hsp->start('query') Function: Retrieves the start for the HSP component requested Returns : integer, or list of two integers (query start and subject start) in list context Args : 'hit' or 'subject' or 'sbjct' to retrieve the start of the subject 'query' to retrieve the query start (default) end Title : end Usage : $hsp->end('query') Function: Retrieves the end for the HSP component requested Returns : integer, or list of two integers (query end and subject end) in list context Args : 'hit' or 'subject' or 'sbjct' to retrieve the end of the subject 'query' to retrieve the query end (default) pvalue Title : pvalue Usage : my $pvalue = $hsp->pvalue(); Function: Returns the P-value for this HSP Returns : undef (Hmmpfam reports do not have p-values) Args : none perl v5.14.2 2012-03-02 Bio::Search::HSP::BlastPullHSP(3pm)