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Bio::Search::HSP::HmmpfamHSP.3pm
Langue: en
Version: 2009-02-27 (fedora - 05/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hspsSYNOPSIS
# generally we use Bio::SearchIO to build these objects use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 'result.hmmer'); while (my $result = $in->next_result) { while (my $hit = $result->next_hit) { print $hit->name, "\n"; print $hit->score, "\n"; print $hit->significance, "\n"; while (my $hsp = $hit->next_hsp) { # process HSPI objects } } }
DESCRIPTION
This object implements a parser for hmmpfam hsp output, a program in the HMMER package.FEEDBACK
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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.
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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:
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AUTHOR - Sendu Bala
Email bix@sendu.me.ukAPPENDIX
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::HmmpfamHSP->new(); Function: Builds a new Bio::Search::HSP::HmmpfamHSP object. Returns : Bio::Search::HSP::HmmpfamHSP Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent) -parent => Bio::PullParserI object (required if no -chunk) -hsp_data => array ref with [rank query_start query_end hit_start hit_end score evalue] 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 gaps in the query, hit, or total alignment. Returns : Integer, number of gaps 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'
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
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