bio::searchio::hmmer(3pm) [debian man page]
Bio::SearchIO::hmmer(3pm) User Contributed Perl Documentation Bio::SearchIO::hmmer(3pm) NAME
Bio::SearchIO::hmmer - A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) SYNOPSIS
# do not use this class directly it is available through Bio::SearchIO use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer', -file => 't/data/L77119.hmmer'); while( my $result = $in->next_result ) { # this is a Bio::Search::Result::HMMERResult object print $result->query_name(), " for HMM ", $result->hmm_name(), " "; while( my $hit = $result->next_hit ) { print $hit->name(), " "; while( my $hsp = $hit->next_hsp ) { print "length is ", $hsp->length(), " "; } } } DESCRIPTION
This object implements a parser for HMMER output. It works with both HMMER2 and HMMER3 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 - Kai Blin Email kai.blin-at-biotech.uni-tuebingen.de APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ perl v5.14.2 2012-03-02 Bio::SearchIO::hmmer(3pm)
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Bio::SearchIO::hmmer2(3pm) User Contributed Perl Documentation Bio::SearchIO::hmmer2(3pm) NAME
Bio::SearchIO::hmmer2 - A parser for HMMER output (hmmpfam, hmmsearch) SYNOPSIS
# do not use this class directly it is available through Bio::SearchIO use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer2', -file => 't/data/L77119.hmmer'); while( my $result = $in->next_result ) { # this is a Bio::Search::Result::HMMERResult object print $result->query_name(), " for HMM ", $result->hmm_name(), " "; while( my $hit = $result->next_hit ) { print $hit->name(), " "; while( my $hsp = $hit->next_hsp ) { print "length is ", $hsp->length(), " "; } } } DESCRIPTION
This object implements a parser for HMMER 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 - 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::SearchIO::hmmer2->new(); Function: Builds a new Bio::SearchIO::hmmer2 object Returns : Bio::SearchIO::hmmer2 Args : -fh/-file => HMMER filename -format => 'hmmer2' next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' end_element Title : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convience method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string within_element Title : within_element Usage : if( $eventgenerator->within_element($element) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block. Returns : boolean Args : string element name in_element Title : in_element Usage : if( $eventgenerator->in_element($element) ) {} Function: Test if we are in a particular element This is different than 'within' because 'in' only tests its immediete parent. Returns : boolean Args : string element name start_document Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none perl v5.14.2 2012-03-02 Bio::SearchIO::hmmer2(3pm)