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::Search::Hit::Fasta(3pm) User Contributed Perl Documentation Bio::Search::Hit::Fasta(3pm) NAME
Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits SYNOPSIS
# You wouldn't normally create these manually; # instead they would be produced by Bio::SearchIO::fasta use Bio::Search::Hit::Fasta; my $hit = Bio::Search::Hit::Fasta->new(id=>'LBL_6321', desc=>'lipoprotein', e_val=>0.01); DESCRIPTION
Bio::Search::Hit::HitI objects are data structures that contain information about specific hits obtained during a library search. Some information will be algorithm-specific, but others will be generally defined, such as the ability to obtain alignment objects corresponding to each hit. SEE ALSO
Bio::Search::Hit::HitI, Bio::Search::Hit::GenericHit, Bio::SearchIO::fasta. 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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Aaron Mackey Email amackey-at-virginia.edu APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ _initialize Function: where the heavy stuff will happen when new is called AUTOLOAD Function: Provide getter/setters for ID,DESC,SIZE,INITN,INIT1,OPT,ZSC,E_VAL perl v5.14.2 2012-03-02 Bio::Search::Hit::Fasta(3pm)