bio::tools::hmmpfam(3pm) [debian man page]
Bio::Tools::Hmmpfam(3pm) User Contributed Perl Documentation Bio::Tools::Hmmpfam(3pm) NAME
Bio::Tools::Hmmpfam - Parser for Hmmpfam program SYNOPSIS
use Bio::Tools::Hmmpfam; my @hmmpfam_feat; my $hmmpfam_parser = Bio::Tools::Hmmpfam->new(-fh =>$filehandle ); while( my $hmmpfam_feat = $hmmpfam_parser->next_result ) { push @hmmpfam_feat, $hmmpfam_feat; } DESCRIPTION
Parser for Hmmpfam program. See also Bio::SearchIO::hmmer. 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 - Balamurugan Kumarasamy Email: fugui@worf.fugu-sg.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 $obj = Bio::Tools::Hmmpfam->new(-fh=>$filehandle); Function: Builds a new Bio::Tools::Hmmpfam object Returns : Bio::Tools::Hmmpfam Args : -filename -fh (filehandle) next_result Title : next_result Usage : my $feat = $hmmpfam_parser->next_result Function: Get the next result set from parser data Returns : L<Bio::SeqFeature::Generic> Args : none create_feature Title : create_feature Usage : my $feat=$hmmpfam_parser->create_feature($feature,$seqname) Function: creates a SeqFeature Generic object Returns : L<Bio::SeqFeature::Generic> Args : seqname Title : seqname Usage : obj->seqname($seqname) Function: Internal(not to be used directly) Returns : Args : seqname perl v5.14.2 2012-03-02 Bio::Tools::Hmmpfam(3pm)
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Bio::Tools::Tmhmm(3pm) User Contributed Perl Documentation Bio::Tools::Tmhmm(3pm) NAME
Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM) SYNOPSIS
use Bio::Tools::Tmhmm; my $parser = Bio::Tools::Tmhmm->new(-fh => $filehandle ); while ( my $tmhmm_feat = $parser->next_result ) { # do something, e.g. push @tmhmm_feat, $tmhmm_feat; } DESCRIPTION
TMHMM is software for the prediction of transmembrane helices in proteins. See <http://www.cbs.dtu.dk/services/TMHMM/> for more details. This module parses the "long output" format of TMHMM 2.0 and creates a Bio:SeqFeature::Generic object for each "TMHelix" feature found from lines like this: my_sequence_id TMHMM2.0 TMhelix 54 76 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 - Torsten Seemann Email torsten.seemann AT infotech.monash.edu.au CONTRIBUTOR - Bala Email savikalpa@fugu-sg.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::Tools::Tmhmm->new(); Function: Builds a new Bio::Tools::Tmhmm object Returns : Bio::Tools::Tmhmm Args : Either of the following as per L<Bio::Root::IO> interface -fh => $filehandle -file => $filename next_result Title : next_result Usage : my $feat = $Tmhmm->next_result Function: Get the next result set from parser data Returns : Bio::SeqFeature::Generic Args : none perl v5.14.2 2012-03-02 Bio::Tools::Tmhmm(3pm)