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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::Seg(3pm)					User Contributed Perl Documentation				      Bio::Tools::Seg(3pm)

NAME
Bio::Tools::Seg - parse "seg" output SYNOPSIS
use Bio::Tools::Seg; my $parser = Bio::Tools::Seg->(-file => 'seg.fasta'); while ( my $f = $parser->next_result ) { if ($f->score < 1.5) { print $f->location->to_FTstring, " is low complexity "; } } DESCRIPTION
"seg" identifies low-complexity regions on a protein sequence. It is usually part of the "WU-BLAST" and "InterProScan" packages. The Bio::Tools::Seg module will only parse the "fasta" output modes of "seg", i.e. "seg -l" (low complexity regions only), "seg -h" (high complexity regions only), or "seg -a" (both low and high). It creates a Bio::SeqFeature::Generic for each FASTA-like entry found in the input file. It is up to the user to appropriately filter these using the feature's score. 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::Seg->new(); Function: Builds a new Bio::Tools::Seg object Returns : Bio::Tools::Seg Args : -fh/-file => $val, # for initing input, see Bio::Root::IO next_result Title : next_result Usage : my $feat = $seg->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::Seg(3pm)
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