bio::tools::footprinter(3pm) [debian man page]
Bio::Tools::FootPrinter(3pm) User Contributed Perl Documentation Bio::Tools::FootPrinter(3pm) NAME
Bio::Tools::FootPrinter - write sequence features in FootPrinter format SYNOPSIS
use Bio::Tools::FootPrinter; my $tool = Bio::Tools::FootPrinter->new(-file=>"footprinter.out"); while (my $result = $tool->next_feature){ foreach my $feat($result->sub_SeqFeature){ print $result->seq_id." ".$feat->start." ".$feat->end." ".$feat->seq->seq." "; } } DESCRIPTION
This module writes sequence features in FootPrinter format. See <http://bio.cs.washington.edu/software.html> for more details. 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 - Shawn Hoon Email shawnh@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::FootPrinter->new(); Function: Builds a new Bio::Tools::FootPrinter object Returns : Bio::Tools::FootPrinter Args : -fh/-file => $val, # for initing input, see Bio::Root::IO next_feature Title : next_feature Usage : my $r = $footprint->next_feature Function: Get the next feature from parser data Returns : L<Bio::SeqFeature::Generic> Args : none _add_feature Title : _add_feature Usage : $footprint->_add_feature($feat) Function: Add feature to array Returns : none Args : none _parse_predictions Title : _parse_predictions Usage : my $r = $footprint->_parse_predictions Function: do the parsing Returns : none Args : none _predictions_parsed Title : _predictions_parsed Usage : $footprint->_predictions_parsed(1) Function: Get/Set for whether predictions parsed Returns : 1/0 Args : none _parse Title : _parse Usage : $footprint->_parse($name,$seq,$pattern) Function: do the actual parsing Returns : L<Bio::SeqFeature::Generic> Args : none perl v5.14.2 2012-03-02 Bio::Tools::FootPrinter(3pm)
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Bio::Tools::Pseudowise(3pm) User Contributed Perl Documentation Bio::Tools::Pseudowise(3pm) NAME
Bio::Tools::Pseudowise - Results of one Pseudowise run SYNOPSIS
use Bio::Tools::Pseudowise; my $parser = Bio::Tools::Pseudowise->new(-file=>"pw.out"); while(my $feat = $parser->next_result){ push @feat, $feat; } DESCRIPTION
Pseudowise is a pseudogene prediction program written by Ewan Birney as part of the Wise Package. This module is the parser for the output of the program. http://www.sanger.ac.uk/software/wise2 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 - Jason Stajich Previous committed by the Fugu Team Re-written by Jason Stajich jason-at-bioperl-dot-org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ analysis_method Usage : $pseudowise->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /pseudowise/i. Returns : String Argument : n/a next_feature Title : next_feature Usage : $seqfeature = $obj->next_feature(); Function: Returns the next feature available in the analysis result, or undef if there are no more features. Example : Returns : A Bio::SeqFeatureI implementing object, or undef if there are no more features. Args : none See Also Bio::SeqFeatureI next_prediction Title : next_prediction Usage : while($gene = $pseudowise->next_prediction()) { # do something } Function: Returns the gene of the Pseudowise result file. Call this method repeatedly until FALSE is returned. Example : Returns : a Bio::SeqFeature::Generic Args : none See Also Bio::SeqFeature::Generic _parse_predictions Title : _parse_predictions() Usage : $obj->_parse_predictions() Function: Parses the prediction section. Automatically called by next_prediction() if not yet done. Example : Returns : _prediction Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns : _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($gene) Function: internal Example : Returns : _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE perl v5.14.2 2012-03-02 Bio::Tools::Pseudowise(3pm)