bio::featureio::vecscreen_simple(3pm) [debian man page]
Bio::FeatureIO::vecscreen_simple(3pm) User Contributed Perl Documentation Bio::FeatureIO::vecscreen_simple(3pm) NAME
Bio::FeatureIO::vecscreen_simple - read/write features from NCBI vecscreen -f 3 output SYNOPSIS
# read features my $fin = Bio::FeatureIO->new(-file=>'vecscreen.out', -format=>'vecscreen_simple'); my @vec_regions; while (my $f = $fin->next_feature) { push @vec_regions, $f; } # write features NOT IMPLEMENTED DESCRIPTION
vecscreen is a system for quickly identifying segments of a nucleic acid sequence that may be of vector origin. NCBI developed vecscreen to minimize the incidence and impact of vector contamination in public sequence databases. GenBank Annotation Staff use vecscreen to verify that sequences submitted for inclusion in the database are free from contaminating vector sequence. Any sequence can be screened for vector contamination using vecscreen. This module provides parsing for vecscreen '-f 3' output, described in the vecscreen documentation as 'Text list, no alignments' 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 - Robert Buels Email rmb32 AT cornell.edu CONTRIBUTORS
Based on ptt.pm by Torsten Seeman APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ _initialize Title : _initialize Function: Reading? parses the header of the input Writing? next_feature Title : next_feature Usage : $io->next_feature() Function: read the next feature from the vecscreen output file Args : none Returns : Bio::SeqFeatureI object write_feature (NOT IMPLEMENTED) Title : write_feature Usage : $io->write_feature($feature) Function: write a Bio::SeqFeatureI object in vecscreen -f 3 format Example : Args : Bio::SeqFeatureI object Returns : perl v5.14.2 2012-03-02 Bio::FeatureIO::vecscreen_simple(3pm)
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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)