Christopher Fields > BioPerl-1.6.923 > Bio::Tools::FootPrinter

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Source   Latest Release: BioPerl-1.6.924

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 $result->seq_id."\t".$feat->start."\t".$feat->end."\t".$feat->seq->seq."\n";
      }
    }

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
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