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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 $result->seq_id."\t".$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:

   http://bugzilla.open-bio.org/
 
 

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