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://github.com/bioperl/bioperl-live/issues

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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq