Bio::Tools::FootPrinteUser Contributed Perl DocumentBio::Tools::FootPrinter(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::Tools::FootPrinter(3)
