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