bio::tools::footprinter(3pm) [debian man page]

Bio::Tools::FootPrinter(3pm)				User Contributed Perl Documentation			      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 $result->seq_id."	".$feat->start."	".$feat->end."	".$feat->seq->seq."
";
	     }
	   }

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

perl v5.14.2							    2012-03-02					      Bio::Tools::FootPrinter(3pm)

Check Out this Related Man Page

Bio::Tools::Hmmpfam(3pm)				User Contributed Perl Documentation				  Bio::Tools::Hmmpfam(3pm)

NAME

       Bio::Tools::Hmmpfam - Parser for Hmmpfam program

SYNOPSIS

	 use Bio::Tools::Hmmpfam;
	 my @hmmpfam_feat;
	 my $hmmpfam_parser = Bio::Tools::Hmmpfam->new(-fh =>$filehandle );
	 while( my $hmmpfam_feat = $hmmpfam_parser->next_result ) {
	       push @hmmpfam_feat, $hmmpfam_feat;
	 }

DESCRIPTION

       Parser for Hmmpfam  program.  See also Bio::SearchIO::hmmer.

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 - Balamurugan Kumarasamy
	Email: fugui@worf.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 $obj = Bio::Tools::Hmmpfam->new(-fh=>$filehandle);
	Function: Builds a new Bio::Tools::Hmmpfam object
	Returns : Bio::Tools::Hmmpfam
	Args	: -filename
		  -fh (filehandle)

   next_result
	Title	: next_result
	Usage	: my $feat = $hmmpfam_parser->next_result
	Function: Get the next result set from parser data
	Returns : L<Bio::SeqFeature::Generic>
	Args	: none

   create_feature
	Title	: create_feature
	Usage	: my $feat=$hmmpfam_parser->create_feature($feature,$seqname)
	Function: creates a SeqFeature Generic object
	Returns : L<Bio::SeqFeature::Generic>
	Args	:

   seqname
	Title	:   seqname
	Usage	:   obj->seqname($seqname)
	Function:   Internal(not to be used directly)
	Returns :
	Args	:   seqname

perl v5.14.2							    2012-03-02						  Bio::Tools::Hmmpfam(3pm)

Linux and UNIX Man Pages

bio::tools::footprinter(3pm) [debian man page]

Check Out this Related Man Page