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

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

NAME

       Bio::Tools::Blat - parser for Blat program

SYNOPSIS

	 use Bio::Tools::Blat;
	 my $blat_parser = Bio::Tools::Blat->new(-fh =>$filehandle );
	 while( my $blat_feat = $blat_parser->next_result ) {
	       push @blat_feat, $blat_feat;
	 }

DESCRIPTION

	Parser for Blat program

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 the
	web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Balamurugan Kumarasamy
	Email: bala@tll.org.sg

APPENDIX

	The rest of the documentation details each of the object methods.
	Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::Tools::Blat->new(-fh=>$filehandle);
	Function: Builds a new Bio::Tools::Blat object
	Returns : Bio::Tools::Blat
	Args	: -filename
		  -fh (filehandle)

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

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

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

NAME

       Bio::Tools::Match - Parses output from Transfac's match(TM)

SYNOPSIS

	 use strict;

	 use Bio::Tools::Match;

	 my $parser = Bio::Tools::Match->new(-file => "match.out");

	 while (my $feat = $parser->next_result) {
	   my $start = $feat->start;
	   my $end = $feat->end;
	   my $core_score = $feat->score;
	   my $matrix_score = ($feat->annotation->get_Annotations('matrix_score'))[0]->value;
	   my $matrix_id = ($feat->annotation->get_Annotations('matrix_id'))[0]->value;
	 }

DESCRIPTION

       This module is used to parse the output from Transfac's match(TM) program. It doesn't support the histogram output of match.

       Each result is a Bio::SeqFeature::Annotated representing a single matrix match.

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 - Sendu Bala
       Email bix@sendu.me.uk

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::Match->new();
	Function: Builds a new Bio::Tools::Match object
	Returns : Bio::Tools::Match
	Args	: -file (or -fh) should contain the contents of a standard match output

   next_result
	Title	: next_result
	Usage	: $result = $obj->next_result();
	Function: Returns the next result available from the input, or undef if there
		  are no more results.
	Returns : Bio::SeqFeature::Annotated object. Features are annotated with tags
		  for 'matrix_score', 'matrix_id' and a 'predicted' tag.
	Args	: none

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