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

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

NAME

       Bio::Tools::Prints - Parser for FingerPRINTScanII program

SYNOPSIS

	 use Bio::Tools::Prints;
	 my $prints_parser = Bio::Tools::Prints->new(-fh =>$filehandle );
	 while( my $prints_feat = $prints_parser->next_result ) {
	       push @prints_feat, $prints_feat;
	 }

DESCRIPTION

	PRINTScan II is a PRINTS fingerprint identification algorithm.
	Copyright (C) 1998,1999  Phil Scordis

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
	bala@tll.org.sg
	juguang@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 $obj = Bio::Tools::Prints->new(-fh=>$filehandle);
	Function: Builds a new Bio::Tools::Prints object
	Returns : Bio::Tools::Prints
	Args	: -filename
		  -fh (filehandle)

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

   print_sac
	Title	: print_sac
	Usage	: $prints_parser->print_sac($print_sac)
	Function: get/set for print_sac
	Returns :
	Args	:

   seqname
	Title	: seqname
	Usage	: $prints_parser->seqname($seqname)
	Function: get/set for seqname
	Returns :
	Args	:

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

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

NAME

       Bio::Tools::Coil - parser for Coil output

SYNOPSIS

	use Bio::Tools::Coil
	my $parser = Bio::Tools::Coil->new();
	while( my $sp_feat = $parser->next_result($file) ) {
	      #do something
	      #eg
	      push @sp_feat, $sp_feat;
	}

DESCRIPTION

	Parser for Coil output

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

	Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
	originally written by Marc Sohrmann (ms2@sanger.ac.uk)
	Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>
       # Please direct questions and support issues to <bioperl-l@bioperl.org>
       #
	Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)

APPENDIX

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

   parse_results
	Title	: parse_results
	Usage	: obj->parse_results
	Function: Parses the coil output. Automatically called by
		  next_result() if not yet done.
	Example :
	Returns :

   next_result
	Title	: next_result
	Usage	: while($feat = $coil->next_result($file)) {
			 # do something
		  }
	Function: Returns the next protein feature of the coil output file
	Returns :
	Args	:

   _result
	Title	: _result
	Usage	: $feat = $obj->_result()
	Function: internal
	Example :
	Returns :

   _add_prediction
	Title	: _add_prediction()
	Usage	: $obj->_add_prediction($feat)
	Function: internal
	Example :
	Returns :

   _predictions_parsed
	Title	: _predictions_parsed
	Usage	: $obj->_predictions_parsed
	Function: internal
	Example :
	Returns : TRUE or FALSE

   create_feature
	Title	: create_feature
	Usage	: obj->create_feature(\%feature)
	Function: Internal(not to be used directly)
	Returns :
	Args	:

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

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