bio::index::embl(3pm) [debian man page]

Bio::Index::EMBL(3pm)					User Contributed Perl Documentation				     Bio::Index::EMBL(3pm)

NAME

       Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).

SYNOPSIS

	   # Complete code for making an index for several
	   # EMBL files
	   use Bio::Index::EMBL;
	   use strict;

	   my $Index_File_Name = shift;
	   my $inx = Bio::Index::EMBL->new(-filename => $Index_File_Name,
					   -write_flag => 'WRITE');
	   $inx->make_index(@ARGV);

	   # Print out several sequences present in the index
	   # in Fasta format
	   use Bio::Index::EMBL;
	   use strict;

	   my $Index_File_Name = shift;
	   my $inx = Bio::Index::EMBL->new(-filename => $Index_File_Name);
	   my $out = Bio::SeqIO->new(-format => 'Fasta',-fh => *STDOUT);

	   foreach my $id (@ARGV) {
	       my $seq = $inx->fetch($id); # Returns Bio::Seq object
	       $out->write_seq($seq);
	   }

	   # alternatively
	   my ($id, $acc);
	   my $seq1 = $inx->get_Seq_by_id($id);
	   my $seq2 = $inx->get_Seq_by_acc($acc);

DESCRIPTION

       Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing EMBL files, and
       retrieving the sequence from them. Heavily snaffled from James Gilbert and his Fasta system. Note: for best results 'use strict'.

       The keys are the identifiers in the ID and AC lines.

FEED_BACK
   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

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

AUTHOR - Ewan Birney
       Email - birney@sanger.ac.uk

APPENDIX

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

   _index_file
	 Title	 : _index_file
	 Usage	 : $index->_index_file( $file_name, $i )
	 Function: Specialist function to index EMBL format files.
		   Is provided with a filename and an integer
		   by make_index in its SUPER class.
	 Example :
	 Returns :
	 Args	 :

   _file_format
	Title	: _file_format
	Usage	: Internal function for indexing system
	Function: Provides file format for this database
	Example :
	Returns :
	Args	:

perl v5.14.2							    2012-03-02						     Bio::Index::EMBL(3pm)

Check Out this Related Man Page

Bio::Index::SwissPfam(3pm)				User Contributed Perl Documentation				Bio::Index::SwissPfam(3pm)

NAME

       Bio::Index::SwissPfam - Interface for indexing swisspfam files

SYNOPSIS

	   use Bio::Index::SwissPfam;
	   use strict;

	   my $Index_File_Name = shift;
	   my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name,
						'-write_flag' => 'WRITE');
	   $inx->make_index(@ARGV);

	   use Bio::Index::SwissPfam;
	   use strict;

	   my $Index_File_Name = shift;
	   my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name);

	   foreach my $id (@ARGV) {
	       my $seq = $inx->fetch($id); # Returns stream
		    while( <$seq> ) {
			if(/^>/) {
			      print;
				 last;
			}
		    }
	   }

DESCRIPTION

       SwissPfam is one of the flat files released with Pfam. This modules provides a way of indexing this module.

       Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing SwissPfam files.
       Only retrieves FileStreams at the moment. Once we have something better (ie, an object!), will use that. Heavily snaffled from Index::Fasta
       system of James Gilbert. Note: for best results 'use strict'.

FEED_BACK
   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

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

AUTHOR - Ewan Birney
APPENDIX

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

   _index_file
	 Title	 : _index_file
	 Usage	 : $index->_index_file( $file_name, $i )
	 Function: Specialist function to index swisspfam format files.
		   Is provided with a filename and an integer
		   by make_index in its SUPER class.
	 Example :
	 Returns :
	 Args	 :

   fetch
	 Title	 : fetch
	 Usage	 : $index->fetch( $id )
	 Function: Returns a Bio::Seq object from the index
	 Example : $seq = $index->fetch( 'dJ67B12' )
	 Returns : Bio::Seq object
	 Args	 : ID

perl v5.14.2							    2012-03-02						Bio::Index::SwissPfam(3pm)

Linux and UNIX Man Pages

bio::index::embl(3pm) [debian man page]

Check Out this Related Man Page