Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::Index::EMBL(3)   User Contributed Perl Documentation  Bio::Index::EMBL(3)

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 funtionality 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://github.com/bioperl/bioperl-live/issues

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 v5.32.0			  2019-12-07		   Bio::Index::EMBL(3)

NAME | SYNOPSIS | DESCRIPTION | FEED_BACK | AUTHOR - Ewan Birney | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Index::EMBL&sektion=3&manpath=FreeBSD+12.2-RELEASE+and+Ports>

home | help