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Bio::DB::EMBL(3)      User Contributed Perl Documentation     Bio::DB::EMBL(3)

NAME
       Bio::DB::EMBL - Database object interface for EMBL entry retrieval

SYNOPSIS
	 use Bio::DB::EMBL;

	 $embl = Bio::DB::EMBL->new();

	 # remember that EMBL_ID does not equal GenBank_ID!
	 $seq = $embl->get_Seq_by_id('BUM'); # EMBL ID
	 print "cloneid is ", $seq->id, "\n";

	 # or changeing to accession number and Fasta format ...
	 $embl->request_format('fasta');
	 $seq = $embl->get_Seq_by_acc('J02231'); # EMBL ACC
	 print "cloneid is ", $seq->id, "\n";

	 # especially when using versions, you better be prepared
	 # in not getting what what want
	 eval {
	     $seq = $embl->get_Seq_by_version('J02231.1'); # EMBL VERSION
	 };
	 print "cloneid is ", $seq->id, "\n" unless $@;

	 # or ... best when downloading very large files, prevents
	 # keeping all of the file in memory

	 # also don't want features, just sequence so let's save bandwith
	 # and request Fasta sequence
	 $embl = Bio::DB::EMBL->new(-retrievaltype => 'tempfile' ,
				   -format => 'fasta');
	 my $seqio = $embl->get_Stream_by_id(['AC013798', 'AC021953'] );
	 while( my $clone =  $seqio->next_seq ) {
	       print "cloneid is ", $clone->id, "\n";
	 }

DESCRIPTION
       Allows the dynamic retrieval of sequence objects Bio::Seq from the EMBL
       database using the dbfetch script at EBI:
       http://www.ebi.ac.uk/cgi-bin/dbfetch <http://www.ebi.ac.uk/cgi-
       bin/dbfetch>.

       In order to make changes transparent we have host type (currently only
       ebi) and location (defaults to ebi) separated out.  This allows later
       additions of more servers in different geographical locations.

       The functionality of this module is inherited from Bio::DB::DBFetch
       which implements Bio::DB::WebDBSeqI.

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 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:

	 http://bugzilla.open-bio.org/

AUTHOR - Heikki Lehvaslaiho
       Email Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>

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

   new
	Title	: new
	Usage	: $gb = Bio::DB::GenBank->new(@options)
	Function: Creates a new genbank handle
	Returns : New genbank handle
	Args	: -delay   number of seconds to delay between fetches (3s)

       NOTE:  There are other options that are used internally.

   Bio::DB::WebDBSeqI methods
       Overriding WebDBSeqI method to help newbies to retrieve sequences.
       EMBL database is all too often passed RefSeq accessions. This redirects
       those calls. See Bio::DB::RefSeq.

   get_Stream_by_acc
	 Title	 : get_Stream_by_acc
	 Usage	 : $seq = $db->get_Seq_by_acc([$acc1, $acc2]);
	 Function: Gets a series of Seq objects by accession numbers
	 Returns : a Bio::SeqIO stream object
	 Args	 : $ref : a reference to an array of accession numbers for
			  the desired sequence entries
	 Note	 : For GenBank, this just calls the same code for get_Stream_by_id()

   _check_id
	 Title	 : _check_id
	 Usage	 :
	 Function:
	 Returns : A Bio::DB::RefSeq reference or throws
	 Args	 : $id(s), $string

perl v5.14.1			  2011-07-22		      Bio::DB::EMBL(3)
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