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

NAME
       Bio::DB::RefSeq - Database object interface for RefSeq retrieval

SYNOPSIS
	 use Bio::DB::RefSeq;

	 $db = Bio::DB::RefSeq->new();

	 # most of the time RefSeq_ID eq RefSeq acc
	 $seq = $db->get_Seq_by_id('NM_006732'); # RefSeq ID
	 print "accession is ", $seq->accession_number, "\n";

	 # or changeing to accession number and Fasta format ...
	 $db->request_format('fasta');
	 $seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq ACC
	 print "seq is ", $seq->seq, "\n";

	 # especially when using versions, you better be prepared
	 # in not getting what what want
	 eval {
	     $seq = $db->get_Seq_by_version('NM_006732.1'); # RefSeq VERSION
	 };
	 print "accesion is ", $seq->accession_number, "\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
	 $db = Bio::DB::RefSeq->new(-retrievaltype => 'tempfile' ,
				      -format => 'fasta');
	 my $seqio = $db->get_Stream_by_id(['NM_006732', 'NM_005252'] );
	 while( my $seq	 =  $seqio->next_seq ) {
	       print "seqid is ", $seq->id, "\n";
	 }

DESCRIPTION
       Allows the dynamic retrieval of sequence objects Bio::Seq from the
       RefSeq database using the dbfetch script at EBI:

       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.

       This module retrieves entries from EBI although it retrives database
       entries produced at NCBI. When read into bioperl objects, the parser
       for GenBank format it used. RefSeq is a NONSTANDARD GenBank file so be
       ready for surprises.

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 _

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