.\" Automatically generated by Pod::Man 4.09 (Pod::Simple 3.35) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. 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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::DB::EMBL \- Database object interface for EMBL entry retrieval .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 1 \& use Bio::DB::EMBL; \& \& $embl = Bio::DB::EMBL\->new(); \& \& # remember that EMBL_ID does not equal GenBank_ID! \& $seq = $embl\->get_Seq_by_id(\*(AqHSFOS\*(Aq); # EMBL ID \& print "cloneid is ", $seq\->id, "\en"; \& \& # or changeing to accession number and Fasta format ... \& $embl\->request_format(\*(Aqfasta\*(Aq); \& $seq = $embl\->get_Seq_by_acc(\*(AqJ02231\*(Aq); # EMBL ACC \& print "cloneid is ", $seq\->id, "\en"; \& \& # especially when using versions, you better be prepared \& # in not getting what what want \& eval { \& $seq = $embl\->get_Seq_by_version(\*(AqJ02231.1\*(Aq); # EMBL VERSION \& }; \& print "cloneid is ", $seq\->id, "\en" unless $@; \& \& # or ... best when downloading very large files, prevents \& # keeping all of the file in memory \& \& # also don\*(Aqt want features, just sequence so let\*(Aqs save bandwidth \& # and request Fasta sequence \& $embl = Bio::DB::EMBL\->new(\-retrievaltype => \*(Aqtempfile\*(Aq , \& \-format => \*(Aqfasta\*(Aq); \& my $seqio = $embl\->get_Stream_by_id([\*(AqAC013798\*(Aq, \*(AqAC021953\*(Aq] ); \& while( my $clone = $seqio\->next_seq ) { \& print "cloneid is ", $clone\->id, "\en"; \& } .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" Allows the dynamic retrieval of sequence objects Bio::Seq from the \&\s-1EMBL\s0 database using the dbfetch script at \s-1EBI:\s0 . .PP 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. .PP The functionality of this module is inherited from Bio::DB::DBFetch which implements Bio::DB::WebDBSeqI. .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "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. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Support" .IX Subsection "Support" Please direct usage questions or support issues to the mailing list: .PP \&\fIbioperl\-l@bioperl.org\fR .PP 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. .SS "Reporting Bugs" .IX Subsection "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: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHOR \- Heikki Lehvaslaiho" .IX Header "AUTHOR - Heikki Lehvaslaiho" Email Heikki Lehvaslaiho .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SS "new" .IX Subsection "new" .Vb 5 \& 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) .Ve .PP \&\s-1NOTE:\s0 There are other options that are used internally. .SS "Bio::DB::WebDBSeqI methods" .IX Subsection "Bio::DB::WebDBSeqI methods" Overriding WebDBSeqI method to help newbies to retrieve sequences. \&\s-1EMBL\s0 database is all too often passed RefSeq accessions. This redirects those calls. See Bio::DB::RefSeq. .SS "get_Stream_by_acc" .IX Subsection "get_Stream_by_acc" .Vb 7 \& 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() .Ve .SS "_check_id" .IX Subsection "_check_id" .Vb 5 \& Title : _check_id \& Usage : \& Function: \& Returns : A Bio::DB::RefSeq reference or throws \& Args : $id(s), $string .Ve