SYNOPSIS
use Bio::DB::SeqHound;
$sh = Bio::DB::SeqHound->new();
$seq = $sh->get_Seq_by_acc("CAA28783"); # Accession Number
# or ...
$seq = $sh->get_Seq_by_gi(4557225); # GI Number
VERSION
1.1DESCRIPTION
SeqHound is a database of biological sequences and structures. This script allows the retrieval of sequence objects (Bio::Seq) from the SeqHound database at the Blueprint Initiative.Bioperl extension permitting use of the SeqHound Database System developed by researchers at
The Blueprint Initiative Samuel Lunenfeld Research Institute Mount Sinai Hospital Toronto, Canada
FEEDBACK/BUGS
known bugs: fail to get sequences for some RefSeq record with CONTIG, example GI = 34871762MAILING LISTS
User feedback is an integral part of the evolution of this Bioperl module. Send your comments and suggestions preferably to seqhound.usergroup mailing lists. Your participation is much appreciated.WEBSITE
For more information on SeqHound http://dogboxonline.unleashedinformatics.com/DISCLAIMER
This software is provided 'as is' without warranty of any kind.AUTHOR
Rong Yao, Hao Lieu, Ian DonaldsonAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new Usage : $sh = Bio::DB::SeqHound->new(@options); Function: Creates a new seqhound handle Returns : New seqhound handle Args :
Routines Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI
get_Seq_by_id
Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN'); Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception Example : Each of these calls retrieves the same sequence record $seq = $db->get_Seq_by_id(56); #retrieval by GI $seq = $db->get_Seq_by_id("X02597"); #retrieval by NCBI accession $seq = $db->get_Seq_by_id("BTACHRE"); #retrieval by sequence "name" a sequence "name" is a secondary identifier (usually assigned by the submitting database external to the NCBI) that may not be visible in the GenBank flat file version of the record but is always present in the ASN.1 format. Note : Since in GenBank.pm, this function accepts a gi, an accession number or a sequence name, SeqHound also satisfies these inputs. If the input uid is a number, it is treated as a gi, if the uid is a string, it is treated as an accession number first. If the search still fails, it is treated as a sequence name. Since SeqHound stores biological data from different source sequence databases like: GenBank, GenPept, SwissProt, EMBL, RefSeq, you can pass ids from the above databases to this function. The Bio::Seq object returned by this function is identical to the Bio::Seq generated by the GenBank.pm and GenPept.pm. The Bio::Seq object returned by this function sometimes has minor difference in the SeqFeature from the Bio::Seq object generated in RefSeq.pm. The Bio::Seq objects created from this function will have the NCBI versions of the SwissProt and EMBL sequence data information.
get_Seq_by_acc
Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('M34830'); Function: Gets a Seq object by accession numbers Returns : a Bio::Seq object Args : the accession number as a string Throws : "id does not exist" exception Note : Since in GenBank.pm, this function accepts an accession number or a sequence name, SeqHound also satisfies these inputs. If the input uid is a string, it is treated as an accession number first. If the search fails, it is treated as a sequence name. Since SeqHound stores biological data from different source sequence databases like: GenBank, GenPept, SwissProt, EMBL, RefSeq, you can pass ids from the above databases to this function. The Bio::Seq object returned by this function is identical to the Bio::Seq generated by the GenBank.pm and GenPept.pm. The Bio::Seq object returned by this function sometimes has minor difference in the SeqFeature from the Bio::Seq object generated in RefSeq.pm. The Bio::Seq objects created from this function will have the NCBI versions of the SwissProt and EMBL sequence data information.
get_Seq_by_gi
Title : get_Seq_by_gi Usage : $seq = $sh->get_Seq_by_gi('405830'); Function: Gets a Bio::Seq object by gi number Returns : A Bio::Seq object Args : gi number (as a string) Throws : "gi does not exist" exception Note : call the same code get_Seq_by_id
get_Seq_by_version
Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_version('X77802'); Function: Gets a Bio::Seq object by sequence version Returns : A Bio::Seq object Args : accession.version (as a string) Throws : "acc.version does not exist" exception Note : SeqHound only keeps the most up-to-date version of a sequence. So for the above example, use $seq = $db->get_Seq_by_acc('X77802'); instead of X77802.1
get_Stream_by_query
Title : get_Stream_by_query Usage : $seq = $db->get_Stream_by_query($query); Function: Retrieves Seq objects from Entrez 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_Stream_by_[id/acc](). Example : $query_string = 'Candida maltosa 26S ribosomal RNA gene'; $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide', -query=>$query_string); $stream = $sh->get_Stream_by_query($query); or $query = Bio::DB::Query::GenBank->new (-db=> 'nucleotide', -ids=>['X02597', 'X63732', 11002, 4557284]); $stream = $sh->get_Stream_by_query($query); Returns : a Bio::SeqIO stream object Args : $query : A Bio::DB::Query::GenBank object. It is suggested that you create a Bio::DB::Query::GenBank object and get the entry count before you fetch a potentially large stream.
get_Stream_by_id
Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id(['J05128', 'S43442', 34996479]); Function: Gets a series of Seq objects by unique identifiers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of unique identifiers for the desired sequence entries, according to genbank.pm this function accepts gi, accession number and sequence name Note : Since in GenBank.pm, this function accepts a gi, an accession number or a sequence name, SeqHound also satisfies these inputs. If the input uid is a number, it is treated as a gi, if the uid is a string, it is treated as an accession number first. If the search still fails, it is treated as a sequence name. Since SeqHound stores biological data from different source sequence databases like: GenBank, GenPept, SwissProt, EMBL, RefSeq, you can pass ids from the above databases to this function. The Bio::Seq object returned by this function is identical to the Bio::Seq generated by the GenBank.pm and GenPept.pm. The Bio::Seq object returned by this function sometimes has minor difference in the SeqFeature from the Bio::Seq object generated in RefSeq.pm. The Bio::Seq objects created from this function will have the NCBI versions of the SwissProt and EMBL sequence data information.
get_Stream_by_acc
Title : get_Stream_by_acc Usage : $seq = $db->get_Stream_by_acc(['M98777', 'M34830']); 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 SeqHound, this just calls the same code for get_Stream_by_id()
get_Stream_by_gi
Title : get_Stream_by_gi Usage : $seq = $db->get_Seq_by_gi([161966, 255064]); Function: Gets a series of Seq objects by gi numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of gi numbers for the desired sequence entries Note : For SeqHound, this just calls the same code for get_Stream_by_id()
get_request
Title : get_request Usage : my $lcontent = $self->get_request; Function: get the output from SeqHound API http call Returns : the result of the remote call from SeqHound Args : %qualifiers = a hash of qualifiers (SeqHound function name, id, query etc) Example : $lcontent = $self->get_request(-funcname=>'SeqHoundGetGenBankff', -query=>'gi', -uid=>555); Note : this function overrides the implementation in Bio::DB::WebDBSeqI.
postprocess_data
Title : postprocess_data Usage : $self->postprocess_data (-funcname => $funcname, -lcontent => $lcontent, -outtype => $outtype); Function: process return String from http seqrem call output type can be a string or a Bio::SeqIO object. Returns : void Args : $funcname is the API function name of SeqHound $lcontent is a string output from SeqHound server http call $outtype is a string or a Bio::SeqIO object Example : $seqio = $self->postprocess_data ( -lcontent => $lcontent, -funcname => 'SeqHoundGetGenBankffList', -outtype => 'Bio::SeqIO'); or $gi = $self->postprocess_data( -lcontent => $lcontent, -funcname => 'SeqHoundFindAcc', -outtype => 'string'); Note : this method overrides the method works for genbank/genpept, this is for SeqHound
_get_gi_from_name
Title : _get_gi_from_name Usage : $self->_get_gi_from_name('J05128'); Function: get the gene identifier from a sequence name in SeqHound database Return : gene identifier or undef Args : a string represented sequence name
_get_gi_from_acc
Title : _get_gi_from_acc Usage : $self->_get_gi_from_acc('M34830') Function: get the gene identifier from an accession number in SeqHound database Return : gene identifier or undef Args : a string represented accession number
_get_Seq_from_gbff
Title : _get_Seq_from_gbff Usage : $self->_get_Seq_from_gbff($str) Function: get the Bio::SeqIO stream object from gi or a list of gi in SeqHound database Return : Bio::SeqIO or undef Args : a string represented gene identifier or a list of gene identifiers Example : $seq = $self->_get_Seq_from_gbff(141740); or $seq = $self->_get_Seq_from_gbff([141740, 255064, 45185482]);
_init_SeqHound
Title : _init_SeqHound Usage : $self->_init_SeqHound(); Function: call SeqHoundInit at blueprint server Return : $result (TRUE or FALSE) Args :
_MaxSizeArray
Title : _MaxSizeArray Usage : $self->_MaxSizeArray(\@arr) Function: get an array with the limit size Return : an array with the limit size Args : a reference to an array