NAME
Bio::DB::SeqHound - Database object interface to SeqHound
SYNOPSIS
use Bio::DB::SeqHound;
$sh = new Bio::DB::SeqHound();
$seq = $sh->get_Seq_by_acc("CAA28783"); # Accession Number
# or ...
$seq = $sh->get_Seq_by_gi(4557225); # GI NumberVERSION
1.1
DESCRIPTION
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, CanadaFEEDBACK/BUGS
known bugs: fail to get sequences for some RefSeq record with CONTIG, example GI = 34871762
<seqhound@blueprint.org>
MAILING 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.
<seqhound.usergroup@lists.blueprint.org>
WEBSITE
For more information on SeqHound http://www.blueprint.org/seqhound/
DISCLAIMER
This software is provided 'as is' without warranty of any kind.
AUTHOR
Rong Yao, Hao Lieu, Ian Donaldson
<seqhound@blueprint.org>
APPENDIX
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_idget_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 X77802.1get_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