Bio::DB::SeqHound(3)

NAME
Bio::DB::SeqHound - Database object interface to SeqHound

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
1.1

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, Canada

FEEDBACK/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://dogboxonline.unleashedinformatics.com/

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_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