Provided by: libbio-perl-perl_1.6.923-1_all bug

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