Bio::DB::TFBS::transfac_pro(3pm)

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new

 Title   : new
 Usage   : my $obj = new Bio::DB::TFBS::transfac_pro();
 Function: Builds a new Bio::DB::TFBS::transfac_pro object 
 Returns : an instance of Bio::DB::TTFBS::transfac_pro
 Args    : -dat_dir   => name of directory where Transfac Pro .dat files
                         (required to initially build indexes)
           -tax_db    => Bio::DB::Taxonomy object, used when initially building
                         indexes, gives better results for species information
                         but not required.
           -index_dir => name of directory where index files should be created
                         or already exist. (defaults to -dat_dir, required if
                         -dat_dir not supplied)
           -force     => 1 replace current indexes even if they exist

Bio::DB::TFBS Interface implementation

get_reference

 Title   : get_reference
 Usage   : my $ref = $obj->get_reference($id);
 Function: Get a literature reference.
 Returns : Bio::Annotation::Reference
 Args    : string - a reference id ('RE...')

get_genemap

 Title   : get_genemap
 Usage   : my $map = $obj->get_genemap($id);
 Function: Get a GeneMap for a gene.
 Returns : Bio::Map::GeneMap
 Args    : string - a gene id ('G...'), and optionally int (number of bp
           upstream)

get_seq

 Title   : get_seq
 Usage   : my $seq = $obj->get_seq($id);
 Function: Get the sequence of a site. The sequence will be annotated with the
           the tags 'relative_start', 'relative_end', 'relative_type' and
           'relative_to'.
 Returns : Bio::Seq
 Args    : string - a site id ('R...')

get_fragment

 Title   : get_fragment
 Usage   : my $seq = $obj->get_fragment($id);
 Function: Get the sequence of a fragment.
 Returns : Bio::Seq
 Args    : string - a site id ('FR...')

get_matrix

 Title   : get_matrix
 Usage   : my $matrix = $obj->get_matrix($id);
 Function: Get a matrix that describes a binding site.
 Returns : Bio::Matrix::PSM::SiteMatrix
 Args    : string - a matrix id ('M...'), optionally a sequence string from
           which base frequencies will be calculated for the matrix model
           (default 0.25 each)

get_aln

 Title   : get_aln
 Usage   : my $aln = $obj->get_aln($id);
 Function: Get the alignment that was used to generate a matrix. Each sequence
           in the alignment will have an accession_number corresponding to the
           Transfac site id, and id() based on that but unique within the
           alignment.
 Returns : Bio::SimpleAlign
 Args    : string - a matrix id ('M...'), optionally true to, when a matrix
           lists no sequences, search for sequences via the matrix's factors,
           picking the sites that best match the matrix

get_factor

 Title   : get_factor
 Usage   : my $factor = $obj->get_factor($id);
 Function: Get the details of a transcription factor.
 Returns : Bio::Map::TranscriptionFactor
 Args    : string - a factor id ('T...')

get_reference_ids

 Title   : get_reference_ids
 Usage   : my @ids = $obj->get_reference_ids(-key => $value);
 Function: Get all the reference ids that are associated with the supplied
           args.
 Returns : list of strings (ids)
 Args    : -key => value, where value is a string id, and key is one of:
           -pubmed -site -gene -matrix -factor

get_site_ids

 Title   : get_site_ids
 Usage   : my @ids = $obj->get_site_ids(-key => $value);
 Function: Get all the site ids that are associated with the supplied
           args.
 Returns : list of strings (ids)
 Args    : -key => value, where value is a string id, and key is one of:
           -id -species -gene -matrix -factor -reference

get_matrix_ids

 Title   : get_matrix_ids
 Usage   : my @ids = $obj->get_matrix_ids(-key => $value);
 Function: Get all the matrix ids that are associated with the supplied
           args.
 Returns : list of strings (ids)
 Args    : -key => value, where value is a string id, and key is one of:
           -id -name -site -factor -reference

get_factor_ids

 Title   : get_factor_ids
 Usage   : my @ids = $obj->get_factor_ids(-key => $value);
 Function: Get all the factor ids that are associated with the supplied
           args.
 Returns : list of strings (ids)
 Args    : -key => value, where value is a string id, and key is one of:
           -id -name -species -interactors -gene -matrix -site -reference
           NB: -gene only gets factor ids for genes that encode factors

get_fragment_ids

 Title   : get_fragment_ids
 Usage   : my @ids = $obj->get_fragment_ids(-key => $value);
 Function: Get all the fragment ids that are associated with the supplied
           args.
 Returns : list of strings (ids)
 Args    : -key => value, where value is a string id, and key is one of:
           -id -species -gene -factor -reference

Helper methods

index_directory

 Title   : index_directory
 Function : Get/set the location that index files are stored. (this module
           will index the supplied database)
 Usage   : $obj->index_directory($newval)
 Returns : value of index_directory (a scalar)
 Args    : on set, new value (a scalar or undef, optional)