Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::DB::TFBS::transfac_pro - An implementation of Bio::DB::TFBS which uses local flat
       files for transfac pro

SYNOPSIS

         use Bio::DB::Taxonomy;

         my $db = new Bio::DB::Taxonomy(-source => 'transfac_pro'
                                        -dat_dir => $directory);

         # we're interested in the gene P5
         my ($gene_id) = $db->get_gene_ids(-name => 'P5'); # G000001

         # we want all the transcription factors that bind to our gene
         my @factor_ids = $db->get_factor_ids(-gene => $gene_id);

         # get info about those TFs
         foreach my $factor_id (@factor_ids) {
           my $factor = $db->get_factor($factor_id);
           my $name = $factor->universal_name;
           # etc. - see Bio::Map::TranscriptionFactor, eg. find out where it binds
         }

         # get a matrix
         my $matrix = $db->get_matrix('M00001');

         # get a binding site sequence
         my $seq = $db->get_site('R00001');

DESCRIPTION

       This is an implementation which uses local flat files and the DB_File module RECNO data
       structures to manage a local copy of the Transfac Pro TFBS database.

       Required database files require a license which can be obtained via
       http://www.biobase-international.com/pages/index.php?id=170

       Within the linux installation tarball you will find a cgibin tar ball, and inside that is
       a data directory containing the .dat files needed by this module. Point to that data
       directory with -dat_dir

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala

       Email bix@sendu.me.uk

CONTRIBUTORS

       Based on Bio::DB::Taxonomy::flatfile by Jason Stajich

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   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 calcualted 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
        Funtion : 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)