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Bio::DB::TFBS::transfac_pro.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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)