Bio::DB::TFBS::transfac_pro man page on Pidora

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Bio::DB::TFBS::transfaUseroContributed Perl DocuBio::DB::TFBS::transfac_pro(3)

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)

perl v5.14.1			  2011-07-22	Bio::DB::TFBS::transfac_pro(3)
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