| Bio::DB::TFBS::transfac_pro(3pm) | User Contributed Perl Documentation | Bio::DB::TFBS::transfac_pro(3pm) |
Bio::DB::TFBS::transfac_pro - An implementation of Bio::DB::TFBS which uses local flat files for transfac pro
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');
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
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
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.
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Based on Bio::DB::Taxonomy::flatfile by Jason Stajich
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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...')
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)
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...')
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...')
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)
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
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...')
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
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
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
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
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
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)
| 2018-10-27 | perl v5.26.2 |