Bio-DB-TFBS
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Makefile.PL
dist.ini
lib/Bio/DB/TFBS.pm
lib/Bio/DB/TFBS/transfac_pro.pm
t/00-compile.t
t/author-mojibake.t
t/author-pod-syntax.t
t/data/taxdump/names.dmp
t/data/taxdump/nodes.dmp
t/data/transfac_pro/factor.dat
t/data/transfac_pro/fragment.dat
t/data/transfac_pro/gene.dat
t/data/transfac_pro/matrix.dat
t/data/transfac_pro/readme.txt
t/data/transfac_pro/reference.dat
t/data/transfac_pro/site.dat
t/transfac_pro.t
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
$sv = Bio::Annotation::SimpleValue->new(-tagname => 'relative_end', -value => $data[5] || ($data[4] || 1 + length($data[2]) - 1));
$annot->add_Annotation($sv);
$sv = Bio::Annotation::SimpleValue->new(-tagname => 'relative_type', -value => $data[3] || 'artificial');
$annot->add_Annotation($sv);
$sv = Bio::Annotation::SimpleValue->new(-tagname => 'relative_to', -value => $data[1]);
$annot->add_Annotation($sv);
return $seq;
}
=head2 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...')
=cut
sub get_fragment {
my ($self, $id) = @_;
$id || return;
my $data = $self->{fragment}->{data}->{$id} || return;
my @data = split(SEPARATOR, $data);
# accession = id gene_id1 gene_id2 species_tax_id_or_raw_string sequence source
return new Bio::Seq( -seq => $data[4],
-accession_number => $id,
-description => 'Between genes '.$data[1].' and '.$data[2],
-species => $data[3],
-id => $data[0],
-alphabet => 'dna' );
}
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
-id -name -species -interactors -gene -matrix -site -reference
NB: -gene only gets factor ids for genes that encode factors
=cut
sub get_factor_ids {
my $self = shift;
return $self->_get_ids('factor', @_);
}
=head2 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
=cut
sub get_fragment_ids {
my $self = shift;
return $self->_get_ids('fragment', @_);
}
=head2 Helper methods
=cut
# internal method which does the indexing
sub _build_index {
my ($self, $dat_dir, $force) = @_;
# MLDBM would give us transparent complex data structures with DB_File,
# allowing just one index file, but its yet another requirement and we
# don't strictly need it
my $index_dir = $self->index_directory;
my $gene_index = "$index_dir/gene.dat.index";
my $reference_index = "$index_dir/reference.dat.index";
my $matrix_index = "$index_dir/matrix.dat.index";
my $factor_index = "$index_dir/factor.dat.index";
my $fragment_index = "$index_dir/fragment.dat.index";
my $site_index = "$index_dir/site.dat.index";
my $reference_dat = "$dat_dir/reference.dat";
if (! -e $reference_index || $force) {
open my $REF, '<', $reference_dat or $self->throw("Could not read reference file '$reference_dat': $!");
my %references;
unlink $reference_index;
my $ref = tie(%references, 'DB_File', $reference_index, O_RDWR|O_CREAT, 0644, $DB_HASH)
or $self->throw("CCould not open file '$reference_index': $!");
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
unlink $reference_gene;
my $gene = tie(%gene, 'DB_File', $reference_gene, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$reference_gene': $!");
my %site;
my $reference_site = $site_index.'.reference';
unlink $reference_site;
my $site = tie(%site, 'DB_File', $reference_site, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$reference_site': $!");
my %fragment;
my $reference_fragment = $fragment_index.'.reference';
unlink $reference_fragment;
my $fragment = tie(%fragment, 'DB_File', $reference_fragment, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$reference_fragment': $!");
my %factor;
my $reference_factor = $factor_index.'.reference';
unlink $reference_factor;
my $factor = tie(%factor, 'DB_File', $reference_factor, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$reference_factor': $!");
my %matrix;
my $reference_matrix = $matrix_index.'.reference';
unlink $reference_matrix;
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
elsif (/^GE TRANSFAC: (\w\d+)/) {
$gene->put($data[0], "$1");
}
elsif (/^BS TRANSFAC: (\w\d+)/) {
$site->put($data[0], "$1");
}
elsif (/^FA TRANSFAC: (\w\d+)/) {
$factor->put($data[0], "$1");
}
elsif (/^FR TRANSFAC: (FR\d+)/) {
$fragment->put($data[0], "$1");
}
elsif (/^MX TRANSFAC: (\w\d+)/) {
$matrix->put($data[0], "$1");
}
elsif (/^\/\//) {
# end of a record, store previous data and reset
# accession = pubmed authors title location
$references{$data[0]} = join(SEPARATOR, ($data[1] || '',
$data[2] || '',
$data[3] || '',
$data[4] || ''));
@data = ();
}
}
close $REF;
$ref = $pub = $gene = $site = $fragment = $factor = $matrix = undef;
untie %references;
untie %pubmed;
untie %gene;
untie %site;
untie %fragment;
untie %factor;
untie %matrix;
}
my $gene_dat = "$dat_dir/gene.dat";
if (! -e $gene_index || $force) {
open my $GEN, '<', $gene_dat or $self->throw("Could not read gene file '$gene_dat': $!");
my %genes;
unlink $gene_index;
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
unlink $gene_site;
my $site = tie(%site, 'DB_File', $gene_site, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$gene_site': $!");
my %factor;
my $gene_factor = $factor_index.'.gene';
unlink $gene_factor;
my $factor = tie(%factor, 'DB_File', $gene_factor, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$gene_factor': $!");
my %fragment;
my $gene_fragment = $fragment_index.'.gene';
unlink $gene_fragment;
my $fragment = tie(%fragment, 'DB_File', $gene_fragment, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$gene_fragment': $!");
my %reference;
my $gene_reference = $reference_index.'.gene';
unlink $gene_reference;
my $reference = tie(%reference, 'DB_File', $gene_reference, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$gene_reference': $!");
# skip the first three header lines
<$GEN>; <$GEN>; <$GEN>;
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
elsif (/^RN .+?(RE\d+)/) {
$reference->put($data[0], "$1");
}
elsif (/^BS .+?(R\d+)/) {
$site->put($data[0], "$1");
}
elsif (/^FA (T\d+)/) {
$factor->put($data[0], "$1");
}
elsif (/^BR (FR\d+)/) {
$fragment->put($data[0], "$1");
}
elsif (/^\/\//) {
# end of a record, store previous data and reset
# accession = id name description species_tax_id_or_raw_string
$genes{$data[0]} = join(SEPARATOR, ($data[1] || '',
$data[2] || '',
$data[3] || '',
$data[4] || ''));
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
unlink $factor_matrix;
my $matrix = tie(%matrix, 'DB_File', $factor_matrix, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$factor_matrix': $!");
my %site;
my $factor_site = $site_index.'.factor';
unlink $factor_site;
my $site = tie(%site, 'DB_File', $factor_site, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$factor_site': $!");
my %fragment;
my $factor_fragment = $fragment_index.'.factor';
unlink $factor_fragment;
my $fragment = tie(%fragment, 'DB_File', $factor_fragment, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$factor_fragment': $!");
my %reference;
my $factor_reference = $reference_index.'.factor';
unlink $factor_reference;
my $reference = tie(%reference, 'DB_File', $factor_reference, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$factor_reference': $!");
# skip the first three header lines
<$FAC>; <$FAC>; <$FAC>;
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
elsif (/^IN (T\d+)/) {
$interact->put($data[0], "$1");
}
elsif (/^MX (M\d+)/) {
$matrix->put($data[0], "$1");
}
elsif (/^BS (R\d+)/) {
$site->put($data[0], "$1");
}
elsif (/^BR (FR\d+)/) {
$fragment->put($data[0], "$1");
}
elsif (/^RN .+?(RE\d+)/) {
$reference->put($data[0], "$1");
}
elsif (/^\/\//) {
# end of a record, store previous data and reset
# accession = id name species sequence
$factors{$data[0]} = join(SEPARATOR, ($data[1] || '',
$data[2] || '',
$data[3] || '',
$sequence));
@data = ();
$sequence = '';
}
}
close $FAC;
$factor = $id = $name = $species = $interact = $gene = $matrix = $site = $fragment = $reference = undef;
untie %factors;
untie %id;
untie %name;
untie %species;
untie %interactors;
untie %gene;
untie %matrix;
untie %site;
untie %fragment;
untie %reference;
}
my $fragment_dat = "$dat_dir/fragment.dat";
if (! -e $fragment_index || $force) {
if (open my $FRA, '<', $fragment_dat) {
my %fragments;
unlink $fragment_index;
my $fragment = tie(%fragments, 'DB_File', $fragment_index, O_RDWR|O_CREAT, 0644, $DB_HASH)
or $self->throw("Could not open file '$fragment_index': $!");
my %id;
my $fragment_id = $fragment_index.'.id';
unlink $fragment_id;
my $id = tie(%id, 'DB_File', $fragment_id, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$fragment_id': $!");
my %qualities;
my $fragment_qualities = $fragment_index.'.qual';
unlink $fragment_qualities;
my $quality = tie(%qualities, 'DB_File', $fragment_qualities, O_RDWR|O_CREAT, 0644, $DB_HASH)
or $self->throw("Could not open file '$fragment_qualities': $!");
my %species;
my $fragment_species = $fragment_index.'.species';
unlink $fragment_species;
my $species = tie(%species, 'DB_File', $fragment_species, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$fragment_species': $!");
my %gene;
my $fragment_gene = $gene_index.'.fragment';
unlink $fragment_gene;
my $gene = tie(%gene, 'DB_File', $fragment_gene, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$fragment_gene': $!");
my %factor;
my $fragment_factor = $factor_index.'.fragment';
unlink $fragment_factor;
my $factor = tie(%factor, 'DB_File', $fragment_factor, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$fragment_factor': $!");
my %reference;
my $fragment_reference = $reference_index.'.fragment';
unlink $fragment_reference;
my $reference = tie(%reference, 'DB_File', $fragment_reference, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$fragment_reference': $!");
# skip the first three header lines
<$FRA>; <$FRA>; <$FRA>;
my @data;
while (<$FRA>) {
if (/^AC (\S+)/) {
$data[0] = $1;
}
elsif (/^ID (\S+)/) {
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
$reference->put($data[0], "$1");
}
elsif (/^BF (T\d+); .+?; Quality: (\d)/) {
$factor->put($data[0], "$1");
$qualities{$data[0].SEPARATOR.$1} = $2;
}
elsif (/^\/\//) {
# end of a record, store previous data and reset
# accession = id gene_id1 gene_id2 species_tax_id_or_raw_string sequence source
$fragments{$data[0]} = join(SEPARATOR, ($data[1] || '',
$data[2] || '',
$data[3] || '',
$data[4] || '',
$data[5] || '',
$data[6] || ''));
@data = ();
}
}
close $FRA;
$fragment = $id = $species = $quality = $gene = $factor = $reference = undef;
untie %fragments;
untie %id;
untie %species;
untie %qualities;
untie %gene;
untie %factor;
untie %reference;
}
else {
$self->warn("Could not read fragment file '$fragment_dat', assuming you have an old version of Transfac Pro with no fragment.dat file");
}
}
}
# connect the internal db handle
sub _db_connect {
my $self = shift;
return if $self->{'_initialized'};
my $index_dir = $self->index_directory;
my $gene_index = "$index_dir/gene.dat.index";
my $reference_index = "$index_dir/reference.dat.index";
my $matrix_index = "$index_dir/matrix.dat.index";
my $factor_index = "$index_dir/factor.dat.index";
my $site_index = "$index_dir/site.dat.index";
my $fragment_index = "$index_dir/fragment.dat.index";
foreach ($gene_index, $reference_index, $matrix_index, $factor_index, $site_index, $fragment_index) {
if (! -e $_) {
#$self->warn("Index files have not been created");
#return 0;
}
}
# reference
{
$self->{reference}->{data} = {};
tie (%{$self->{reference}->{data}}, 'DB_File', $reference_index, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$reference_index': $!");
my $reference_pubmed = $reference_index.'.pubmed';
$self->{reference}->{pubmed} = tie (%{$self->{reference}->{pubmed}}, 'DB_File', $reference_pubmed, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$reference_pubmed': $!");
my $reference_gene = $gene_index.'.reference';
$self->{gene}->{reference} = tie (%{$self->{gene}->{reference}}, 'DB_File', $reference_gene, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$reference_gene': $!");
my $reference_site = $site_index.'.reference';
$self->{site}->{reference} = tie (%{$self->{site}->{reference}}, 'DB_File', $reference_site, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$reference_site': $!");
my $reference_fragment = $fragment_index.'.reference';
$self->{fragment}->{reference} = tie (%{$self->{fragment}->{reference}}, 'DB_File', $reference_fragment, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$reference_fragment': $!");
my $reference_factor = $factor_index.'.reference';
$self->{factor}->{reference} = tie (%{$self->{factor}->{reference}}, 'DB_File', $reference_factor, undef, 0644, $DB_BTREE) || $self->throw("Cannot open file '$reference_factor': $!");
my $reference_matrix = $matrix_index.'.reference';
$self->{matrix}->{reference} = tie (%{$self->{matrix}->{reference}}, 'DB_File', $reference_matrix, undef, 0644, $DB_BTREE) || $self->throw("Cannot open file '$reference_matrix': $!");
}
# gene
{
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
my $gene_name = $gene_index.'.name';
$self->{gene}->{name} = tie(%{$self->{gene}->{name}}, 'DB_File', $gene_name, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_name': $!");
my $gene_species = $gene_index.'.species';
$self->{gene}->{species} = tie(%{$self->{gene}->{species}}, 'DB_File', $gene_species, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_species': $!");
my $gene_site = $site_index.'.gene';
$self->{site}->{gene} = tie(%{$self->{site}->{gene}}, 'DB_File', $gene_site, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_site': $!");
my $gene_fragment = $fragment_index.'.gene';
$self->{fragment}->{gene} = tie(%{$self->{fragment}->{gene}}, 'DB_File', $gene_fragment, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_fragment': $!");
my $gene_factor = $factor_index.'.gene';
$self->{factor}->{gene} = tie(%{$self->{factor}->{gene}}, 'DB_File', $gene_factor, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_factor': $!");
my $gene_reference = $reference_index.'.gene';
$self->{reference}->{gene} = tie(%{$self->{reference}->{gene}}, 'DB_File', $gene_reference, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_reference': $!");
}
# site
{
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
my $site_matrix = $matrix_index.'.site';
$self->{matrix}->{site} = tie(%{$self->{matrix}->{site}}, 'DB_File', $site_matrix, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$site_matrix': $!");
my $site_factor = $factor_index.'.site';
$self->{factor}->{site} = tie(%{$self->{factor}->{site}}, 'DB_File', $site_factor, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$site_factor': $!");
my $site_reference = $reference_index.'.site';
$self->{reference}->{site} = tie(%{$self->{reference}->{site}}, 'DB_File', $site_reference, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$site_reference': $!");
}
# fragment (may not be in older databases)
if (-e $fragment_index) {
$self->{fragment}->{data} = {};
tie (%{$self->{fragment}->{data}}, 'DB_File', $fragment_index, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$fragment_index': $!");
my $fragment_id = $fragment_index.'.id';
$self->{fragment}->{id} = tie(%{$self->{fragment}->{id}}, 'DB_File', $fragment_id, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$fragment_id': $!");
my $fragment_species = $fragment_index.'.species';
$self->{fragment}->{species} = tie(%{$self->{fragment}->{species}}, 'DB_File', $fragment_species, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file $fragment_species': $!");
#*** quality not actually used by anything (yet)
my $fragment_qualities = $fragment_index.'.qual';
$self->{fragment_quality} = {};
tie(%{$self->{fragment_quality}}, 'DB_File', $fragment_qualities, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$fragment_qualities': $!");
my $fragment_gene = $gene_index.'.fragment';
$self->{gene}->{fragment} = tie(%{$self->{gene}->{fragment}}, 'DB_File', $fragment_gene, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$fragment_gene': $!");
my $fragment_factor = $factor_index.'.fragment';
$self->{factor}->{fragment} = tie(%{$self->{factor}->{fragment}}, 'DB_File', $fragment_factor, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$fragment_factor': $!");
my $fragment_reference = $reference_index.'.fragment';
$self->{reference}->{fragment} = tie(%{$self->{reference}->{fragment}}, 'DB_File', $fragment_reference, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$fragment_reference': $!");
}
else {
die "no fragment_index at '$fragment_index'\n";
}
# matrix
{
$self->{matrix}->{data} = {};
tie (%{$self->{matrix}->{data}}, 'DB_File', $matrix_index, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$matrix_index': $!");
my $matrix_id = $matrix_index.'.id';
$self->{matrix}->{id} = tie(%{$self->{matrix}->{id}}, 'DB_File', $matrix_id, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$matrix_id': $!");
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
my $factor_gene = $gene_index.'.factor';
$self->{gene}->{factor} = tie(%{$self->{gene}->{factor}}, 'DB_File', $factor_gene, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_gene': $!");
my $factor_matrix = $matrix_index.'.factor';
$self->{matrix}->{factor} = tie(%{$self->{matrix}->{factor}}, 'DB_File', $factor_matrix, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_matrix': $!");
my $factor_site = $site_index.'.factor';
$self->{site}->{factor} = tie(%{$self->{site}->{factor}}, 'DB_File', $factor_site, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_site': $!");
my $factor_fragment = $fragment_index.'.factor';
$self->{fragment}->{factor} = tie(%{$self->{fragment}->{factor}}, 'DB_File', $factor_fragment, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_fragment': $!");
my $factor_reference = $reference_index.'.factor';
$self->{reference}->{factor} = tie(%{$self->{reference}->{factor}}, 'DB_File', $factor_reference, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_reference': $!");
}
$self->{'_initialized'} = 1;
}
=head2 index_directory
t/transfac_pro.t view on Meta::CPAN
my @matrices = $db->get_matrix_ids(-reference => $ref_id);
is join(' ', sort @matrices), 'M01123 M01124 M01125';
my @factors = $db->get_factor_ids(-reference => $ref_id);
like "@factors", qr/T08800/;
@ref_ids = $db->get_reference_ids(-matrix => 'M01123');
is join(' ', sort @ref_ids), "$ref_id RE0047626";
@ref_ids = $db->get_reference_ids(-factor => 'T08800');
is join(' ', sort @ref_ids), "$ref_id RE0047634 RE0047637 RE0047645";
$ref_id = 'RE0023998';
my %fragments = map { $_ => 1 } $db->get_fragment_ids(-reference => $ref_id);
ok $fragments{'FR0002267'};
@ref_ids = $db->get_reference_ids(-fragment => 'FR0002267');
is "@ref_ids", $ref_id;
}
# gene.dat
{
ok my ($gene_id) = $db->get_gene_ids(-name => 'P5');
is $gene_id, 'G000001';
#*** get_genemap with ensembl lookup being fantastically slow
#ok defined Bio::Map::Gene->set_from_db; # will try and do ensembl lookups for gene info
t/transfac_pro.t view on Meta::CPAN
($gene_id) = $db->get_gene_ids(-id => 'AAV$P5');
is $gene_id, 'G000001';
my @gene_ids = $db->get_gene_ids(-species => '9606');
is @gene_ids, 5;
is [sort @gene_ids]->[0], 'G000060'; # in real data this would be G000174, but since our taxdump doesn't have chicken in it, G000060 was changed to human
($gene_id) = $db->get_gene_ids(-site => 'R03174');
is $gene_id, 'G000001';
($gene_id) = $db->get_gene_ids(-factor => 'T00267');
is $gene_id, 'G000060';
my %gene_ids = map { $_ => 1 } $db->get_gene_ids(-fragment => 'FR0002267');
ok $gene_ids{'G020751'};
# get_gene_ids(-reference => ...) already tested
my @site_ids = $db->get_site_ids(-gene => 'G000001');
is join(' ', sort @site_ids), 'R03174 R03175 R03176';
my @factor_ids = $db->get_factor_ids(-gene => 'G000060');
is join(' ', sort @factor_ids), 'T00267 T08293'; # only found for genes that encode factors
my %fragment_ids = map { $_ => 1 } $db->get_fragment_ids(-gene => 'G020751');
ok $fragment_ids{'FR0002267'};
# get_reference_ids(-gene => ...) already tested
}
# site.dat
{
ok my ($site_id) = $db->get_site_ids(-id => 'HS$IFI616_01');
is $site_id, 'R00001';
ok my $seq = $db->get_seq($site_id);
isa_ok $seq, 'Bio::Seq';
is $seq->id, 'HS$IFI616_01';
t/transfac_pro.t view on Meta::CPAN
my %matrix_ids = map { $_ => 1 } $db->get_matrix_ids(-factor => 'T00526');
ok $matrix_ids{M00001};
# get_matrix_ids(-reference => ...) already tested
# get_site_ids(-matrix => ...) already tested
my @factor_ids = $db->get_factor_ids(-matrix => 'M00001');
is join(' ', sort @factor_ids), 'T00526 T09177';
# get_reference_ids(-matrix => ...) already tested
}
# fragment.dat
{
ok my ($fragment_id) = $db->get_fragment_ids(-id => 'FR0002267');
is $fragment_id, 'FR0002267'; # id and accession are the same for fragments
ok my $seq = $db->get_fragment($fragment_id);
isa_ok $seq, 'Bio::SeqI';
is $seq->id, 'FR0002267';
is $seq->seq, 'GTCTACAACACTCTTGCGGACGGAGAGCCGAAGAGCAAAGCGTCGCCGGGTAAGACGAACGCTCAAGGGGGTACGAGCAGCGTAACGACGGAAACGGTGACGCCCCGGGATTTGGGGCTCAGCTAGGGTCGCCGAGTAGGGGGCCGCGGGGACAACGGGGGCGACACGCCGCTTTCCCTGCGTCTGTGGAGCCTATGGTACGGCGTAACCGGTTGTGTGATGAACTG...
is $seq->species, 9606;
# -id -species -gene -factor -reference
my @fragment_ids = $db->get_fragment_ids(-species => '9606');
is @fragment_ids, 2;
is [sort @fragment_ids]->[0], 'FR0000001';
my %fragment_ids = map { $_ => 1 } $db->get_fragment_ids(-factor => 'T03828');
ok $fragment_ids{'FR0002267'};
# get_fragment_ids(-gene => ...) already tested
# get_fragment_ids(-reference => ...) already tested
my ($factor_id) = $db->get_factor_ids(-fragment => 'FR0002267');
is $factor_id, 'T03828';
# get_gene_ids(-fragment => ...) already tested
# get_reference_ids(-fragment => ...) already tested
}
# factor.dat
{
ok my ($factor_id) = $db->get_factor_ids(-id => 'T00001');
is $factor_id, 'T00001'; # id and accession are the same for factors
ok my $factor = $db->get_factor($factor_id);
isa_ok $factor, 'Bio::Map::TranscriptionFactor';
is $factor->id, 'T00001';
is $factor->universal_name, 'AAF';
t/transfac_pro.t view on Meta::CPAN
($factor_id) = $db->get_factor_ids(-name => 'AAF');
is $factor_id, 'T00001';
my @factor_ids = $db->get_factor_ids(-species => '9606');
is @factor_ids, 7;
is [sort @factor_ids]->[0], 'T00001';
@factor_ids = $db->get_factor_ids(-interactors => 'T03200');
is [sort @factor_ids]->[0], 'T00002';
# get_factor_ids(-gene => ...) already tested
# get_factor_ids(-site => ...) already tested
# get_factor_ids(-matrix => ...) already tested
# get_factor_ids(-fragment => ...) already tested
# get_factor_ids(-reference => ...) already tested
# get_*_ids(-factor => ...) already tested
}
}
# how to get something like ok $psmIO->release, '10.2--2006-06-30'; ?
# or all factors, all sites, all matrices, all genes etc.?
( run in 0.991 second using v1.01-cache-2.11-cpan-364913b4093 )