XrefParser::UniProtDatabaseParser Class Reference
Public Member Functions | |
| public | run () |
Detailed Description
Definition at line 5 of file UniProtDatabaseParser.pm.
Member Function Documentation
◆ run()
| public XrefParser::UniProtDatabaseParser::run | ( | ) |
Undocumented method
Code:
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sub run {
my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $dbi = $ref_arg->{dbi};
my $xref_source = $ref_arg->{xref_source};
if((!defined $source_id) or (!defined $species_id) or (!defined $xref_source)){
croak "Need to pass source_id, species_id and xref_source";
}
my @source_ids;
my $sp_source_id = $self->get_source_id_for_source_name('Uniprot/SWISSPROT','sequence_mapped', $dbi);
push @source_ids, $sp_source_id;
my $sptr_source_id = $self->get_source_id_for_source_name('Uniprot/SPTREMBL', 'sequence_mapped', $dbi);
push @source_ids, $sptr_source_id;
my $sptr_non_display_source_id = $self->get_source_id_for_source_name('Uniprot/SPTREMBL', 'protein_evidence_gt_2', $dbi);
push @source_ids, $sptr_non_display_source_id;
my $sp_direct_source_id = $self->get_source_id_for_source_name('Uniprot/SWISSPROT', 'direct', $dbi);
push @source_ids, $sp_direct_source_id;
my $sptr_direct_source_id = $self->get_source_id_for_source_name('Uniprot/SPTREMBL', 'direct', $dbi);
push @source_ids, $sptr_direct_source_id;
my $isoform_source_id = $self->get_source_id_for_source_name('Uniprot_isoform');
push @source_ids, $isoform_source_id;
my $get_xref_sql = "SELECT xref_id, accession, version, label, description, info_type ".
"FROM xref WHERE species_id = ? AND source_id = ?";
my $get_xref_sth = $xref_source->prepare($get_xref_sql);
my $get_dependent_sql = "SELECT x.xref_id, x.accession, x.version, x.label, x.description, x.source_id, x.species_id, dx.linkage_source_id FROM xref x, dependent_xref dx ".
"WHERE dx.dependent_xref_id = x.xref_id and dx.master_xref_id = ?";
my $get_dependent_sth = $xref_source->prepare($get_dependent_sql);
my $get_sequence_sql = "SELECT sequence, sequence_type, status FROM primary_xref WHERE xref_id = ?";
my $get_sequence_sth = $xref_source->prepare($get_sequence_sql);
my $get_synonym_sql = "SELECT synonym FROM synonym WHERE xref_id = ?";
my $get_synonym_sth = $xref_source->prepare($get_synonym_sql);
my $get_direct_sql = "SELECT ensembl_stable_id, linkage_xref FROM translation_direct_xref WHERE general_xref_id = ?";
my $get_direct_sth = $xref_source->prepare($get_direct_sql);
my ($xref_id, $accession, $version, $label, $description, $info_type, $parsed_seq, $type, $status, $dep_xref_id, $dep_accession, $dep_version, $dep_label, $dep_description, $dep_source_id, $dep_species_id, $linkage_source_id, $synonym, $stable_id, $linkage_xref);
my @xrefs;
my $count = 0;
foreach my $xref_source_id (@source_ids) {
$get_xref_sth->execute($species_id, $xref_source_id);
$get_xref_sth->bind_columns(\$xref_id, \$accession, \$version, \$label, \$description, \$info_type);
while ($get_xref_sth->fetch) {
my $xref = {};
$count++;
$xref->{ACCESSION} = $accession;
$xref->{LABEL} = $label;
$xref->{VERSION} = $version;
$xref->{SPECIES_ID} = $species_id;
$xref->{INFO_TYPE} = $info_type;
$xref->{SOURCE_ID} = $xref_source_id;
$xref->{DESCRIPTION} = $description;
# Add sequence if there is some
$get_sequence_sth->execute($xref_id);
$get_sequence_sth->bind_columns(\$parsed_seq, \$type, \$status);
while ($get_sequence_sth->fetch) {
$xref->{SEQUENCE_TYPE} = $type;
$xref->{STATUS} = $status;
$xref->{SEQUENCE} = $parsed_seq;
}
# Look for synonyms
$get_synonym_sth->execute($xref_id);
$get_synonym_sth->bind_columns(\$synonym);
while ($get_synonym_sth->fetch) {
push (@{$xref->{SYNONYMS} }, $synonym);
}
# Look for direct xref
$get_direct_sth->execute($xref_id);
$get_direct_sth->bind_columns(\$stable_id, \$linkage_xref);
while ($get_direct_sth->fetch) {
my %direct;
my $isoform;
$direct{STABLE_ID} = $stable_id;
$direct{ENSEMBL_TYPE} = 'Translation';
$direct{LINKAGE_TYPE} = $linkage_xref;
$direct{SOURCE_ID} = $xref_source_id;
push (@{$xref->{DIRECT_XREFS}}, \%direct);
}
#Add any dependent xrefs
$get_dependent_sth->execute($xref_id);
$get_dependent_sth->bind_columns(\$dep_xref_id, \$dep_accession, \$dep_version, \$dep_label, \$dep_description, \$dep_source_id, \$dep_species_id, \$linkage_source_id);
while ($get_dependent_sth->fetch) {
if ($dep_species_id != $species_id) { next; }
my %dep;
$dep{ACCESSION} = $dep_accession;
$dep{LABEL} = $dep_label;
$dep{VERSION} = $dep_version;
$dep{DESCRIPTION} = $dep_description;
$dep{SOURCE_ID} = $dep_source_id;
$dep{LINKAGE_SOURCE_ID} = $linkage_source_id;
$get_synonym_sth->execute($dep_xref_id);
$get_synonym_sth->bind_columns(\$synonym);
while ($get_synonym_sth->fetch) {
push (@{$dep{SYNONYMS} }, $synonym);
}
push @{$xref->{DEPENDENT_XREFS}}, \%dep;
}
push @xrefs, $xref;
if ($count > 1000) {
$self->upload_xref_object_graphs( \@xrefs, $dbi );
$count = 0;
undef @xrefs;
}
}
}
$self->upload_xref_object_graphs(\@xrefs, $dbi) if scalar(@xrefs) > 0;
return 0; # successfull
}
The documentation for this class was generated from the following file:
- ensembl/misc-scripts/xref_mapping/XrefParser/UniProtDatabaseParser.pm
