diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
index 71d793818afd551b3dbcca71dfef1d304ad0f91f..d04724738b66d942d51430ceb782d84de823687e 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
@@ -135,7 +135,7 @@ sub create_xrefs {
# Create a hash of all valid names and taxon_ids for this species
my %species2name = $self->species_id2name($dbi);
if (defined $species_name) { push @{$species2name{$species_id}}, $species_name; }
- if (!defined $species2name{$species_id}) { next; }
+ if (!defined $species2name{$species_id}) { return; }
my %species2tax = $self->species_id2taxonomy($dbi);
push @{$species2tax{$species_id}}, $species_id;
my @names = @{$species2name{$species_id}};
@@ -164,30 +164,48 @@ sub create_xrefs {
local $/ = "\/\/\n";
- my $type;
- if ($file =~ /protein/) {
+ my $type = $self->type_from_file($file);
+ return unless $type;
- $type = 'peptide';
+ while ( my $entry = $refseq_io->getline() ) {
- } elsif ($file =~ /rna/) {
+ my $xref = $self->xref_from_record(
+ $entry,
+ \%name2species_id, \%taxonomy2species_id,
+ $pred_mrna_source_id, $pred_ncrna_source_id,
+ $mrna_source_id, $ncrna_source_id,
+ $pred_peptide_source_id, $peptide_source_id,
+ $entrez_source_id, $wiki_source_id, $add_dependent_xref_sth,
+ $species_id, $type, \%refseq_ids,\%entrez_ids,\%wiki_ids
+ );
- $type = 'dna';
+ push @xrefs, $xref if $xref;
- } elsif($file =~ /RefSeq_protein/){
-
- $type = 'peptide';
-
- }else{
- print STDERR "Could not work out sequence type for $file\n";
- return;
- }
+ } # while <REFSEQ>
+ $refseq_io->close();
- while ( $_ = $refseq_io->getline() ) {
+ print "Read " . scalar(@xrefs) ." xrefs from $file\n" if($verbose);
- my $xref;
+ return \@xrefs;
- my $entry = $_;
+}
+sub type_from_file {
+ my ($self, $file) = @_;
+ return 'peptide' if $file =~ /RefSeq_protein/;
+ return 'dna' if $file =~ /rna/;
+ return 'peptide' if $file =~ /protein/;
+ print STDERR "Could not work out sequence type for $file\n";
+ return;
+}
+sub xref_from_record {
+ my ( $self, $entry, $name2species_id, $taxonomy2species_id,
+ $pred_mrna_source_id, $pred_ncrna_source_id,
+ $mrna_source_id, $ncrna_source_id,
+ $pred_peptide_source_id, $peptide_source_id,
+ $entrez_source_id, $wiki_source_id, $add_dependent_xref_sth,
+ $species_id, $type, $refseq_ids,$entrez_ids,$wiki_ids
+) = @_;
chomp $entry;
my ($species) = $entry =~ /\s+ORGANISM\s+(.*)\n/;
@@ -196,12 +214,12 @@ sub create_xrefs {
$species =~ s/\s*\(.+\)//; # Ditch anything in parens
$species =~ s/\s+/_/g;
$species =~ s/\n//g;
- my $species_id_check = $name2species_id{$species};
+ my $species_id_check = $name2species_id->{$species};
# Try going through the taxon ID if species check didn't work.
if ( !defined $species_id_check ) {
my ($taxon_id) = $entry =~ /db_xref="taxon:(\d+)"/;
- $species_id_check = $taxonomy2species_id{$taxon_id};
+ $species_id_check = $taxonomy2species_id->{$taxon_id};
}
# skip xrefs for species that aren't in the species table
@@ -209,6 +227,7 @@ sub create_xrefs {
&& defined $species_id_check
&& $species_id == $species_id_check )
{
+ my $xref = {};
my ($acc) = $entry =~ /ACCESSION\s+(\S+)/;
my ($ver) = $entry =~ /VERSION\s+(\S+)/;
my ($refseq_pair) = $entry =~ /DBSOURCE\s+REFSEQ: accession (\S+)/;
@@ -243,7 +262,7 @@ sub create_xrefs {
$description =~ s/\s+/ /g;
$description = substr($description, 0, 255) if (length($description) > 255);
- my ($seq) = $_ =~ /^\s*ORIGIN\s+(.+)/ms; # /s allows . to match newline
+ my ($seq) = $entry =~ /^\s*ORIGIN\s+(.+)/ms; # /s allows . to match newline
my @seq_lines = split /\n/, $seq;
my $parsed_seq = "";
foreach my $x (@seq_lines) {
@@ -311,12 +330,12 @@ sub create_xrefs {
# Add xrefs for RefSeq mRNA as well where available
$refseq_pair =~ s/\.[0-9]*// if $refseq_pair;
if (defined $refseq_pair) {
- if ($refseq_ids{$refseq_pair}) {
- foreach my $refseq_id (@{ $refseq_ids{$refseq_pair} }) {
- foreach my $entrez_id (@{ $entrez_ids{$ll} }) {
+ if ($refseq_ids->{$refseq_pair}) {
+ foreach my $refseq_id (@{ $refseq_ids->{$refseq_pair} }) {
+ foreach my $entrez_id (@{ $entrez_ids->{$ll} }) {
$add_dependent_xref_sth->execute($refseq_id, $entrez_id);
}
- foreach my $wiki_id (@{ $wiki_ids{$ll} }) {
+ foreach my $wiki_id (@{ $wiki_ids->{$ll} }) {
$add_dependent_xref_sth->execute($refseq_id, $wiki_id);
}
}
@@ -328,19 +347,8 @@ sub create_xrefs {
# Don't add SGD Xrefs, as they are mapped directly from SGD ftp site
# Refseq's do not tell whether the mim is for the gene of morbid so ignore for now.
-
- push @xrefs, $xref;
-
- }# if defined species
-
- } # while <REFSEQ>
-
- $refseq_io->close();
-
- print "Read " . scalar(@xrefs) ." xrefs from $file\n" if($verbose);
-
- return \@xrefs;
-
+ return $xref;
+ }
}
# --------------------------------------------------------------------------------
diff --git a/misc-scripts/xref_mapping/XrefParser/WormbaseCElegansBase.pm b/misc-scripts/xref_mapping/XrefParser/WormbaseCElegansBase.pm
new file mode 100644
index 0000000000000000000000000000000000000000..53558bddbdae544f6cf7d5247a0b52162a448136
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/WormbaseCElegansBase.pm
@@ -0,0 +1,67 @@
+=head1 LICENSE
+
+Copyright [2018] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+use strict;
+use warnings;
+package XrefParser::WormbaseCElegansBase;
+
+sub swap_dependency {
+ my ($self, $source_ids, $dbi, $xref, @source_ids_skip) = @_;
+ $source_ids = [$source_ids] unless ref $source_ids eq 'ARRAY';
+
+ my @matching_source_id_dependents;
+ my @other_dependents;
+ for my $dependent_xref (@{$xref->{DEPENDENT_XREFS} || []}){
+ my $source_id_here = $dependent_xref->{SOURCE_ID};
+ if(grep {$_ == $source_id_here } @$source_ids
+ and $self->get_xref($dependent_xref->{ACCESSION}, $dependent_xref->{SOURCE_ID}, $xref->{SPECIES_ID})){
+ $dependent_xref->{SPECIES_ID} = $xref->{SPECIES_ID};
+ push @matching_source_id_dependents, $dependent_xref;
+ } elsif (grep {$_ == $source_id_here} @source_ids_skip){
+ #skip
+ } else {
+ push @other_dependents, $dependent_xref;
+ }
+ }
+ my @result;
+ for my $matching_source_id_dependent (@matching_source_id_dependents) {
+ my $source_id = $matching_source_id_dependent->{SOURCE_ID};
+ my $xref_as_dependent_here = {
+ %$xref, INFO_TYPE => "DEPENDENT",
+ LINKAGE_SOURCE_ID => $source_id,
+ DEPENDENT_XREFS => undef,
+ };
+ my @dependents_here = ({
+ %$xref, INFO_TYPE => "DEPENDENT",
+ LINKAGE_SOURCE_ID => $source_id,
+ DEPENDENT_XREFS => undef,
+ });
+ for my $d (@other_dependents){
+ push @dependents_here, {
+ %$d, INFO_TYPE => "DEPENDENT", LINKAGE_SOURCE_ID => $source_id,
+ };
+ }
+ push @result, {
+ %$matching_source_id_dependent,
+ LABEL=>undef, INFO_TYPE => "MISC",
+ DEPENDENT_XREFS =>\@dependents_here,
+ };
+ }
+
+ return @result;
+}
+1;
diff --git a/misc-scripts/xref_mapping/XrefParser/WormbaseCElegansRefSeqGPFFParser.pm b/misc-scripts/xref_mapping/XrefParser/WormbaseCElegansRefSeqGPFFParser.pm
new file mode 100644
index 0000000000000000000000000000000000000000..da456fc3fc6115632e4b9876efcc2a570b59c458
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/WormbaseCElegansRefSeqGPFFParser.pm
@@ -0,0 +1,68 @@
+=head1 LICENSE
+
+Copyright [2018] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+
+package XrefParser::WormbaseCElegansRefSeqGPFFParser;
+use strict;
+use warnings;
+use parent qw/XrefParser::WormbaseCElegansBase XrefParser::RefSeqGPFFParser/;
+my $SOURCE_IDS;
+my $ACCESSION_FROM_ENTRY_PATTERN;
+sub run {
+ my ($self, $arg_ref) = @_;
+ my $type = $self->type_from_file(@{$arg_ref->{files}});
+ if($type eq 'peptide'){
+ $SOURCE_IDS = [ $self->get_source_id_for_source_name('protein_id') ];
+ $ACCESSION_FROM_ENTRY_PATTERN = qr/This record has been curated by WormBase. The\s+reference sequence is identical to (.*?)\./;
+ } elsif ($type eq 'dna'){
+ $SOURCE_IDS = [
+ $self->get_source_id_for_source_name('wormbase_cds'),
+ $self->get_source_id_for_source_name('wormbase_transcript'),
+ ];
+ $ACCESSION_FROM_ENTRY_PATTERN = qr/standard_name="(.*?)"/;
+ }
+ die %$arg_ref unless @$SOURCE_IDS;
+ return $self->SUPER::run($arg_ref);
+}
+sub upload_xref_object_graphs {
+ my ($self, $xrefs, $dbi) = @_;
+ my @adapted_xrefs;
+ for my $xref ( @$xrefs) {
+ push @adapted_xrefs, $self->swap_dependency($SOURCE_IDS, $dbi, $xref, @$SOURCE_IDS);
+ }
+ return $self->SUPER::upload_xref_object_graphs(\@adapted_xrefs, $dbi);
+}
+
+sub xref_from_record {
+ my ($self, $entry, @args) = @_;
+ return &modify_xref_with_dependent(
+ $SOURCE_IDS, $entry,
+ $self->SUPER::xref_from_record($entry, @args),
+ $ACCESSION_FROM_ENTRY_PATTERN,
+ );
+}
+
+sub modify_xref_with_dependent {
+ my ($source_ids, $entry, $xref, $get_accession_pattern) = @_;
+ return unless $xref;
+ my ($accession) = $entry =~ $get_accession_pattern;
+ return unless $accession;
+ $xref->{DEPENDENT_XREFS} //= [];
+ push @{$xref->{DEPENDENT_XREFS}}, map {{ACCESSION => $accession, SOURCE_ID=>$_}} @$source_ids;
+ return $xref;
+}
+1;
diff --git a/misc-scripts/xref_mapping/XrefParser/WormbaseCElegansUniProtParser.pm b/misc-scripts/xref_mapping/XrefParser/WormbaseCElegansUniProtParser.pm
new file mode 100644
index 0000000000000000000000000000000000000000..68b2c7e45b4109104466d81d250a7236836538d0
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/WormbaseCElegansUniProtParser.pm
@@ -0,0 +1,44 @@
+=head1 LICENSE
+
+Copyright [2018] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+use strict;
+use warnings;
+package XrefParser::WormbaseCElegansUniProtParser;
+
+# UniProt xrefs are sometimes - really - dependent xrefs of
+# INSDC entries which we get from somewhere else
+# Attempt to find the parent (has to already be present in the xref table)
+# INSDC and UniProt entries have the same protein sequence, and
+# UniProt lists INSDC as a parent. We get INSDC entries from somewhere else,
+# so make UniProt entries dependent on INSDC entries.
+# Note:
+# INSDC entries have coordinates, and UniProt entries don't.
+# So for perfect homologs, there can be many INSDC entries per UniProt.
+
+use parent qw/XrefParser::WormbaseCElegansBase XrefParser::UniProtParser/;
+
+sub upload_xref_object_graphs {
+ my ($self, $xrefs, $dbi) = @_;
+ my $source_id = $self->get_source_id_for_source_name('protein_id');
+ my $source_id_skip = $self->get_source_id_for_source_name('EMBL');
+ my @adapted_xrefs;
+ for my $xref ( @$xrefs) {
+ push @adapted_xrefs, $self->swap_dependency($source_id, $dbi, $xref, $source_id_skip);
+ }
+ return $self->SUPER::upload_xref_object_graphs(\@adapted_xrefs, $dbi);
+}
+1;
diff --git a/misc-scripts/xref_mapping/XrefParser/WormbaseDirectParser.pm b/misc-scripts/xref_mapping/XrefParser/WormbaseDirectParser.pm
index 0d570d862f638facab43264116f0f2fa0bdc0817..7b5e1d88ed1ebb80141d73727a543448a6ad5a7f 100644
--- a/misc-scripts/xref_mapping/XrefParser/WormbaseDirectParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WormbaseDirectParser.pm
@@ -28,151 +28,96 @@ use XrefParser::BaseParser;
use base qw( XrefParser::BaseParser );
-
sub run {
my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $files = $ref_arg->{files};
- my $verbose = $ref_arg->{verbose};
if((!defined $source_id) or (!defined $species_id) or (!defined $files)){
croak "Need to pass source_id, species_id and files as pairs";
}
- $verbose |=0;
my $file = @{$files}[0];
-
- my $wormbasegene_src_id = $self->get_source_id_for_source_name('wormbase_gene');
- my $wormbasegseq_src_id = $self->get_source_id_for_source_name('wormbase_gseqname');
- my $wormbaselocus_src_id = $self->get_source_id_for_source_name('wormbase_locus');
- my $wormbasetran_src_id = $self->get_source_id_for_source_name('wormbase_transcript');
- my $wormpep_src_id = $self->get_source_id_for_source_name('wormpep_id');
-
- my $xref_wgene_sth = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=$wormbasegene_src_id AND species_id=$species_id");
- my $xref_gseq_sth = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=$wormbasegseq_src_id AND species_id=$species_id");
- my $xref_wloc_sth = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=$wormbaselocus_src_id AND species_id=$species_id");
- my $xref_wtran_sth = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=$wormbasetran_src_id AND species_id=$species_id");
- my $xref_wpep_sth = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=$wormpep_src_id AND species_id=$species_id");
-
- my $pep_io = $self->get_filehandle($file);
-
- if ( !defined $pep_io ) {
- print STDERR "ERROR: Could not open $file\n";
- return 1; # 1 error
+ my @fields = qw/wormbase_gene wormbase_gseqname wormbase_locus wormbase_transcript wormbase_cds wormpep_id protein_id/;
+ my %src_ids;
+ my $sth = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=? AND species_id=$species_id");
+ for my $field (@fields){
+ $src_ids{$field} = $self->get_source_id_for_source_name($field);
}
+ my $data = $self->get_data(@$files);
+ for my $gene_id (keys %$data){
+ $self->add_xref_and_direct_xref(
+ $sth, $species_id, "gene", $src_ids{wormbase_gene},
+ $gene_id, $gene_id
+ );
+ $self->add_xref_and_direct_xref(
+ $sth, $species_id, "gene", $src_ids{wormbase_gseqname},
+ $gene_id, $data->{$gene_id}->{wormbase_gseqname}
+ );
+ $self->add_xref_and_direct_xref(
+ $sth, $species_id, "gene", $src_ids{wormbase_locus},
+ $gene_id, $data->{$gene_id}->{wormbase_locus}
+ );
+ for my $transcript (@{$data->{$gene_id}->{transcripts}}){
+ $self->add_xref_and_direct_xref(
+ $sth, $species_id, "transcript", $src_ids{wormbase_transcript},
+ $transcript->{transcript_id}, $transcript->{transcript_id}
+ );
+ $self->add_xref_and_direct_xref(
+ $sth, $species_id, "transcript", $src_ids{wormbase_cds},
+ $transcript->{wormbase_cds}, $transcript->{wormbase_cds}, $transcript->{transcript_id}
+ );
+ $self->add_xref_and_direct_xref(
+ $sth, $species_id, "translation", $src_ids{wormpep_id},
+ $transcript->{wormpep_id}, $transcript->{wormpep_id}, $transcript->{transcript_id}
+ );
+ $self->add_xref_and_direct_xref(
+ $sth, $species_id, "translation", $src_ids{protein_id},
+ $transcript->{protein_id}, $transcript->{protein_id}, $transcript->{transcript_id}
+ );
+ }
+ }
+}
+sub get_data {
+ my ($self, $file) = @_;
+ my $pep_io = $self->get_filehandle($file) or croak "Could not open: $file";
- my ($x_count, $d_count);
-
- my (%wbgene2seqid, %wbgene2loc, %tran2wbtran, %tran2wpep);
+ my $data = {};
while ( $_ = $pep_io->getline() ) {
next if /^\/\//;
-
- my ($gseqid, $wbgeneid, $locus, $wbtranscript, $wormpep) = split(/\t/, $_);
-
- # Each WBGeneid should have only one sequence name and (optionally) one locus name
- $wbgene2seqid{$wbgeneid} = $gseqid;
- $wbgene2loc{$wbgeneid} = $locus if $locus ne '.';
-
- $tran2wbtran{$wbtranscript} = 1;
- $tran2wpep{$wbtranscript} = $wormpep if $wormpep ne '.';
-
+ my ($gseqid, $wbgeneid, $locus, $wbtranscript, $wormpep, $insdc_parent, $insdc_locus_tag, $protein_id, $uniprot_id) = split(/\t/, $_);
+
+ $data->{$wbgeneid}->{transcripts} //=[];
+ push @{$data->{$wbgeneid}->{transcripts}}, {
+ transcript_id => $wbtranscript,
+ ($wormpep ne '.' && $wbtranscript =~ /^(.*?)(\.\d+)?$/ ? (wormbase_cds => $1 ) : ()),
+ ($wormpep ne '.' ? (wormpep_id => $wormpep) : ()),
+ ($protein_id ne '.' ? (protein_id => $protein_id) : ()),
+ };
+ $data->{$wbgeneid}->{wormbase_gseqname} = $gseqid;
+ $data->{$wbgeneid}->{wormbase_locus} = $locus if $locus ne '.';
}
$pep_io->close();
-
- foreach my $wbgid (keys %wbgene2seqid) {
- # reuse or create xref
- $xref_wgene_sth->execute($wbgid);
- my $xref_id = ($xref_wgene_sth->fetchrow_array())[0];
- if (!$xref_id) {
- $xref_id = $self->add_xref({ acc => $wbgid,
- label => $wbgid,
- source_id => $wormbasegene_src_id,
- species_id => $species_id,
- info_type => "DIRECT"} );
- $x_count++;
- }
- $self->add_direct_xref($xref_id, $wbgid, "gene", "");
- $d_count++;
-
- my $gseqname = $wbgene2seqid{$wbgid};
-
- $xref_gseq_sth->execute($wbgid);
- $xref_id = ($xref_gseq_sth->fetchrow_array())[0];
- if (not $xref_id) {
- $xref_id = $self->add_xref({ acc => $wbgid,
- label => $gseqname,
- source_id => $wormbasegseq_src_id,
- species_id => $species_id,
- info_type => "DIRECT"} );
- $x_count++;
- }
- $self->add_direct_xref($xref_id, $wbgid, "gene", "");
- $d_count++;
-
-
- if (exists $wbgene2loc{$wbgid}) {
- my $loc_sym = $wbgene2loc{$wbgid};
-
- $xref_wloc_sth->execute($wbgid);
- $xref_id = ($xref_wloc_sth->fetchrow_array())[0];
- if (!$xref_id) {
- $xref_id = $self->add_xref({ acc => $wbgid,
- label => $loc_sym,
- source_id => $wormbaselocus_src_id,
- species_id => $species_id,
- info_type => "DIRECT"} );
- $x_count++;
- }
- }
-
- # and direct xref
- $self->add_direct_xref($xref_id, $wbgid, "gene", "");
- $d_count++;
- }
-
-
- foreach my $tid (keys %tran2wbtran) {
- $xref_wtran_sth->execute($tid);
- my $xref_id = ($xref_wtran_sth->fetchrow_array())[0];
- if (!$xref_id) {
- $xref_id = $self->add_xref({ acc => $tid,
- label => $tid,
- source_id => $wormbasetran_src_id,
- species_id => $species_id,
- info_type => "DIRECT"} );
- $x_count++;
- }
-
- # and direct xref
- $self->add_direct_xref($xref_id, $tid, "transcript", "");
- $d_count++;
- }
-
- foreach my $tid (keys %tran2wpep) {
- my $wpep = $tran2wpep{$tid};
-
- $xref_wpep_sth->execute($wpep);
-
- my $xref_id = ($xref_wpep_sth->fetchrow_array())[0];
- if (!$xref_id) {
- $xref_id = $self->add_xref({ acc => $wpep,
- label => $wpep,
- source_id => $wormpep_src_id,
- species_id => $species_id,
- info_type => "DIRECT"} );
- $x_count++;
- }
-
- # and direct xref
- $self->add_direct_xref($xref_id, $tid, "translation", "");
- $d_count++;
- }
-
- print "Added $d_count direct xrefs and $x_count xrefs\n" if($verbose);
- return 0;
+ return $data;
}
+sub add_xref_and_direct_xref {
+ my ($self, $sth, $species_id, $object_type, $source_id, $object_id, $label, $primary_id) = @_;
+ $primary_id //= $object_id;
+ return unless $label;
+ $sth->execute($primary_id, $source_id);
+ $self->add_direct_xref(
+ ($sth->fetchrow_array())[0]
+ || $self->add_xref({
+ acc => $object_id,
+ label => $label,
+ source_id => $source_id,
+ species_id => $species_id,
+ info_type => "DIRECT"
+ })
+ , $primary_id, $object_type, "");
+}
1;
diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini
index 69889a109487bb49b4fcd8204f121f1878ba6c5c..fe7c917c79d9953d6d4630ed68ac13435511716b 100644
--- a/misc-scripts/xref_mapping/xref_config.ini
+++ b/misc-scripts/xref_mapping/xref_config.ini
@@ -1652,6 +1652,14 @@ order = 50
priority = 1
parser = comes from WormbaseDirectParser
+[source wormbase_cds::wormbase]
+# Used by wormbase core species
+name = wormbase_cds
+download = N
+order = 50
+priority = 1
+parser = comes from WormbaseDirectParser
+
[source Gramene_Pathway::arabidopsis_thaliana]
# Used by Arabidopsis thaliana, Gramene-specific
name = Gramene_Pathway
diff --git a/modules/t/xref_parser.t b/modules/t/xref_parser.t
index 2c77b54ea78293c4083a393f618bd1af2df086fb..03f16c15bb263d87e35f3ebc97112b94fa5f4a9a 100644
--- a/modules/t/xref_parser.t
+++ b/modules/t/xref_parser.t
@@ -55,32 +55,37 @@ my %xref_tables_expected_empty_by_default = (
);
my $tmp_dir = tempdir(CLEANUP=>1);
sub store_in_temporary_file {
- my $path = "$tmp_dir/tmp";
+ my ($content, %opts) = @_;
+ my $path = join("/", $tmp_dir, $opts{tmp_file_name} || "tmp");
open(my $fh, ">", $path) or die $path;
- print $fh @_;
+ print $fh $content;
close($fh);
return $path;
}
+# Happens to match the species id of the core database
+my $SPECIES_ID = 1;
+my $SPECIES_NAME = "Homo sapiens";
sub test_parser {
- my ($parser, $content, $source_id, $expected, $test_name) = @_;
+ my ($parser, $content, $expected, $test_name, %opts) = @_;
require_ok($parser);
$parser->new($database)->run({
- files => [store_in_temporary_file($content)],
- source_id => $source_id,
- species_id => 1 #Happens to be right, but doesn't matter anyway - we are not testing the mapping
+ files =>[store_in_temporary_file($content, %opts)],
+ source_id => "Source id (unused but sometimes required)",
+ species_id => $SPECIES_ID,
+ species => $SPECIES_NAME,
});
my $expected_table_counts = {%xref_tables_expected_empty_by_default, %$expected};
subtest "$parser $test_name" => sub {
plan tests => scalar(keys %$expected_table_counts);
for my $table (keys %$expected_table_counts){
my $actual_count = count_rows($dba, $table);
- $dba->dbc->prepare("delete from $table;")->execute() if $actual_count;
+ $dba->dbc->prepare("delete from $table;")->execute() if ($actual_count and not $opts{skip_clean});
my $expected_count = $expected_table_counts->{$table};
is($actual_count, $expected_count, "$table has $expected_count rows") or diag "$table has $actual_count rows";
}
}
}
-test_parser("XrefParser::WormbaseDirectParser", "", "source_id (unused)", {}, "null case");
+test_parser("XrefParser::WormbaseDirectParser", "", {}, "null case");
my $wormbase_celegans_xrefs_head= <<EOF;
//
// WormBase Caenorhabditis elegans XREFs for WS265
@@ -99,14 +104,264 @@ my $wormbase_celegans_xrefs_head= <<EOF;
// Missing or not applicable data (e.g. protein identifiers for non-coding RNAs) is denoted by a "."
//
2L52.1 WBGene00007063 . 2L52.1b CE50569 BX284602 CELE_2L52.1 CTQ86426 A0A0K3AWR5
-2L52.1 WBGene00007063 . 2L52.1a CE32090 BX284602 CELE_2L52.1 CCD61130 A4F336
+2L52.1 WBGene00007063 . 2L52.1a.1 CE32090 BX284602 CELE_2L52.1 CCD61130 A4F336
+2L52.1 WBGene00007063 . 2L52.1a.2 CE32090 BX284602 CELE_2L52.1 CCD61130 A4F336
2L52.2 WBGene00200402 . 2L52.2 . BX284602 CELE_2L52.2 . .
EOF
-test_parser("XrefParser::WormbaseDirectParser", $wormbase_celegans_xrefs_head, "source_id (unused)", {
-xref=>9,
-gene_direct_xref => 6,
-transcript_direct_xref => 3,
-translation_direct_xref => 2,
-}, "Direct xrefs: genes: count currently off due to some questionable duplicates, transcripts: as in column 4, translations: as in column 5. At least one direct xref per xref (but should be one to one)");
+my $wormbase_celegans_xrefs_expected_count = {
+xref=>14,
+gene_direct_xref => 4,
+transcript_direct_xref => 7,
+translation_direct_xref => 6,
+};
+test_parser("XrefParser::WormbaseDirectParser", $wormbase_celegans_xrefs_head,
+ $wormbase_celegans_xrefs_expected_count, "Direct xrefs: genes: columns 1,2,3, transcripts: column 4 once as transcript and also once as CDS for coding genes, translations: column 5 and 7. xrefs: sum of these minus one reused CDS and two reused proteins"
+);
+
+my $uniprot_elegans_record = <<EOF;
+ID A0A0K3AWR5_CAEEL Unreviewed; 220 AA.
+AC A0A0K3AWR5;
+DT 11-NOV-2015, integrated into UniProtKB/TrEMBL.
+DT 11-NOV-2015, sequence version 1.
+DT 18-JUL-2018, entry version 14.
+DE SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:CTQ86426.1};
+GN ORFNames=2L52.1 {ECO:0000313|EMBL:CTQ86426.1,
+GN ECO:0000313|WormBase:2L52.1b},
+GN CELE_2L52.1 {ECO:0000313|EMBL:CTQ86426.1};
+OS $SPECIES_NAME.
+OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
+OC Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
+OX NCBI_TaxID=$SPECIES_ID {ECO:0000313|EMBL:CTQ86426.1, ECO:0000313|Proteomes:UP000001940};
+RN [1] {ECO:0000313|EMBL:CTQ86426.1, ECO:0000313|Proteomes:UP000001940}
+RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
+RC STRAIN=Bristol N2 {ECO:0000313|EMBL:CTQ86426.1,
+RC ECO:0000313|Proteomes:UP000001940};
+RX PubMed=9851916; DOI=https://doi.org/10.1126/science.282.5396.2012;
+RG The C. elegans sequencing consortium;
+RA Sulson J.E., Waterston R.;
+RT "Genome sequence of the nematode C. elegans: a platform for
+RT investigating biology.";
+RL Science 282:2012-2018(1998).
+CC -----------------------------------------------------------------------
+CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
+CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
+CC -----------------------------------------------------------------------
+DR EMBL; BX284602; CTQ86426.1; -; Genomic_DNA.
+DR RefSeq; NP_001300487.1; NM_001313558.1.
+DR UniGene; Cel.25279; -.
+DR EnsemblMetazoa; 2L52.1b; 2L52.1b; WBGene00007063.
+DR GeneID; 181792; -.
+DR CTD; 181792; -.
+DR WormBase; 2L52.1b; CE50569; WBGene00007063; -.
+DR Proteomes; UP000001940; Chromosome II.
+DR ExpressionAtlas; A0A0K3AWR5; baseline and differential.
+PE 4: Predicted;
+KW Complete proteome {ECO:0000313|Proteomes:UP000001940};
+KW Reference proteome {ECO:0000313|Proteomes:UP000001940}.
+SQ SEQUENCE 220 AA; 26028 MW; E12D5EA7F6FFF373 CRC64;
+ MSDNEEVYVN FRGMNCISTG KSASMVPSKR RNWPKRVKKR LSTQRNNQKT IRPPELNKNN
+ IEIKDMNSNN LEERNREECI QPVSVEKNIL HFEKFKSNQI CIVRENNKFR EGTRRRRKNS
+ GESEDLKIHE NFTEKRRPIR SCKQNISFYE MDGDIEEFEV FFDTPTKSKK VLLDIYSAKK
+ MPKIEVEDSL VNKFHSKRPS RACRVLGSME EVPFDVEIGY
+//
+EOF
+test_parser("XrefParser::UniProtParser", $uniprot_elegans_record, {
+ xref => 3,
+ primary_xref => 1,
+ dependent_xref => 2,
+},"Example UniProt record");
+(my $uniprot_elegans_record_embl = $uniprot_elegans_record) =~ s/DR EMBL;.*?\n//;
+test_parser("XrefParser::UniProtParser", $uniprot_elegans_record_embl, {
+ xref => 1,
+ primary_xref => 1,
+},"EMBL entries are the dependent xrefs");
+my @recognised_sources = (
+ "PDB; 3HRI; X-ray; 2.85 A; A/B/C/D/E/F=44-477.",
+ "MEROPS; C26.956; -.",
+);
+for my $l (@recognised_sources) {
+ (my $uniprot_elegans_record_extra_line = $uniprot_elegans_record) =~ s/DR(.*?)\n/DR$1\nDR $l/;
+ test_parser("XrefParser::UniProtParser", $uniprot_elegans_record_extra_line, {
+ xref => 4,
+ primary_xref => 1,
+ dependent_xref => 3,
+ }, "Pick up as extra xref + dependent xref: $l" );
+}
+sub test_elegans_uniprot {
+ my ($expected_count, $extra_line) = @_;
+ my $uniprot_elegans_record_here = $uniprot_elegans_record;
+ $uniprot_elegans_record_here =~ s/DR(.*?)\n/DR$1\nDR $extra_line/ if $extra_line;
+ test_parser("XrefParser::WormbaseCElegansUniProtParser",
+ $uniprot_elegans_record_here,
+ {},
+ "No UniProt entries without corresponding INSDC entries $extra_line"
+ );
+ test_parser("XrefParser::WormbaseDirectParser",
+ $wormbase_celegans_xrefs_head,
+ $wormbase_celegans_xrefs_expected_count,
+ "Test again to set up the next test",
+ skip_clean => 1,
+ );
+ test_parser("XrefParser::WormbaseCElegansUniProtParser",
+ $uniprot_elegans_record_here,
+ $expected_count,
+ "Correct xrefs and dependent xrefs $extra_line",
+ );
+}
+my $wormbase_and_uniprot_expected_count = {
+ %$wormbase_celegans_xrefs_expected_count,
+ xref => $wormbase_celegans_xrefs_expected_count->{xref}+1,
+ dependent_xref => 1 #protein id still there, no parent sequence ID
+};
+test_elegans_uniprot($wormbase_and_uniprot_expected_count, "");
+for my $l (@recognised_sources) {
+ test_elegans_uniprot({
+ %$wormbase_and_uniprot_expected_count,
+ xref => $wormbase_and_uniprot_expected_count->{xref}+1,
+ dependent_xref => $wormbase_and_uniprot_expected_count->{dependent_xref}+1,
+ },$l);
+}
+test_elegans_uniprot({
+ %$wormbase_and_uniprot_expected_count,
+ dependent_xref => $wormbase_and_uniprot_expected_count->{dependent_xref}+1,
+ }, "EMBL; BX284602; CCD61130.1; -; Genomic_DNA",
+);
+
+my $refseq_protein_elegans_record = <<EOF;
+LOCUS NP_493629 427 aa linear INV 19-AUG-2018
+DEFINITION Uncharacterized protein CELE_2L52.1 [Caenorhabditis elegans].
+ACCESSION NP_493629
+VERSION NP_493629.2
+DBLINK BioProject: PRJNA158
+ BioSample: SAMEA3138177
+DBSOURCE REFSEQ: accession NM_061228.2
+KEYWORDS RefSeq.
+SOURCE Caenorhabditis elegans
+ ORGANISM Caenorhabditis elegans
+ Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
+ Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
+REFERENCE
+ <snipped>
+COMMENT REVIEWED REFSEQ: This record has been curated by WormBase. The
+ reference sequence is identical to CCD61130.
+FEATURES Location/Qualifiers
+ source 1..427
+ /organism="Caenorhabditis elegans"
+ /strain="Bristol N2"
+ /db_xref="taxon:$SPECIES_ID"
+ /chromosome="II"
+ Protein 1..427
+ /product="hypothetical protein"
+ /calculated_mol_wt=49887
+ CDS 1..427
+ /gene="2L52.1"
+ /locus_tag="CELE_2L52.1"
+ /standard_name="2L52.1a"
+ /coded_by="NM_061228.2:1..1284"
+ /note="Confirmed by transcript evidence"
+ /db_xref="EnsemblGenomes-Gn:WBGene00007063"
+ /db_xref="EnsemblGenomes-Tr:2L52.1a"
+ /db_xref="GeneID:181792"
+ /db_xref="GOA:A4F336"
+ /db_xref="InterPro:IPR013087"
+ /db_xref="UniProtKB/TrEMBL:A4F336"
+ /db_xref="WormBase:WBGene00007063"
+ORIGIN
+ 1 msmvrnvsnq sekleilsck wvgclkstev fktveklldh vtadhipevi vnddgseevv
+ 61 cqwdccemga srgnlqkkke wmenhfktrh vrkakifkcl iedcpvvkss sqeiethlri
+ 121 shpinpkker lkefksstdh ieptqanrvw tivngevqwk tpprvkkktv iyyddgpryv
+ 181 fptgcarcny dsdeselesd efwsatemsd neevyvnfrg mncistgksa smvpskrrnw
+ 241 pkrvkkrlst qrnnqktirp pelnknniei kdmnsnnlee rnreeciqpv sveknilhfe
+ 301 kfksnqiciv rennkfregt rrrrknsges edlkihenft ekrrpirsck qnisfyemdg
+ 361 dieefevffd tptkskkvll diysakkmpk ievedslvnk fhskrpsrac rvlgsmeevp
+ 421 fdveigy
+//
+EOF
+
+my $refseq_mrna_elegans_record = <<EOF;
+LOCUS NM_001313558 663 bp mRNA linear INV 19-AUG-2018
+DEFINITION Caenorhabditis elegans Uncharacterized protein (2L52.1), partial
+ mRNA.
+ACCESSION NM_001313558
+VERSION NM_001313558.1
+DBLINK BioProject: PRJNA158
+ BioSample: SAMEA3138177
+KEYWORDS RefSeq.
+SOURCE Caenorhabditis elegans
+ ORGANISM Caenorhabditis elegans
+ Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
+ Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
+REFERENCE 1 (bases 1 to 663)
+ <snipped>
+COMMENT REVIEWED REFSEQ: This record has been curated by WormBase. This
+ record is derived from an annotated genomic sequence (NC_003280).
+ COMPLETENESS: incomplete on both ends.
+FEATURES Location/Qualifiers
+ source 1..663
+ /organism="Caenorhabditis elegans"
+ /mol_type="mRNA"
+ /strain="Bristol N2"
+ /db_xref="taxon:$SPECIES_ID"
+ /chromosome="II"
+ gene <1..>663
+ /gene="2L52.1"
+ /locus_tag="CELE_2L52.1"
+ /db_xref="GeneID:181792"
+ /db_xref="WormBase:WBGene00007063"
+ CDS 1..663
+ /gene="2L52.1"
+ /locus_tag="CELE_2L52.1"
+ /standard_name="2L52.1a"
+ /note="Confirmed by transcript evidence"
+ /codon_start=1
+ /product="hypothetical protein"
+ /protein_id="NP_001300487.1"
+ /db_xref="EnsemblGenomes-Gn:WBGene00007063"
+ /db_xref="EnsemblGenomes-Tr:2L52.1b"
+ /db_xref="GeneID:181792"
+ /db_xref="UniProtKB/TrEMBL:A0A0K3AWR5"
+ /db_xref="WormBase:WBGene00007063"
+ /translation="MSDNEEVYVNFRGMNCISTGKSASMVPSKRRNWPKRVKKRLSTQ
+ RNNQKTIRPPELNKNNIEIKDMNSNNLEERNREECIQPVSVEKNILHFEKFKSNQICI
+ VRENNKFREGTRRRRKNSGESEDLKIHENFTEKRRPIRSCKQNISFYEMDGDIEEFEV
+ FFDTPTKSKKVLLDIYSAKKMPKIEVEDSLVNKFHSKRPSRACRVLGSMEEVPFDVEI
+ GY"
+ORIGIN
+ 1 atgtcagata atgaagaagt atatgtgaac ttccgtggaa tgaactgtat ctcaacagga
+ 61 aagtcggcca gtatggtccc gagcaaacga agaaattggc caaaaagagt gaagaaaagg
+ 121 ctatcgacac aaagaaacaa tcagaaaact attcgaccac cagagctgaa taaaaataat
+ 181 atagagataa aagatatgaa ctcaaataac cttgaagaac gcaacagaga agaatgcatt
+ 241 cagcctgttt ctgttgaaaa gaacatcctg cattttgaaa aattcaaatc aaatcaaatt
+ 301 tgcattgttc gggaaaacaa taaatttaga gaaggaacga gaagacgcag aaagaattct
+ 361 ggtgaatcgg aagacttgaa aattcatgaa aactttactg aaaaacgaag acccattcga
+ 421 tcatgcaaac aaaatataag tttctatgaa atggacgggg atatagaaga atttgaagtg
+ 481 tttttcgata ctcccacaaa aagcaaaaaa gtacttctgg atatctacag tgcgaagaaa
+ 541 atgccaaaaa ttgaggttga agattcatta gttaataagt ttcattcaaa acgtccatca
+ 601 agagcatgtc gagttcttgg aagtatggaa gaagtaccat ttgatgtgga aataggatat
+ 661 tga
+//
+EOF
+sub test_refseq {
+ my ($record, $type) = @_;
+ my $file = "something_that_says_$type";
+ test_parser("XrefParser::RefSeqGPFFParser",$record, {
+ xref =>1,
+ primary_xref => 1,
+ }, "$type: Example record" , tmp_file_name => $file);
+ test_parser("XrefParser::WormbaseCElegansRefSeqGPFFParser",$record, {
+ }, "$type no entries without WormBase records" , tmp_file_name => $file);
+
+ test_parser("XrefParser::WormbaseDirectParser", $wormbase_celegans_xrefs_head,
+ $wormbase_celegans_xrefs_expected_count, "$type test again to set up the next test",
+ skip_clean => 1);
+ test_parser("XrefParser::WormbaseCElegansRefSeqGPFFParser",$record, {
+ %$wormbase_celegans_xrefs_expected_count,
+ xref => $wormbase_celegans_xrefs_expected_count->{xref}+1,
+ dependent_xref => 1,
+ }, "$type RefSeq entries hang off INSDC entries", tmp_file_name => $file);
+}
+test_refseq($refseq_protein_elegans_record, "protein");
+test_refseq($refseq_mrna_elegans_record, "mrna");
done_testing();
+