From 34ba09a898ec9ea7eb66adc37ea51a68cf3c2017 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Mon, 13 Dec 2004 10:42:19 +0000
Subject: [PATCH] Renamed run_matching to build_list_and_map.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 36 ++++++++++---------
misc-scripts/xref_mapping/xref_mapper.pl | 2 +-
2 files changed, 20 insertions(+), 18 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 357f2ef0b9..743c8ebb66 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -55,7 +55,7 @@ sub dump_seqs{
-=head2 run_matching
+=head2 build_list_and_map
Arg[1]: xref object which holds info on method and files.
@@ -66,7 +66,8 @@ sub dump_seqs{
=cut
-sub run_matching{
+sub build_list_and_map {
+
my ($self) = @_;
my @list=();
@@ -685,6 +686,7 @@ sub store {
my ($self, $xref) = @_;
# get current max object_xref_id
+ # TODO use selectall_arrayref
my $max_object_xref_id = 0;
my $sth = $self->dbi()->prepare("SELECT MAX(object_xref_id) FROM object_xref");
$sth->execute();
@@ -742,7 +744,7 @@ sub store {
open(FILE, $file);
$total_files++;
- # files are named Method_(dna|prot)_N.map
+ # files are named Method_(dna|peptide)_N.map
my $type = get_ensembl_object_type($file);
# get or create the appropriate analysis ID
@@ -918,13 +920,13 @@ sub dump_core_xrefs {
my $xref_sth = $xref_dbi->prepare($sql);
$xref_sth->execute();
- my ($xref_id, $accession, $version, $label, $description, $source_id, $species_id);
+ my ($xref_id, $accession, $version, $label, $description, $source_id, $species_id, $master_xref_id);
$xref_sth->bind_columns(\$xref_id, \$accession, \$version, \$label, \$description, \$source_id, \$species_id);
# note the xref_id we write to the file is NOT the one we've just read
# from the internal xref database as the ID may already exist in the core database
# so we add on $xref_id_offset
- while (my @row = $xref_sth->fetchrow_array()) {
+ while ($xref_sth->fetch()) {
print XREF ($xref_id+$xref_id_offset) . "\t" . $accession . "\t" . $label . "\t" . $description . "\n";
$source_ids{$source_id} = $source_id;
@@ -932,23 +934,23 @@ sub dump_core_xrefs {
}
# Now get the dependent xrefs for each of these xrefs and write them as well
- $sql = "SELECT DISTINCT(x.xref_id), x.accession, x.label, x.description, x.source_id FROM dependent_xref dx, xref x WHERE x.xref_id=dx.dependent_xref_id AND master_xref_id $id_str";
+ $sql = "SELECT DISTINCT(x.xref_id), dx.master_xref_id, x.accession, x.label, x.description, x.source_id FROM dependent_xref dx, xref x WHERE x.xref_id=dx.dependent_xref_id AND master_xref_id $id_str";
my $dep_sth = $xref_dbi->prepare($sql);
$dep_sth->execute();
- $dep_sth->bind_columns(\$xref_id, \$accession, \$label, \$description, \$source_id);
- while (my @row = $dep_sth->fetchrow_array()) {
+ $dep_sth->bind_columns(\$xref_id, \$master_xref_id, \$accession, \$label, \$description, \$source_id);
+ while ($dep_sth->fetch()) {
print XREF ($xref_id+$xref_id_offset) . "\t" . $accession . "\t" . $label . "\t" . $description . "\tDEPENDENT\n";
$source_ids{$source_id} = $source_id;
# create an object_xref linking this (dependent) xref with any objects it maps to
# write to file and add to object_xref_mappings
- if (defined $xref_to_objects{$xref_id+$xref_id_offset}) {
- my @objects = keys( %{$xref_to_objects{$xref_id+$xref_id_offset}} );
- print "xref $accession has " . scalar(@objects) . " associated ensembl objects\n";
- foreach my $object_id (@objects) {
+ if (defined $xref_to_objects{$master_xref_id}) { # XXX check
+ my @ensembl_object_ids = keys( %{$xref_to_objects{$master_xref_id}} ); # XXX check
+ print "xref $accession has " . scalar(@ensembl_object_ids) . " associated ensembl objects\n";
+ foreach my $object_id (@ensembl_object_ids) {
my $type = $ensembl_object_types{$object_id};
print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t" . ($xref_id+$xref_id_offset) . "\tDEPENDENT\n";
$object_xref_id++;
@@ -966,7 +968,7 @@ sub dump_core_xrefs {
$syn_sth->execute();
$syn_sth->bind_columns(\$xref_id, \$accession);
- while (my @row = $syn_sth->fetchrow_array()) {
+ while ($syn_sth->fetch()) {
print EXTERNAL_SYNONYM ($xref_id+$xref_id_offset) . "\t" . $accession . "\n";
@@ -1014,7 +1016,7 @@ sub dump_core_xrefs {
my ($source_name, $release, $source_id);
$source_sth->bind_columns(\$source_name, \$release, \$source_id);
- while (my @row = $source_sth->fetchrow_array()) {
+ while ($source_sth->fetch()) {
print EXTERNAL_DB "$edb_id\t$source_name\t$release\tXREF\n";
# TODO knownxref etc??
$edb_id++;
@@ -1083,7 +1085,7 @@ sub build_transcript_display_xrefs {
my ($xref_id, $source_name);
$sth->bind_columns(\$xref_id, \$source_name);
- while (my @row = $sth->fetchrow_array()) {
+ while ($sth->fetch()) {
$xref_to_source{$xref_id} = $source_name;
}
@@ -1098,7 +1100,7 @@ sub build_transcript_display_xrefs {
my ($translation_id, $transcript_id);
$sth->bind_columns(\$translation_id, \$transcript_id);
- while (my @row = $sth->fetchrow_array()) {
+ while ($sth->fetch()) {
$translation_to_transcript{$translation_id} = $transcript_id;
}
@@ -1196,7 +1198,7 @@ sub build_gene_display_xrefs {
$sth->bind_columns(\$gene_id, \$transcript_id);
my %genes_to_transcripts;
- while (my @row = $sth->fetchrow_array()) {
+ while ($sth->fetch()) {
push @{$genes_to_transcripts{$gene_id}}, $transcript_id;
}
diff --git a/misc-scripts/xref_mapping/xref_mapper.pl b/misc-scripts/xref_mapping/xref_mapper.pl
index 748770867d..51ad27563c 100644
--- a/misc-scripts/xref_mapping/xref_mapper.pl
+++ b/misc-scripts/xref_mapping/xref_mapper.pl
@@ -100,7 +100,7 @@ if(defined($species)){
for my $species ( @all_species ) {
$species->xref($xref); # attach xref object to species object
$species->dump_seqs();
- $species->run_matching();
+ $species->build_list_and_map();
$species->store();
}
--
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