From 1ac3b437eb68a37c97bdf23d012c1055942b0c1c Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Thu, 16 Dec 2004 11:02:30 +0000
Subject: [PATCH] Fixed calculation of transcript display_xrefs; wasn't
considering translation-transcript relationship properly.
Now use | as separator character in composite hash keys; : was a bad choice since it appears in GO xrefs.
Don't write xref/object_xrefs for sources that have no corresponding external_db entry (but warn about this).
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 147 ++++++++++++------
1 file changed, 96 insertions(+), 51 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 49e70d3e51..4731268a01 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -791,7 +791,7 @@ sub parse_mappings {
$ensembl_object_types{$target_id} = $type;
# store mapping for later - note NON-OFFSET xref_id is used
- my $key = $type . ":" . $target_id;
+ my $key = $type . "|" . $target_id;
my $xref_id = $query_id;
push @{$object_xref_mappings{$key}}, $xref_id;
@@ -965,9 +965,11 @@ sub dump_core_xrefs {
if (!$xrefs_written{$xref_id}) {
my $external_db_id = $source_to_external_db{$source_id};
- print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
- $xrefs_written{$xref_id} = 1;
- $source_ids{$source_id} = $source_id;
+ if ($external_db_id) { # skip "unknown" sources
+ print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
+ $xrefs_written{$xref_id} = 1;
+ $source_ids{$source_id} = $source_id;
+ }
}
}
@@ -981,6 +983,8 @@ sub dump_core_xrefs {
while ($dep_sth->fetch()) {
my $external_db_id = $source_to_external_db{$source_id};
+ next if (!$external_db_id);
+
$label = $accession if (!$label);
if (!$xrefs_written{$xref_id}) {
@@ -991,17 +995,17 @@ sub dump_core_xrefs {
# 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 $xref_to_objects{$master_xref_id}) { # XXX check
- my @ensembl_object_ids = keys( %{$xref_to_objects{$master_xref_id}} ); # XXX check
+ if (defined $xref_to_objects{$master_xref_id}) {
+ my @ensembl_object_ids = keys( %{$xref_to_objects{$master_xref_id}} );
#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};
- my $full_key = $type.":".$object_id.":".$xref_id;
+ my $full_key = $type."|".$object_id."|".$xref_id;
if (!$object_xrefs_written{$full_key}) {
print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t" . ($xref_id+$xref_id_offset) . "\tDEPENDENT\n";
$object_xref_id++;
# Add this mapping to the list - note NON-OFFSET xref_id is used
- my $key = $type . ":" . $object_id;
+ my $key = $type . "|" . $object_id;
push @{$object_xref_mappings->{$key}}, $xref_id;
$object_xrefs_written{$full_key} = 1;
}
@@ -1097,9 +1101,10 @@ sub build_transcript_display_xrefs {
print "Got " . scalar(keys %xref_to_source) . " xref-source mappings\n";
- # Cache the list of translation->transcript mappings
+ # Cache the list of translation->transcript mappings & vice versa
print "Building translation to transcript mappings\n";
my %translation_to_transcript;
+ my %transcript_to_translation;
my $sth = $self->dbi()->prepare("SELECT translation_id, transcript_id FROM translation");
$sth->execute();
@@ -1108,23 +1113,20 @@ sub build_transcript_display_xrefs {
while ($sth->fetch()) {
$translation_to_transcript{$translation_id} = $transcript_id;
+ $transcript_to_translation{$transcript_id} = $translation_id if ($translation_id);
}
print "Building transcript display_xrefs\n";
my @priorities = $self->transcript_display_xref_sources();
- open (TRANSCRIPT_DX, ">transcript_display_xref.sql");
-
my $n = 0;
- # go through each object/xref mapping
- # store the best ones as we go along
- # hash keyed on transcript id, value is xref_id:source prioirity index
- # xref is stored with offset added
- # Note xrefs to translations are also considered; transcript ID is always stored
- my %transcript_display_xrefs;
+
+ # go through each object/xref mapping and store the best ones as we go along
+ my %obj_to_best_xref;
+
foreach my $key (keys %{$object_xref_mappings}) {
- my ($type, $obj) = split /:/, $key;
+ my ($type, $object_id) = split /\|/, $key;
next if ($type !~ /(Transcript|Translation)/i);
@@ -1134,6 +1136,7 @@ sub build_transcript_display_xrefs {
my ($best_xref, $best_xref_priority_idx);
$best_xref_priority_idx = 99999;
foreach my $xref (@xrefs) {
+
my $source = $xref_to_source{$xref};
if ($source) {
my $i = find_in_list($source, @priorities);
@@ -1145,29 +1148,67 @@ sub build_transcript_display_xrefs {
warn("Couldn't find a source for xref $xref \n");
}
}
+ # store object type, id, and best xref id and source priority
+ if ($best_xref) {
+ $obj_to_best_xref{$key} = $best_xref . "|" . $best_xref_priority_idx;
+ }
- if (!$best_xref) {
- #warn("Couldn't find a display xref for transcript id $obj\n");
- } else {
+ }
+
+ # Now go through each of the calculated best xrefs and convert any that are
+ # calculated against translations to be associated with their transcript,
+ # if the priority of the translation xref is higher than that of the transcript
+ # xref.
+ # Needs to be done this way to avoid clobbering higher-priority transcripts.
+
+ # hash keyed on transcript id, value is xref_id|source prioirity index
+ my %transcript_display_xrefs;
+
+ # Write a .sql file that can be executed, and a .txt file that can be processed
+ open (TRANSCRIPT_DX, ">transcript_display_xref.sql");
+ open (TRANSCRIPT_DX_TXT, ">transcript_display_xref.txt");
+
+ foreach my $key (keys %obj_to_best_xref) {
+
+ my ($type, $object_id) = split /\|/, $key;
+ my ($best_xref, $best_xref_priority_idx) = split /\|/, $obj_to_best_xref{$object_id};
+
+ # If transcript has a translation, use the best xref out of the transcript & translation
+ if ($type =~ /Transcript/i) {
+ my $transcript_id = $object_id;
+ my $translation_id = $transcript_to_translation{$transcript_id};
+ if ($translation_id) {
+ my ($translation_xref, $translation_priority) = split /\|/, $obj_to_best_xref{"Translation|$translation_id"};
+ my ($transcript_xref, $transcript_priority) = split /\|/, $obj_to_best_xref{"Transcript|$transcript_id"};
+
+ if ($translation_priority < $transcript_priority) {
+ $best_xref = $translation_xref;
+ $best_xref_priority_idx = $translation_priority;
+ } else {
+ $best_xref = $transcript_xref;
+ $best_xref_priority_idx = $transcript_priority;
+ }
- # If transcript, store directly
- # If translation, lookup transcript id
- my $object_id;
- if ($type =~ /Transcript/i) {
- $object_id = $obj;
- } elsif ($type =~ /Translation/i) {
- $object_id = $translation_to_transcript{$obj};
}
+ }
+
+ if ($best_xref) {
+
# Write record with xref_id_offset
print TRANSCRIPT_DX "UPDATE transcript SET display_xref_id=" . ($best_xref+$xref_id_offset) . " WHERE transcript_id=" . $object_id . ";\n";
+ print "wrote " . $best_xref . " (plus offset) for 95625\n" if ($object_id eq 95625);
+ print TRANSCRIPT_DX_TXT ($best_xref+$xref_id_offset) . "\t" . $object_id . "\n";
$n++;
- my $value = ($best_xref+$xref_id_offset) . ":" . $best_xref_priority_idx;
+
+ my $value = ($best_xref+$xref_id_offset) . "|" . $best_xref_priority_idx;
$transcript_display_xrefs{$object_id} = $value;
+
}
}
close(TRANSCRIPT_DX);
+ close(TRANSCRIPT_DX_TXT);
print "Wrote $n transcript display_xref entries to transcript_display_xref.sql\n";
@@ -1213,6 +1254,7 @@ sub build_gene_display_xrefs {
print "Assigning display_xrefs to genes\n";
open (GENE_DX, ">gene_display_xref.sql");
+ open (GENE_DX_TXT, ">gene_display_xref.txt");
my $hit = 0;
my $miss = 0;
my $trans_no_xref = 0;
@@ -1231,9 +1273,10 @@ sub build_gene_display_xrefs {
} else {
$trans_xref++;
}
- my ($xref_id, $priority) = split (/:/, $transcript_display_xrefs->{$transcript_id});
+ my ($xref_id, $priority) = split (/\|/, $transcript_display_xrefs->{$transcript_id});
#print "gene $gene_id orig:" . $transcript_display_xrefs->{$transcript_id} . " xref id: " . $xref_id . " pri " . $priority . "\n";
# 2 separate if clauses to avoid having to fetch transcripts unnecessarily
+
if (($priority lt $best_xref_priority_idx)) {
$best_xref_priority_idx = $priority;
@@ -1252,21 +1295,21 @@ sub build_gene_display_xrefs {
}
}
- if (!$best_xref) {
- #XXXwarn("Couldn't find a display xref for gene id $gene_id\n");
- $miss++;
- } else{
- # Write record
+ if ($best_xref) {
+ # Write record
print GENE_DX "UPDATE gene SET display_xref_id=" . $best_xref . " WHERE gene_id=" . $gene_id . ";\n";
+ print GENE_DX_TXT $best_xref . "\t" . $gene_id ."\n";
$hit++;
}
}
close (GENE_DX);
+ close (GENE_DX_TXT);
print "Transcripts with no xrefs: $trans_no_xref with xrefs: $trans_xref\n";
print "Wrote $hit gene display_xref entries to gene_display_xref.sql\n";
- print "Couldn't find display_xrefs for $miss genes\n";
+ print "Couldn't find display_xrefs for $miss genes\n" if ($miss > 0);
+ print "Found display_xrefs for all genes\n" if ($miss eq 0);
}
@@ -1291,19 +1334,20 @@ sub transcript_display_xref_sources {
}
-# Find the index of an item in a list(ref), or -1 if it's not in the list
+# Find the index of an item in a list(ref), or 999999 if it's not in the list.
+# Only look for exact matches (case insensitive)
sub find_in_list {
my ($item, @list) = @_;
for (my $i = 0; $i < scalar(@list); $i++) {
- if ($list[$i] =~ /$item/) {
+ if (lc($list[$i]) eq lc($item)) {
return $i;
}
}
- return -1;
+ return 999999;
}
@@ -1337,7 +1381,7 @@ sub map_source_to_external_db {
} else {
- print STDERR "Can't find external_db entry for source name $source_name\n"
+ print STDERR "Can't find external_db entry for source name $source_name; xrefs for this source will not be written. Consider adding $source_name to external_db\n"
}
@@ -1379,29 +1423,30 @@ sub do_upload {
# gene_display_xref.sql etc
foreach my $table ("gene", "transcript") {
- my $file = getcwd() . "/" . $table . "_display_xref.sql";
+ my $file = getcwd() . "/" . $table . "_display_xref.txt";
my $sth;
if ($deleteexisting) {
$sth = $self->dbi()->prepare("UPDATE $table SET display_xref_id=NULL");
- print "Setting all existing display_xref_id in $table to NULL\n";
+ print "Setting all existing display_xref_id in $table to null\n";
$sth->execute();
}
- # is this nicer than using the mysql client?
print "Setting $table display_xrefs from $file\n";
- open(DISPLAY_XREF, $file);
- while(<DISPLAY_XREF>) {
-
- $sth = $self->dbi()->prepare($_);
- $sth->execute();
-
+ # TODO this better
+ #my $str = "mysql -u " .$self->user() ." -p" . $self->password() . " -h " . $self->host() ." -P " . $self->port() . " " .$self->dbname() . " < $file";
+ #system $str;
+
+ $sth = $self->dbi()->prepare("UPDATE $table SET display_xref_id=? WHERE ${table}_id=?");
+ open(DX_TXT, $file);
+ while (<DX_TXT>) {
+ my ($xref_id, $object_id) = split;
+ $sth->execute($xref_id, $object_id);
}
- close(DISPLAY_XREF);
-
+ close(DX_TXT);
}
}
--
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