From b8a73799a2a80b8db18c8311a822db6599a809a4 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 20 Oct 2004 10:19:48 +0000
Subject: [PATCH] Fixes to xref dumping.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 92 ++++++++++++++-----
1 file changed, 67 insertions(+), 25 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index a45d447e11..7c23eee4a4 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -149,7 +149,7 @@ sub get_set_lists{
# ["method2",[$self->species,"*"]],
# ["method3",["*","*"]]];
- return [["ExonerateBest1",["homo_sapiens","RefSeq"]]];
+ return [["ExonerateUngappedBest1", ["homo_sapiens","UniProtSwissProt"]]];
# return [["ExonerateBest1",["*","*"]]];
}
@@ -419,9 +419,11 @@ sub fetch_and_dump_seq{
# store ensembl protein file name and open it
#
$self->ensembl_protein_file($self->dir."/".$self->species."_protein.fasta");
+
if(defined($self->dumpcheck()) and -e $self->ensembl_protein_file() and -e $self->ensembl_dna_file()){
return;
}
+
open(PEP,">".$self->ensembl_protein_file())
|| die("Could not open dna file for writing: ".$self->ensembl_protein_file."\n");
@@ -441,6 +443,7 @@ sub fetch_and_dump_seq{
print DNA ">" . $transcript->dbID() . "\n" .$seq."\n";
my $trans = $transcript->translation();
my $translation = $transcript->translate();
+
if(defined($translation)){
my $pep_seq = $translation->seq();
$pep_seq =~ s/(.{60})/$1\n/g;
@@ -699,6 +702,17 @@ sub store {
print "Maximum existing object_xref_id = $max_object_xref_id\n";
}
+ my $max_xref_id = 0;
+ my $core_sth = $self->dbi->prepare("SELECT MAX(xref_id) FROM xref");
+ $core_sth->execute();
+ my $max_xref_id = ($core_sth->fetchrow_array())[0];
+ if (!defined $max_xref_id) {
+ print "Can't get highest existing xref_id, using 0\n)";
+ } else {
+ print "Maximum existing xref_id = $max_xref_id\n";
+ }
+ my $xref_id_offset = $max_xref_id + 1;
+
#my $ox_sth = $dbi->prepare("INSERT INTO object_xref(ensembl_id, ensembl_object_type, xref_id) VALUES(?,?,?)");
#my $ix_sth = $dbi->prepare("INSERT INTO identity_xref VALUES(?,?,?,?,?,?,?,?,?,?,?)");
@@ -743,14 +757,18 @@ sub store {
# TODO make sure query & target are the right way around
- print OBJECT_XREF "$object_xref_id\t$target_id\t$type\t$query_id\n";
- print IDENTITY_XREF "$object_xref_id\t$query_id\t$target_id\t$query_start\t$query_end\t$target_start\t$target_end\t$cigar_line\t$score\t\\N\t$analysis_id\n";
+ # note we add on $xref_id_offset to avoid clashes
+ print OBJECT_XREF "$object_xref_id\t$target_id\t$type\t" . ($query_id+$xref_id_offset) . "\n";
+ print IDENTITY_XREF "$object_xref_id\t" . ($query_id+$xref_id_offset) . "\t$target_id\t$query_start\t$query_end\t$target_start\t$target_end\t$cigar_line\t$score\t\\N\t$analysis_id\n";
# TODO - evalue?
$object_xref_id++;
$ensembl_object_types{$target_id} = $type;
#push @{$primary_xref_ids{$query_id}}, $target_id;
+
+ # note the NON-OFFSET xref_id is stored here as the values are used in
+ # a query against the original xref database
$primary_xref_ids{$query_id}{$target_id} = $target_id;
# Store in database
@@ -773,7 +791,10 @@ sub store {
print "Read $total_lines lines from $total_files exonerate output files\n";
# write relevant xrefs to file
- $self->dump_xrefs(\%primary_xref_ids, $object_xref_id+1, \%ensembl_object_types);
+ $self->dump_xrefs(\%primary_xref_ids, $object_xref_id+1, $xref_id_offset, \%ensembl_object_types);
+
+ # write comparison info. Can be removed after development
+ dump_comparison();
}
@@ -840,7 +861,7 @@ sub get_analysis_id {
sub dump_xrefs {
- my ($self, $xref_ids_hashref, $start_object_xref_id, $ensembl_object_types_hashref) = @_;
+ my ($self, $xref_ids_hashref, $start_object_xref_id, $xref_id_offset, $ensembl_object_types_hashref) = @_;
my @xref_ids = keys %$xref_ids_hashref;
my %xref_to_objects = %$xref_ids_hashref;
my %ensembl_object_types = %$ensembl_object_types_hashref;
@@ -851,18 +872,6 @@ sub dump_xrefs {
my $xref_dbi = $self->xref()->dbi();
my $core_dbi = $self->dbi();
- # get current highest internal ID from xref
- my $max_xref_id = 0;
- my $core_sth = $core_dbi->prepare("SELECT MAX(xref_id) FROM xref");
- $core_sth->execute();
- my $max_xref_id = ($core_sth->fetchrow_array())[0];
- if (!defined $max_xref_id) {
- print "Can't get highest existing xref_id, using 0\n)";
- } else {
- print "Maximum existing xref_id = $max_xref_id\n";
- }
- my $core_xref_id = $max_xref_id + 1;
-
# keep a unique list of source IDs to build the external_db table later
my %source_ids;
@@ -897,10 +906,11 @@ sub dump_xrefs {
# 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 = $xref_sth->fetchrow_array()) {
- print XREF "$core_xref_id\t$accession\t$label\t$description\n";
+
+ print XREF ($xref_id+$xref_id_offset) . "\t" . $accession . "\t" . $label . "\t" . $description . "\n";
$source_ids{$source_id} = $source_id;
- $core_xref_id++;
}
@@ -912,16 +922,17 @@ sub dump_xrefs {
$dep_sth->bind_columns(\$xref_id, \$accession, \$label, \$description, \$source_id);
while (my @row = $dep_sth->fetchrow_array()) {
- print XREF "$core_xref_id\t$accession\t$label\t$description\tDEPENDENT\n";
+
+print XREF ($xref_id+$xref_id_offset) . "\t" . $accession . "\t" . $label . "\t" . $description . "DEPENDENT\n";
$source_ids{$source_id} = $source_id;
- $core_xref_id++;
+
# create an object_xref linking this (dependent) xref with any objects it maps to
- if (defined $xref_to_objects{$xref_id}) {
- my @objects = keys( %{$xref_to_objects{$xref_id}} );
+ 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) {
my $type = $ensembl_object_types{$object_id};
- print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t$core_xref_id DEPENDENT\n";
+ print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t" . ($xref_id+$xref_id_offset) . "DEPENDENT\n";
$object_xref_id++;
}
}
@@ -960,7 +971,7 @@ sub dump_xrefs {
my $source_sql = "SELECT name, release FROM source WHERE source_id $source_id_str";
my $source_sth = $xref_dbi->prepare($source_sql);
- print STDERR $source_sql."\n";
+ #print STDERR $source_sql."\n";
$source_sth->execute();
my ($source_name, $release);
@@ -974,7 +985,38 @@ sub dump_xrefs {
close(EXTERNAL_DB);
+}
+
+# produce output for comparison with existing ensembl mappings
+# format is (with header)
+# xref_accession ensembl_type ensembl_id
+
+sub dump_comparison {
+
+ print "Dumping comparison data\n";
+
+ open (COMPARISON, ">comparison/xref_mappings.txt");
+
+ # get the xref accession for each xref as the xref_ids are ephemeral
+
+ # first read all the xrefs that were dumped and get an xref_id->accession map
+ my %xref_id_to_accesson;
+ open (XREF, "xref.txt");
+ while (<XREF>) {
+ my ($xref_id,$accession,$label,$description) = split;
+ $xref_id_to_accesson{$xref_id} = $accession;
+ }
+ close (XREF);
+
+ open (OBJECT_XREF, "object_xref.txt");
+ while (<OBJECT_XREF>) {
+ my ($object_xref_id,$object_id,$type,$xref_id) = split;
+ print COMPARISON $xref_id_to_accesson{$xref_id} . "\t" . $type . "\t" . $object_id . "\n";
+ }
+
+ close (OBJECT_XREF);
+ close (COMPARISON);
}
--
GitLab