From a1411221c7a289c7ccc07e2c6ea8c6273ddc62ae Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 8 Dec 2004 15:57:15 +0000
Subject: [PATCH] Changed xref dumping to generate SQL to retrieve only those
xrefs we need.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 124 +++++++++---------
1 file changed, 59 insertions(+), 65 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 90997234f8..c1470265e1 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -149,8 +149,8 @@ sub get_species_id_from_species_name{
sub get_set_lists{
my ($self) = @_;
-# return [["ExonerateGappedBest1", ["homo_sapiens","Uniprot/SWISSPROT"]]];
-return [["ExonerateGappedBest1", ["homo_sapiens","*"]]];
+ # return [["ExonerateGappedBest1", ["homo_sapiens","Uniprot/SWISSPROT"]]];
+ return [["ExonerateGappedBest1", ["homo_sapiens","*"]]];
}
@@ -246,7 +246,7 @@ sub dump_xref{
foreach my $list (@lists){
# print "method->".@$list[0]."\n";
$method[$i] = shift @$list;
- my $j = 1;
+ my $j = 0;
my @source_id=();
my @species_id=();
foreach my $element (@$list){
@@ -297,72 +297,64 @@ sub dump_xref{
sub dump_subset{
+
my ($self,$xref,$rspecies_id,$rsource_id,$index) = @_;
-
- open(XDNA,">".$xref->dir()."/xref_".$index."_dna.fasta")
- || die "Could not open xref_".$index."_dna.fasta";
- my $sql = "select p.xref_id, p.sequence, x.species_id , x.source_id ";
- $sql .= " from primary_xref p, xref x ";
- $sql .= " where p.xref_id = x.xref_id and ";
- $sql .= " p.sequence_type ='dna' ";
- if(defined($self->maxdump())){
- $sql .= "limit ".$self->maxdump()." ";
- }
-
-# for (my $j =1; $j<scalar(@$rspecies_id); $j++){
-# print $j."\t".$$rspecies_id[$j]."\t".$$rsource_id[$j]."\n";
-# }
- # return $xref->dir."/xref_".$i."_dna.fasta";
-
- my $sth = $xref->dbi()->prepare($sql);
- $sth->execute();
- while(my @row = $sth->fetchrow_array()){
- my $pass = 0;
- for (my $j =1; $j<scalar(@$rspecies_id); $j++){
- if($$rspecies_id[$j] < 0 or $row[2] == $$rspecies_id[$j]){
- if($$rsource_id[$j] < 0 or $row[3] == $$rsource_id[$j]){
- $pass = 1;
- }
- }
+ # generate or condition list for species and sources
+ my $final_clause;
+ my $use_all = 0;
+ my @or_list;
+ for (my $j = 0; $j < scalar(@$rspecies_id); $j++){
+ my @condition;
+ if($$rspecies_id[$j] > 0){
+ push @condition, "x.species_id=" . $$rspecies_id[$j];
}
- if($pass){
- $row[1] =~ s/(.{60})/$1\n/g;
- print XDNA ">".$row[0]."\n".$row[1]."\n";
+ if($$rsource_id[$j] > 0){
+ push @condition, "x.source_id=" . $$rsource_id[$j];
}
- }
- close XDNA;
+ # note if both source and species are * (-1) there's no need for a final clause
+
+ if ( !@condition ) {
+ $use_all = 1;
+ last;
+ }
+
+ push @or_list, join (" AND ", @condition);
- open(XPRO,">".$xref->dir."/xref_".$index."_prot.fasta")
- || die "Could not open xref_".$index."_prot.fasta";
- my $sql = "select p.xref_id, p.sequence, x.species_id , x.source_id ";
- $sql .= " from primary_xref p, xref x ";
- $sql .= " where p.xref_id = x.xref_id and ";
- $sql .= " p.sequence_type ='peptide' ";
- if(defined($self->maxdump())){
- $sql .= "limit ".$self->maxdump()." ";
}
-
-
- $sth = $xref->dbi()->prepare($sql);
- $sth->execute();
- while(my @row = $sth->fetchrow_array()){
- my $pass = 0;
- for (my $j =1; $j<scalar(@$rspecies_id); $j++){
- if($$rspecies_id[$j] < 0 or $row[2] == $$rspecies_id[$j]){
- if($$rsource_id[$j] < 0 or $row[3] == $$rsource_id[$j]){
- $pass = 1;
- }
- }
+
+ $final_clause = " AND ((" . join(") OR (", @or_list) . "))" unless ($use_all) ;
+
+
+ for my $sequence_type ('dna', 'peptide') {
+
+ my $filename = $xref->dir() . "/xref_" . $index . "_" . $sequence_type . ".fasta";
+ open(XREF_DUMP,">$filename") || die "Could not open $filename";
+
+ my $sql = "SELECT p.xref_id, p.sequence, x.species_id , x.source_id ";
+ $sql .= " FROM primary_xref p, xref x ";
+ $sql .= " WHERE p.xref_id = x.xref_id AND ";
+ $sql .= " p.sequence_type ='$sequence_type' ";
+ $sql .= $final_clause;
+
+ if(defined($self->maxdump())){
+ $sql .= " LIMIT ".$self->maxdump()." ";
}
- if($pass){
+
+ my $sth = $xref->dbi()->prepare($sql);
+ $sth->execute();
+ while(my @row = $sth->fetchrow_array()){
+
$row[1] =~ s/(.{60})/$1\n/g;
- print XPRO ">".$row[0]."\n".$row[1]."\n";
+ print XREF_DUMP ">".$row[0]."\n".$row[1]."\n";
+
}
+
+ close(XREF_DUMP);
+ $sth->finish();
+
}
- $sth->finish();
- close XPRO;
}
@@ -425,7 +417,7 @@ sub fetch_and_dump_seq{
}
open(PEP,">".$self->ensembl_protein_file())
- || die("Could not open dna file for writing: ".$self->ensembl_protein_file."\n");
+ || die("Could not open protein file for writing: ".$self->ensembl_protein_file."\n");
my $gene_adap = $db->get_GeneAdaptor();
my @gene_ids = @{$gene_adap->list_dbIDs()};
@@ -450,13 +442,16 @@ sub fetch_and_dump_seq{
print PEP ">".$trans->dbID()."\n".$pep_seq."\n";
}
}
- if(defined($max) and $i > $max){
- goto FIN;
- }
+
+ last if(defined($max) and $i > $max);
+
}
-FIN:
+
close DNA;
close PEP;
+
+ print time() . " after \n";
+ exit(0);
}
@@ -1225,7 +1220,6 @@ sub build_gene_display_xrefs {
my $best_transcript_length = -1;
foreach my $transcript_id (@transcripts) {
if (!$transcript_display_xrefs->{$transcript_id}) {
- #print "No display_xref assigned to transcript $transcript_id\n";
$trans_no_xref++;
next;
} else {
@@ -1246,7 +1240,7 @@ sub build_gene_display_xrefs {
if (!$best_xref) {
#XXXwarn("Couldn't find a display xref for gene id $gene_id\n");
$miss++;
- } else {
+ } else{
# Write record
print GENE_DX "UPDATE gene SET display_xref_id=" . $best_xref . " WHERE gene_id=" . $gene_id . ";\n";
$hit++;
--
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