From 3a1f746a77fb02a4ad937c513dddfb64b280748c Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 6 Jul 2006 07:19:26 +0000
Subject: [PATCH] removed debug die command
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 55 ++++++++++++++++++-
1 file changed, 54 insertions(+), 1 deletion(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 88f142df53..544b48edb4 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -508,7 +508,6 @@ sub fetch_and_dump_seq{
}
close DNA;
close PEP;
- die "FINISHED DUMP\n";
# print "$rna RNA genes ignored for mapping purposes\n";
}
@@ -3085,6 +3084,14 @@ EOS
my $okay =0;
my $both = 0;
my $poss = 0;
+
+
+ #sql needed to get the dependent xrefs for those missed.
+ my $dep_sql = "SELECT dx.dependent_xref_id, FROM dependent_xref dx, xref x WHERE x.xref_id=dx.dependent_xref_id AND master_xref_id = ?";
+ my $dep_sth = $self->xref->dbc->prepare($dep_sql);
+
+
+
while ($xref_sth->fetch()) {
if(!defined($xrefs_written{$xref_id1}) or !defined($xrefs_written{$xref_id2})){
if (!defined($xrefs_written{$xref_id1}) and !defined($xrefs_written{$xref_id2})){
@@ -3152,6 +3159,19 @@ EOS
print OBJECT_XREF2 $transcript_2_translation{$ens_int_id}."\tTranslation\t" ;
print OBJECT_XREF2 $good2missed{$goodxref};
print OBJECT_XREF2 "\n";
+
+
+ $dep_sth->execute($good2missed{$goodxref}-$xref_id_offset);
+ my $dep_xref;
+ $dep_sth->bind_columns(\$dep_xref);
+ while($dep_sth->fetch){
+ $max_object_xref_id++;
+ print OBJECT_XREF2 "$max_object_xref_id\t";
+ print OBJECT_XREF2 $transcript_2_translation{$ens_int_id}."\tTranslation\t" ;
+ print OBJECT_XREF2 $dep_xref+$xref_id_offset;
+ print OBJECT_XREF2 "\n";
+ }
+
print TRIAGE_UPDATE "DELETE unmapped_object FROM unmapped_object ";
print TRIAGE_UPDATE "WHERE identifier = '".$good2missed_acc{$goodxref}."' ";
print TRIAGE_UPDATE "AND external_db_id = $ex_db_id ;\n";
@@ -3163,6 +3183,18 @@ EOS
print OBJECT_XREF2 $translation_2_transcript{$ens_int_id}."\tTranscript\t" ;
print OBJECT_XREF2 $good2missed{$goodxref};
print OBJECT_XREF2 "\n";
+
+ $dep_sth->execute($good2missed{$goodxref}-$xref_id_offset);
+ my $dep_xref;
+ $dep_sth->bind_columns(\$dep_xref);
+ while($dep_sth->fetch){
+ $max_object_xref_id++;
+ print OBJECT_XREF2 "$max_object_xref_id\t";
+ print OBJECT_XREF2 $translation_2_transcript{$ens_int_id}."\tTranscript\t" ;
+ print OBJECT_XREF2 $dep_xref+$xref_id_offset;
+ print OBJECT_XREF2 "\n";
+ }
+
print TRIAGE_UPDATE "DELETE unmapped_object FROM unmapped_object ";
print TRIAGE_UPDATE "WHERE identifier = '".$good2missed_acc{$goodxref}."' ";
print TRIAGE_UPDATE "AND external_db_id = $ex_db_id ;\n";
@@ -3189,6 +3221,16 @@ EOS
print OBJECT_XREF2 $transcript_2_translation{$ens_int_id}."\tTranslation\t" ;
print OBJECT_XREF2 $good2missed{$goodxref};
print OBJECT_XREF2 "\n";
+ $dep_sth->execute($good2missed{$goodxref}-$xref_id_offset);
+ my $dep_xref;
+ $dep_sth->bind_columns(\$dep_xref);
+ while($dep_sth->fetch){
+ $max_object_xref_id++;
+ print OBJECT_XREF2 "$max_object_xref_id\t";
+ print OBJECT_XREF2 $transcript_2_translation{$ens_int_id}."\tTranslation\t" ;
+ print OBJECT_XREF2 $dep_xref+$xref_id_offset;
+ print OBJECT_XREF2 "\n";
+ }
print TRIAGE_UPDATE "DELETE unmapped_object FROM unmapped_object ";
print TRIAGE_UPDATE "WHERE identifier like '".$good2missed_acc{$goodxref}."' ";
print TRIAGE_UPDATE "AND external_db_id = $ex_db_id ;\n";
@@ -3200,6 +3242,16 @@ EOS
print OBJECT_XREF2 $translation_2_transcript{$ens_int_id}."\tTranscript\t" ;
print OBJECT_XREF2 $good2missed{$goodxref};
print OBJECT_XREF2 "\n";
+ $dep_sth->execute($good2missed{$goodxref}-$xref_id_offset);
+ my $dep_xref;
+ $dep_sth->bind_columns(\$dep_xref);
+ while($dep_sth->fetch){
+ $max_object_xref_id++;
+ print OBJECT_XREF2 "$max_object_xref_id\t";
+ print OBJECT_XREF2 $translation_2_transcript{$ens_int_id}."\tTranscript\t" ;
+ print OBJECT_XREF2 $dep_xref+$$xref_id_offset;
+ print OBJECT_XREF2 "\n";
+ }
print TRIAGE_UPDATE "DELETE unmapped_object FROM unmapped_object ";
print TRIAGE_UPDATE "WHERE identifier like '".$good2missed_acc{$goodxref}."' ";
print TRIAGE_UPDATE "AND external_db_id = $ex_db_id ;\n";
@@ -3361,6 +3413,7 @@ PSQL
}
close(XREF);
}
+
1;
--
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