From 72a6bf7737cd828f83bf68930a36abe261c722ee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 15 Mar 2007 15:02:07 +0000
Subject: [PATCH] When writing to XREF, default to '' (empty string) for stuff
that might be undefined. Removes a whole lot of warnings when running with
-w.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 108 +++++++++++++++---
1 file changed, 93 insertions(+), 15 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 53fc265feb..abcc7479b2 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -1627,10 +1627,16 @@ PSQL
if(!defined($updated_source{$external_db_id})){
$self->cleanup_sources_file($external_db_id);
}
- print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession .
- "\t" . $label . "\t" . $version . "\t" . $description . "\tMISC\tNo match\n";
-
- #dump out dependencies aswell
+
+ print XREF ( $xref_id + $xref_id_offset ) . "\t"
+ . ( $external_db_id || '' ) . "\t"
+ . ( $accession || '' ) . "\t"
+ . ( $label || '' ) . "\t"
+ . ( $version || '' ) . "\t"
+ . ( $description || '' ) . "\t" . "MISC" . "\t"
+ . "No match\n";
+
+ #dump out dependencies aswell
$XXXxref_id_to_accession{$xref_id} = $accession;
if(!defined($accession) or $accession eq ""){
@@ -1742,7 +1748,15 @@ sub dump_orphan_xrefs() {
$self->cleanup_sources_file($external_db_id);
}
if(!defined($priority_xref_source_id{$xref_id})){
- print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\tMISC\tNo match\n";
+
+ print XREF ( $xref_id + $xref_id_offset ) . "\t"
+ . ( $external_db_id || '' ) . "\t"
+ . ( $accession || '' ) . "\t"
+ . ( $label || '' ) . "\t"
+ . ( $version || '' ) . "\t"
+ . ( $description || '' ) . "\t" . "MISC" . "\t"
+ . "No match\n";
+
$xrefs_written{$xref_id} = 1;
$count++;
}
@@ -1901,7 +1915,17 @@ sub dump_direct_xrefs {
}
next; # do not store XREF or OBJECT. do much later
}
- print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description ."\t". "DIRECT" . "\t" . "Externally assigned relationship between $ensembl_stable_id and $accession" . "\n";
+
+ print XREF ( $xref_id + $xref_id_offset ) . "\t"
+ . ( $external_db_id || '' ) . "\t"
+ . ( $accession || '' ) . "\t"
+ . ( $label || '' ) . "\t"
+ . ( $version || '' ) . "\t"
+ . ( $description || '' ) . "\t"
+ . "DIRECT" . "\t"
+ . "Externally assigned relationship between "
+ . $ensembl_stable_id . " and "
+ . $accession . "\n";
$xrefs_written{$xref_id} = 1;
}
@@ -1936,7 +1960,18 @@ sub dump_direct_xrefs {
if(!defined($updated_source{$external_db_id})){
$self->cleanup_sources_file($external_db_id);
}
- print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description ."\t". "DIRECT" . "\t" . "Externally assigned relationship between $ensembl_stable_id and $accession" ."\n";
+
+ print XREF ( $xref_id + $xref_id_offset ) . "\t"
+ . ( $external_db_id || '' ) . "\t"
+ . ( $accession || '' ) . "\t"
+ . ( $label || '' ) . "\t"
+ . ( $version || '' ) . "\t"
+ . ( $description || '' ) . "\t"
+ . "DIRECT" . "\t"
+ . "Externally assigned relationship between "
+ . $ensembl_stable_id . " and "
+ . $accession . "\n";
+
$xrefs_written{$xref_id} = 1;
}
$ensembl_internal_id = $stable_id_to_internal_id{$type}->{$stable_id};
@@ -2229,7 +2264,16 @@ sub dump_core_xrefs {
if(!defined($updated_source{$external_db_id})){
$self->cleanup_sources_file($external_db_id);
}
- print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\t" . "SEQUENCE_MATCH\t" . "Relationship generated from exonerate mapping" . "\n";
+
+ print XREF ( $xref_id + $xref_id_offset ) . "\t"
+ . ( $external_db_id || '' ) . "\t"
+ . ( $accession || '' ) . "\t"
+ . ( $label || '' ) . "\t"
+ . ( $version || '' ) . "\t"
+ . ( $description || '' ) . "\t"
+ . "SEQUENCE_MATCH" . "\t"
+ . "Relationship generated from exonerate mapping\n";
+
$xrefs_written{$xref_id} = 1;
$source_ids{$source_id} = $source_id;
}
@@ -2270,7 +2314,17 @@ sub dump_core_xrefs {
}
if(!defined($priority_xref_source_id{$xref_id})){
- print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\t" . "DEPENDENT" . "\t" . "Generated via $master_accession\n";
+
+ print XREF ( $xref_id + $xref_id_offset ) . "\t"
+ . ( $external_db_id || '' ) . "\t"
+ . ( $accession || '' ) . "\t"
+ . ( $label || '' ) . "\t"
+ . ( $version || '' ) . "\t"
+ . ( $description || '' ) . "\t"
+ . "DEPENDENT" . "\t"
+ . "Generated via "
+ . $master_accession . "\n";
+
}
$xrefs_written{$xref_id} = 1;
$source_ids{$source_id} = $source_id;
@@ -4041,7 +4095,17 @@ sub dump_all_dependencies{
}
if(!defined($priority_xref_source_id{$xref_id})){
- print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\t" . "DEPENDENT" . "\t" . "Generated via $master_accession\n";
+
+ print XREF ( $xref_id + $xref_id_offset ) . "\t"
+ . ( $external_db_id || '' ) . "\t"
+ . ( $accession || '' ) . "\t"
+ . ( $label || '' ) . "\t"
+ . ( $version || '' ) . "\t"
+ . ( $description || '' ) . "\t"
+ . "DEPENDENT" . "\t"
+ . "Generated via "
+ . $master_accession . "\n";
+
push @return, ($xref_id+$xref_id_offset);
$xrefs_written{$xref_id} = 1;
}
@@ -4155,8 +4219,14 @@ PSQL
$self->cleanup_sources_file($external_db_id);
}
if(!defined($priority_xref_source_id{$xref_id})){
- print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession .
- "\t" . $label . "\t" . $version . "\t" . $description . "\tMISC\tNo match\n";
+
+ print XREF ( $xref_id + $xref_id_offset ) . "\t"
+ . ( $external_db_id || '' ) . "\t"
+ . ( $accession || '' ) . "\t"
+ . ( $label || '' ) . "\t"
+ . ( $version || '' ) . "\t"
+ . ( $description || '' ) . "\t" . "MISC" . "\t"
+ . "No match\n";
#dump out dependencies aswell
@@ -4437,9 +4507,17 @@ PSQL
if (!$xrefs_written{$xref_id}) {
- print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" .
- $label . "\t" . $version . "\t" . $description . "\t" . "DEPENDENT" . "\t" .
- "No mapping ".$unmapped_primary_xref{$xref_id}. "\n";
+
+ print XREF ( $xref_id + $xref_id_offset ) . "\t"
+ . ( $external_db_id || '' ) . "\t"
+ . ( $accession || '' ) . "\t"
+ . ( $label || '' ) . "\t"
+ . ( $version || '' ) . "\t"
+ . ( $description || '' ) . "\t"
+ . "DEPENDENT" . "\t"
+ . "No mapping "
+ . $unmapped_primary_xref{$xref_id} . "\n";
+
$xrefs_written{$xref_id} = 1;
}
if(!defined($object_succesfully_mapped{$xref_id})){
--
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