From fd07aecafaa4c4f2e68f536d76ed2ed117071296 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 9 Dec 2004 09:51:52 +0000
Subject: [PATCH] tidy up of code
---
misc-scripts/xref_mapping/xref_mapper.pl | 95 +++++++++++-------------
1 file changed, 42 insertions(+), 53 deletions(-)
diff --git a/misc-scripts/xref_mapping/xref_mapper.pl b/misc-scripts/xref_mapping/xref_mapper.pl
index e3ca0745bc..748770867d 100644
--- a/misc-scripts/xref_mapping/xref_mapper.pl
+++ b/misc-scripts/xref_mapping/xref_mapper.pl
@@ -38,9 +38,8 @@ if(defined($dumpcheck) && defined($maxdump)){
open(FILE, $file) or die("Could not open input file '$file'");
my @all_species;
-my $xref;
-#my $output=undef;
-my $new=undef;
+my $xref=undef;
+my $species=undef;
my $type;
while( my $line = <FILE> ) {
chomp($line);
@@ -49,67 +48,57 @@ while( my $line = <FILE> ) {
# print $line."\n";
my ($key, $value) = split("=",$line);
-
- if($key eq "species" || $key eq "xref"){
- if(defined($new)){ #save old one
- if($type eq "species"){
- push @all_species, $new;
- }
- else{
- $xref = $new;
- }
- $new = undef;
+
+ if($key eq "species"){
+ $type = "species";
+ if(defined($species)){
+ push @all_species, $species;
+ $species = undef;
}
- if($key eq "species"){
- $type = "species";
- eval "require XrefMapper::$value";
- my $module;
- if($@) {
- warn("Could not require mapper module XrefMapper::$value\n" .
- "Using XrefMapper::BasicMapper instead:\n$@");
- require XrefMapper::BasicMapper;
- $module = "BasicMapper";
- }
- else{
- $module = $value;
- }
- {
- no strict 'refs';
- $new = "XrefMapper::$module"->new();
- $new->species($value);
- }
- if(defined($dumpcheck)){
- $new->dumpcheck("yes");
- }
- if(defined($maxdump)){
- $new->maxdump($maxdump);
- }
- if(defined($use_existing_mappings)){
- $new->use_existing_mappings("yes");
- }
+ eval "require XrefMapper::$value";
+ my $module;
+ if($@) {
+ warn("Could not require mapper module XrefMapper::$value\n" .
+ "Using XrefMapper::BasicMapper instead:\n$@");
+ require XrefMapper::BasicMapper;
+ $module = "BasicMapper";
}
else{
- $type= "xref";
- $new = new XrefMapper::db();
+ $module = $value;
+ }
+ {
+ no strict 'refs';
+ $species = "XrefMapper::$module"->new();
+ $species->species($value);
+ }
+ if(defined($dumpcheck)){
+ $species->dumpcheck("yes");
+ }
+ if(defined($maxdump)){
+ $species->maxdump($maxdump);
+ }
+ if(defined($use_existing_mappings)){
+ $species->use_existing_mappings("yes");
}
}
- else{
- $new->$key($value);
+ elsif($key eq "xref"){
+ $type = "xref";
+ $xref = new XrefMapper::db();
}
-}
-
-if(defined($new)){ #save last one
- if($type eq "species"){
- push @all_species, $new;
+ elsif($type eq "species"){ # processing species data
+ $species->$key($value);
}
- else{
- $xref = $new;
+ elsif($type eq "xref"){ # processing xref data
+ $xref->$key($value);
}
- $new = undef;
}
+if(defined($species)){
+ push @all_species, $species;
+}
+
for my $species ( @all_species ) {
- $species->xref($xref);
+ $species->xref($xref); # attach xref object to species object
$species->dump_seqs();
$species->run_matching();
$species->store();
--
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