more cruft removal

misc-scripts/idmapping/create_contigids.pl

-my %contigs;
-while (<>) {
-    chomp;
-    if ($_ =~ /(\S+)\.\d+\.\d+\.\d+/) {
-	push (@{$contigs{$1}},$_);
-    }
-    elsif ($_ =~ /(\S+)\.\d+\.(\d+)/) {
-	if ($2 =~ /^1/) {
-	    push (@{$contigs{$1}},$_);
-	}
-	else {
-	    #print "Couldn't parse line $_\n";
-	} 
-    }
-    else {
-	#print "Couldn't parse line $_\n";
-    }
-}
-my %idmap;
-foreach my $clone (keys %contigs) {
-    my %clone;
-    my $c=0;
-    foreach my $line (@{$contigs{$clone}}) {
-	#print "Parsing line $line\n";
-	if ($line =~ /\S+\.\d+\.(\d+)\.\d+/) {
-	    $clone{$1}=$line;
-	}
-	elsif ($_ =~ /(\S+)\.\d+\.(\d+)/) {
-	    $clone{1}=$line;
-	    $c++;
-	}
-	if ($c > 1) {
-	    #print "BARF\n";
-	}
-    }
-    #print "Sorted by start lines for clone $clone:\n";
-    my $c=1;
-    foreach $line (sort {$a <=> $b} (keys %clone)) {
-	my $id = "0000$c";
-	while (length ($id) > 5) {
-	    $id =~ s/^0//g;
-	}
-	my $final = "$clone.$id";
-	$idmap{$line}=$final;
-	print $clone{$line}." $final\n";
-	$c++;
-    }
-    #print "\n";
-}
-	    
-	

misc-scripts/idmapping/dbsql_dbold.pl

-#USe with:
-#mkdir temp/
-#cd temp/
-#ls ../*.pm | xargs -i perl /work2/elia/src/ensembl/misc-scripts/utilities/dbsql_dbold.pl {}
-#mv -f *.pm ../
-#rm -rf temp/
-
-my $file=shift(@ARGV);
-open (FILE,"<$file");
-$file =~ /(\w+\.pm)/;
-my $new = $1;
-open (NEW,">$new");
-while (<FILE>) {
-    $line =$_; 
-    $line =~ s/DBSQL/DBOLD/g; 
-    print NEW $line;
-}

misc-scripts/idmapping/map_ids.pl

-my %map;
-my $file = pop (@ARGV);
-foreach my $f (@ARGV) {
-    #print "Reading $f\n";
-    open ($f,"<$f");
-    while (<$f>) {
-	chomp;
-	$_ =~ /(\S+)\s+(\S+)/;
-	$map{$1}=$2;
-    }
-    close ($f);
-}
-open (FILE,"<$file");
-while (<FILE>) {
-    chomp;
-    my @tabs = split(/\t/);
-    my $line;
-    foreach my $tab (@tabs) {
-	if ($map{$tab}) {
-	    $line .= $map{$tab}."\t";
-	}
-	else {
-	    $line .= $tab."\t";
-	}
-    }
-    $line =~ s/\t$//g;
-    print "$line\n";
-}

misc-scripts/idmapping/revmap_ids.pl

-my %map;
-my $file = pop (@ARGV);
-foreach my $f (@ARGV) {
-    #print "Reading $f\n";
-    open ($f,"<$f");
-    while (<$f>) {
-	chomp;
-	$_ =~ /(\S+)\s+(\S+)/;
-	$map{$2}=$1;
-    }
-    close ($f);
-}
-open (FILE,"<$file");
-while (<FILE>) {
-    chomp;
-    my @tabs = split(/\t/);
-    my $line;
-    foreach my $tab (@tabs) {
-	if ($map{$tab}) {
-	    $line .= $map{$tab}."\t";
-	}
-	else {
-	    $line .= $tab."\t";
-	}
-    }
-    $line =~ s/\t$//g;
-    print "$line\n";
-}