More fiddles

misc-scripts/golden_path/fin_agp2ensembl

@@ -34,15 +34,14 @@ my (@agps);
 my $gptype = "NCBI35";
 my $raw = "e_ctg.dat";
 my $agp_dir = "./fin_agp";
-my $agp_prefix = "chr";
 
 my %clone;
 my %used_ctg_ids;
 
 my @chrs = qw/
-     1  2  3  4  5  6  7  8  9 10
-    11 12 13 14 15 16 17 18 19 20
-     X  Y DR52 DR53 PAR MT
+     chr1  chr2  chr3  chr4  chr5  chr6  chr7  chr8  chr9 chr10
+    chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20
+     chrX  chrY DR52 DR53 PAR chrMT
 /;
 my @chr_info;
 my $chr_id = 1;
@@ -74,7 +73,7 @@ close CTG;
 
 foreach my $chr (@chrs) {
 
-    my $agp = "$agp_dir/$agp_prefix$chr.agp";
+    my $agp = "$agp_dir/$chr.agp";
     my $global_end;
     my $prev_end;
 
@@ -93,8 +92,11 @@ foreach my $chr (@chrs) {
 
 	next if $status eq "N";
 
-	die "Unfinished seq! $_" unless $status eq "F";
-	die "Bad chr name" unless $chr_name eq "$agp_prefix$chr";
+	next unless $status eq "F";
+	if ($chr_name ne "$chr"){
+	  print "Bad chr name in $agp: $chr_name\n";
+	  next;
+        }
 
 	$global_end = $chr_end;