script to create 1-step assembly path from 2-step path between chromosome and contig coord systems

misc-scripts/chimp/chimp_chr_ctg_assembly.pl

+use strict;
+use warnings;
+
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+
+
+my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(@ARGV);
+
+my $slice_adaptor = $db->get_SliceAdaptor();
+
+foreach my $slice (@{$slice_adaptor->fetch_all('chromosome')}) {
+  my $asm_sr_id = $slice->get_seq_region_id();
+
+  print STDERR ".";
+
+  foreach my $segment (@{$slice->project('contig')}) {
+    my $asm_start = $segment->from_start();
+    my $asm_end   = $segment->from_end();
+    my $cmp_sr_id = $segment->to_Slice->get_seq_region_id();
+    my $cmp_start = $segment->to_Slice->start();
+    my $cmp_end   = $segment->to_Slice->end();
+    my $ori       = $segment->to_Slice->strand();
+
+    print join("\t", $asm_sr_id, $cmp_sr_id, $asm_start, $asm_end,
+               $cmp_start, $cmp_end, $ori), "\n";
+  }
+}
+
+print STDERR "done\n";