organism_helpers.rb in rbbt-sources-3.0.17

- old
+ new

@@ -562,19 +562,18 @@
     chr_transcript_ranges[chr][transcript] ||= transcript_ranges
   end
 
   transcript_sequence = {}
   chr_transcript_ranges.each do |chr, transcript_ranges|
-
     begin
-      raise "LRG, GL, HG, and HSCHR chromosomes not supported: #{chr}" if chr =~ /^(?:LRG_|GL0|HG|HSCHR)/
+      raise "LRG, GL, HG, NT, and HSCHR chromosomes not supported: #{chr}" if chr =~ /^(?:LRG_|GL0|HG|HSCHR|NT)/
       p = File.expand_path("./chromosome_#{chr}")
       Organism.root.annotate p
       p.sub!(%r{.*/organisms/},'share/organisms/')
       chr_str = p.produce.read
     rescue Exception
-      Log.debug("Chr #{ chr } failed (#{transcript_ranges.length} transcripts not covered): #{$!.message}")
-      Log.exception $!
+      Log.warn("Chr #{ chr } failed (#{transcript_ranges.length} transcripts not covered): #{$!.message}")
+      raise $! unless $!.message =~ /not supported/
       next
     end
 
     transcript_ranges.each do |transcript, ranges|
       strand = transcript_strand[transcript]