Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Browse files

Make all types case insensitive

  • Loading branch information...
commit d698774ff109ad0ec05fc8ab5c3c996b8e9eb48b 1 parent 035a1c2
@pjotrp authored
View
2  lib/bio/db/gff/digest/gffparser.rb
@@ -31,7 +31,7 @@ def store_record rec
@count_ids.add(id)
@count_seqnames.add(rec.seqname)
- is_component = COMPONENT_TYPES.include?(rec.feature_type)
+ is_component = COMPONENT_TYPES.include?(rec.feature_type.upcase)
if is_component
# check for container ID
warn("Container <#{rec.feature_type}> has no ID, so using sequence name instead",id) if rec.id == nil
View
6 lib/bio/db/gff/gffcomponent.rb
@@ -38,8 +38,8 @@ module Gff3Component
include Logger
COMPONENT_TYPES = Set.new(%w{
- gene SO:0000704 contig transcript Component region
- })
+ gene SO:0000704 contig transcript component region
+ }.map { |s| s.upcase })
# Walk the component list to find a matching component/container for a
# record. First use the parent ID. If that is missing go by sequence
@@ -89,7 +89,7 @@ module Gff3Features
polyA_site SO:0000553
five_prime_UTR SO:0000204 three_prime_UTR SO:0000205
exon SO:0000147
- })
+ }.map { |s| s.upcase })
end
end
Please sign in to comment.
Something went wrong with that request. Please try again.