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[jalview.git]
/
forester
/
ruby
/
evoruby
/
exe
/
select_same_gn.rb
diff --git
a/forester/ruby/evoruby/exe/select_same_gn.rb
b/forester/ruby/evoruby/exe/select_same_gn.rb
index
8fcb6be
..
7dbe9f1
100755
(executable)
--- a/
forester/ruby/evoruby/exe/select_same_gn.rb
+++ b/
forester/ruby/evoruby/exe/select_same_gn.rb
@@
-19,6
+19,7
@@
module Evoruby
f = MsaFactory.new()
IGNORE_SEQS_LACKING_GN = false
f = MsaFactory.new()
IGNORE_SEQS_LACKING_GN = false
+ IGNORE_FRAGMENTS = false
IGNORE_SPECIES = true
msa = nil
IGNORE_SPECIES = true
msa = nil
@@
-58,8
+59,7
@@
module Evoruby
all_names << name
end
all_names << name
end
- if fragment_re.match( name )
-
+ if IGNORE_FRAGMENTS && fragment_re.match( name )
outfile.puts("ignored because fragment: " + name)
frag_counter += 1
next
outfile.puts("ignored because fragment: " + name)
frag_counter += 1
next
@@
-121,7
+121,10
@@
module Evoruby
gn_to_seqs[gn].add_sequence(seq)
end
gn_to_seqs[gn].add_sequence(seq)
end
- outfile.puts( "Sequences ignored because \"fragment\" in desc : " + frag_counter.to_s )
+ if IGNORE_FRAGMENTS
+ outfile.puts( "Sequences ignored because \"fragment\" in desc : " + frag_counter.to_s )
+ end
+
if IGNORE_SEQS_LACKING_GN
outfile.puts( "Sequences ignored because no \"GN=\" in desc : " + no_gn_counter.to_s )
end
if IGNORE_SEQS_LACKING_GN
outfile.puts( "Sequences ignored because no \"GN=\" in desc : " + no_gn_counter.to_s )
end