f = MsaFactory.new()
IGNORE_SEQS_LACKING_GN = false
+ IGNORE_FRAGMENTS = false
IGNORE_SPECIES = true
msa = nil
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
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