1.1 --- a/utils/extract_pfam.py	Tue Jul 12 17:12:05 2011 +0400
     1.2 +++ b/utils/extract_pfam.py	Tue Jul 12 17:56:42 2011 +0400
     1.3 @@ -139,15 +139,16 @@
     1.4      assert len(aln.sequences) >= options.min_depth, "Alignment too thin"
     1.5  
     1.6  def output_aln(aln):
     1.7 -    filename = "pfam_%s_%s.markup" % (aln.ac, aln.id)
     1.8 -    with open(filename, "w") as outfile:
     1.9 +    with open(aln.filename, "w") as outfile:
    1.10          aln.to_file(outfile, format="markup")
    1.11 -        print "Wrote %s" % filename
    1.12 +        print "Wrote %s" % aln.filename
    1.13  
    1.14  def process_aln(aln):
    1.15      out_aln = Alignment()
    1.16      out_aln.ac = aln.ac
    1.17      out_aln.id = aln.id
    1.18 +    out_aln.filename = "pfam_%s_%s.markup" % (out_aln.ac, out_aln.id)
    1.19 +    assert not os.path.exists(out_aln.filename), "File already exists"
    1.20      for seq in aln:
    1.21          try:
    1.22              out_seq = None