1.1 --- a/utils/convert_homology.py	Mon Jul 18 19:26:21 2011 +0400
     1.2 +++ b/utils/convert_homology.py	Mon Jul 18 19:53:06 2011 +0400
     1.3 @@ -23,6 +23,22 @@
     1.4          seq2_number = str(column[seq2].number)
     1.5          mon_map[seq1.name, seq1_number] = seq2_number
     1.6  
     1.7 +def col2_num(seq1_name, mon1_num, col1_num):
     1.8 +    key = seq1_name, str(mon1_num)
     1.9 +    if key not in mon_map:
    1.10 +        return
    1.11 +    seq2_name = seq1_name + "_2"
    1.12 +    mon2_num = int(mon_map[key])
    1.13 +    for seq2 in aln2.sequences:
    1.14 +        if seq2.name != seq2_name:
    1.15 +            continue
    1.16 +        mon2 = seq2[mon2_num - 1]
    1.17 +        for col2 in aln2.columns:
    1.18 +            if seq2 in col2 and col2[seq2] is mon2:
    1.19 +                return aln2_num[col2]
    1.20 +        return
    1.21 +    raise AssertionError, "seq2_name %s not found" % seq2_name
    1.22 +
    1.23  col_map = {}
    1.24  aln1_num = aln1.add_markup('number')
    1.25  aln2_num = aln2.add_markup('number')
    1.26 @@ -33,22 +49,9 @@
    1.27              continue
    1.28          if seq1 not in col1:
    1.29              continue
    1.30 -        key = seq1.name, str(col1[seq1].number)
    1.31 -        if key not in mon_map:
    1.32 -            continue
    1.33 -        num2 = None
    1.34 -        try:
    1.35 -            for seq2 in aln2.sequences:
    1.36 -                if seq2.name.startswith(seq1.name):
    1.37 -                    mon2 = seq2[col1[seq1].number]
    1.38 -                    for col2 in aln2.columns:
    1.39 -                        if col2[seq2] is mon2:
    1.40 -                            num2 = str(aln2_num[col2])
    1.41 -                            raise Exception
    1.42 -        except Exception:
    1.43 -            pass
    1.44 +        num2 = col2_num(seq1.name, col1[seq1].number, aln1_num[col1])
    1.45          if num2 is not None:
    1.46 -            col_map[num1] = num2
    1.47 +            col_map[num1] = str(num2)
    1.48  
    1.49  print sorted(col_map.items(), key=lambda (a,b): int(a))
    1.50