[Biopython] Exonerate Parser Error

[Wibowo Arindrarto]

Hi Zheng,

> I'm trying to use Bio.SearchIO to parse a file generated by exonerate. It
> is a pairwise alignment between a protein sequence and nucleotide sequence.
> I notice that if I put the protein sequence first, SearchIO can happily
> parse the file, but if the nucleotide sequence comes first, it will raise
> an error.

Formatting on the plaintext mail seems inadequate for me at the
moment. Would you mind sending me the file that contains the
alignment? If it's too big, partial files are ok, too.

Looking at our test cases, this particular case may have slipped
testing. We do test for several cases of dna2protein (which could
explain why it works when the nucleotide sequence comes first), but
not protein2dna. Please let me know if I can also use your example as
a test in our test corpus :).

Cheers,
Bow