[Biopython] Exonerate Parser Error

[Wibowo Arindrarto]

Hi Zheng,

Thank you for the files :). I found out what was causing the error and
have pushed a patch along with some tests to our codebase
(https://github.com/biopython/biopython/commit/377889b05235c2e6f192916fb610d0da01b45c6d).
You should be able to parse your file using the latest `master`
branch.

Hope this helps,
Bow

On Thu, Mar 20, 2014 at 9:42 PM, Zheng Ruan <zruan1991 at gmail.com> wrote:
> Hi Bow,
>
> I'm happy to provide the example for testing. See attachment.
>
> The command to generate the output above.
> exonerate --showvulgar no --showalignment yes nuc.fa pro.fa
>
> I'll check the test suite to see if I can find why.
>
> Best,
> Zheng
>
>
> On Thu, Mar 20, 2014 at 4:33 PM, Wibowo Arindrarto <w.arindrarto at gmail.com>
> wrote:
>>
>> > 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 :).
>>
>> Oops, I meant the reverse ~ we have several test cases for protein2dna
>> which may explain why it works when the protein sequence comes first
>> ;).
>
>