[Biopython] Exonerate Parser Error

[Zheng Ruan]

Thanks Bow,

That works for me. But it seems the parser doesn't take the nucleotide
information into the hsps. All I get is a pairwise alignment between two
proteins. Nucleotide information is useful because I want to know the codon
-- amino acid correspondence. In the case of frameshift the situation may
not be that straightforward. Maybe you have other concern of not doing this.

Best,
Zheng


On Thu, Mar 20, 2014 at 7:30 PM, Wibowo Arindrarto
<w.arindrarto at gmail.com>wrote:

> 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
> >> ;).
> >
> >
>