[Biopython-dev] SeqIO Abi Parser

[Peter Cock]

On Thu, Aug 4, 2011 at 12:30 PM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
> Hi Peter,
> Ah yes, I didn't know there could be handles without .seek() and .tell(),
> and I thought those two are the proper way of traversing files, so I used
> them. I also didn't realize you could use SeqIO with network handles, too.
> This is really neat :).

Yes - having a handle focused API makes some clever stuff possible :)
Of course, parsing sequences directly from network handles isn't always
a good idea, but it can be useful.

> In any case, sure, I'd love to make some changes to the current AbiIO code
> so it works without .seek() and .tell(). Is there any other input types that
> does not use .seek() and .tell() other than network handles?

I suspect some specialised handles for accessing compressed files might
have similar limitations. In the case of gzip at least, I think it does support
seek and tell.

> Here's my new branch from the current master:
> https://github.com/bow/biopython/tree/seqio-abi_handlefix
> nothing different for now but I'll push my updates soon.

Don't rush yourself - I'm away for a long weekend so won't be testing
any updates till next week anyway.

Thanks,

Peter