[Biopython-dev] Seq object ungap method

[Peter]

On Wed, Nov 11, 2009 at 5:37 AM, Eric Talevich <eric.talevich at gmail.com> wrote:
> On Fri, Nov 6, 2009 at 2:00 PM, Peter <biopython at maubp.freeserve.co.uk>
> wrote:
>>
>> Hi all,
>>
>> Something we discussed last year was adding an ungap method
>> to the Seq object. See for example this thread:
>>
>> http://lists.open-bio.org/pipermail/biopython/2008-September/004515.html
>>
>> I've (finally) taken the time to actually implement this, and have
>> posted it on a github branch for comment:
>>
>> http://github.com/peterjc/biopython/tree/ungap
>>
>
> Neat!

So worth checking in then?

> Some trivial comments:
> 1. There's a typo on line 897 in Seq.py: s/stil/still/

Thanks.

> 2. Each colon character has a space before it in this function. I've never
> seen you use that style before. (Other Biopython code doesn't do that.)

I think some other bits of Biopython do this, but I agree, we should
be consistent and removing the spaces matches PEP8.

> 3. In the exception messages, and other places in Biopython, the
> concatenated string (or compound expression) is contained in parentheses,
> but there's also a backslash at the end of each line. I don't think the
> backslash is necessary, since the parens already group the multi-line
> expression.

Again, you are right, and it would perhaps be worth tidying up cases
of that. But not critical.

Peter