[Biopython-dev] SwissProt parser: Feature ID kept in description string

[Michiel de Hoon]

I have no objections.
--Michiel.

--- On Mon, 9/13/10, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: SwissProt parser: Feature ID kept in description string
> To: "Biopython-Dev Mailing List" <biopython-dev at biopython.org>, "Michiel de Hoon" <mjldehoon at yahoo.com>
> Date: Monday, September 13, 2010, 6:29 AM
> Hi Michiel at al,
> 
> I'm looking at the SwissProt plain text parser (for Bug
> 2235, making
> SeqFeature objects in SeqIO for "swiss" format), and
> noticed something
> that puzzles me in the new parser in
> Bio/SwissProt/__init__.py:
> 
> The parser spots /FTId= entries and extracts the feature
> ID, which
> is good, but leaves this string in the description string,
> which I find
> odd. Essentially I'd like to change this bit:
> 
>     if line[29:35]==r"/FTId=":
>         ft_id =
> line[35:70].rstrip()[:-1]
>     else:
>         ft_id =""
> 
> too:
> 
>     if line[29:35]==r"/FTId=":
>         ft_id =
> line[35:70].rstrip()[:-1]
>         description = ""
>     else:
>         ft_id =""
> 
> What do you think?
> 
> Peter
>