[Biopython-dev] Re: swissprot not working ?

[Michal Kurowski]

Brad Chapman [chapmanb at arches.uga.edu] wrote:
> Hi Michal;
> Thanks for writing. Since you caught me right at the end of writing
> e-mails, you get an extra fast response :-)

Seems I'm really lucky ;-).

> In short, the problems you are having look like bugs that we have
> noticed and squashed since the 1.00a2 release. I'll get into more
> detail below, but if you want to "just fix the problems," getting the
> latest CVS version should work for you. The biopython source is
> available via anonymous CVS, with instructions at:
> 
> http://cvs.biopython.org/
> 

I'm going there right away.

> There is a (now infamous) bug that snuck into 1.00a2 in which the
> first 5 lines of a file will be eaten (under some conditions). The
> traceback you are seeing is caused during retrieval of the swissprot
> records in the swissprot.py example. The record is retrieved, but is
> short the first 5 lines, so the swissprot parser thinks it is malformed.

I was having the same type of errors when trying my own scripts. After
a small invastigation I found that SProt.py module is a culprit. At
least it seems to ;-).

> 
> > 2) installation won't go smoothly. ( I'm sure I've got TextTools
> >    installed ;-). The log is in a attachment.
> 
> The installation looks good (hey, a majority of the tests passed :-),
> but these are also a few bugs in the tests:

I was using the last "alpha" release previously and I don't remember
anything like that ( but now I've got diffrent TextTools ).

> Thanks for reporting these problems. We definately like to get
> feedback about this sort of thing. I hope this clears things up
> and that you enjoy using Biopython! 

I surely do.
Thanks a lot,

-- 
Michal Kurowski
<mkur at bio.iimcb.gov.pl>