[Biopython-dev] next release closer (?)

[Cayte]

----- Original Message ----- 
From: "Andrew Dalke" <dalke at acm.org>
To: <biopython-dev at biopython.org>
Sent: Monday, November 20, 2000 9:38 PM
Subject: Re: [Biopython-dev] next release closer (?)


> Jeff on the error Cayte's getting:
> >>    I get an error from test_prosite.  My OS is Win98.
> >>
> >> test test_prosite crashed -- exceptions.TypeError : an integer is
> required
> >
> >I don't know.  Andrew?
> >
> >One thing you can try, is to run:
> >python test_prosite.py
> >
> >and see the full stack dump that's generated.
> 
> I would need to see the stack trace.  I cannot reproduce the error using
> the current CVS version.
> 
> I don't see the string "an integer is required" anywhere in the Prosite
> code, nor in the rest of the biopython distribution.  Looking at the
> source code for Python, that only arises during a conversion to int.
> So I would need to find out which call to int is failing and the text
> that it's trying to convert.
> 
C:\biopython-0.90-d03\Tests>python test_prosite.py
Patterns: 'A.' 'A' '(A)'
Traceback (most recent call last):
  File "test_prosite.py", line 88, in ?
    m = p.search(Seq.Seq(x))
  File "c:\biopyt~1.90-\Bio\Prosite\Pattern.py", line 168, in search
    m = self.grouped_re.search(buffer(seq.data), pos, endpos)
TypeError: an integer is required

                                     Cayte