[BioPython] AttributeError: 'module' object has no attribute 'parse'

[I. Friedberg]

Anybody's Debian-fu strong enough to create a clean 1.43 package?

Iddo

On 6/12/07, richa <richa at musc.edu> wrote:
>
> Compiled from source and the no more error messages.  Thank you all for
> your help and advise.
>
> -Adam Richards (richa)
>
> Christof Winter wrote:
> > richa wrote:
> >> Hi all,
> >>
> >> Just installed biopython on ubuntu feisty.  Dependencies and package
> >> seemed to install without a problem.  Many of the test files that
> >> come with it work fine, but the SeqIO object runs into a problem.
> >> For example, the following code causes an error saying that the
> >> 'module' object has no attribute 'parse'.
> >>
> >> Is this a problem of syntax or is it an installation issue?
> >>
> >> from Bio import SeqIO
> >> handle = open("ls_orchid.fasta", "rU")
> >> for record in SeqIO.parse(handle, "fasta") :
> >>    print record.id
> >
> > Dear richa:
> >
> > It is an installation issue. I got exactly the same error. I am
> > running Debian Linux with the python-biopython package installed:
> >
> > $ dpkg -l | grep biopython
> > ii  python-biopython                 1.42-2
> >
> > After upgrading to the newest version with
> > $ sudo apt-get install python-biopython
> >
> > $ dpkg -l | grep biopython
> > ii  python-biopython                 1.43-1
> >
> > the error is gone!
> >
> > By the way: this was the content of my old Bio/SeqIO/__init__.py:
> >
> > """Sequence input/output designed to look similar to the bioperl design.
> >
> > At present, these are all hand written.  I would like to have
> > autogenerated parsers in the futures, esp. with the ability to parse
> > only subsets of the data, and to support event generated parsers.
> >
> > Note that once a parser is given an input string, it is free to read
> > as much of the data as it wants to read, unless otherwise mentioned.
> > """
> >
> > Nothing more. Now it matches the newest version as posted by Peter.
> >
> > Cheers,
> > Christof
> >
>
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>



-- 

I. Friedberg

"The only problem with troubleshooting is that
sometimes trouble shoots back."