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

[Christof Winter]

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