[BioPython] AttributeError: 'module' object has no attribute 'parse'
Peter
biopython at maubp.freeserve.co.uk
Tue Jun 12 17:09:17 UTC 2007
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
That should work. Odd...
What version of Python are you using?
It might be helpful to see the full error message, it should include the
path to a file .../Bio/SeqIO/__init__.py
If you have a quick look in that file and double check there is a
function "parse" (e.g. search for "def parse("), and it looks something
like the latest version, which is online here:
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/SeqIO/__init__.py?rev=1.19&cvsroot=biopython&content-type=text/vnd.viewcvs-markup
You said you were using Ubuntu Feisty - did you install Biopython from
source code by downloading the tar ball, or using "apt-get"?
If you used apt-get then you could try removing the package, and then
installing from source instead (fairly simple). If that works then maybe
there is a problem in the Feisty package.
Peter
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