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

richa richa at musc.edu
Tue Jun 12 12:31:35 EDT 2007


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



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