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dimchris / mdanalysis

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fasta2select problem #112

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1.Opening a python shell
2.Writing the commands

import MDAnalysis.analysis.align
D=Analysis.analysis.align.fasta2select("test.fasta", is_aligned=True)

The expected output is a dictonary with two keys: 'mobile' and 'reference'

The obtained output is:
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File 
"/ibpc/etna/oteri/PKG/MDAnalysis/0.7.5.1/lib/python2.7/site-packages/MDAnalysis-
0.7.5.1-py2.7-linux-x86_64.egg/MDAnalysis/analysis/align.py", line 570, in 
fasta2select
>     alignment = Bio.SeqIO.to_alignment(
> AttributeError: 'module' object has no attribute 'to_alignment'

I am using MDAnalysis 0.7.5.1 on debian

Changing line 579 of align.py 
from  

 alignment = Bio.SeqIO.to_alignment(

 to
  alignment = Bio.SeqIO.MultipleSeqAlignment(

solves the problem.

I attacch the file used

Original issue reported on code.google.com by francesc...@gmail.com on 4 Jun 2012 at 8:25

Attachments:

GoogleCodeExporter commented 9 years ago 
This issue was closed by revision 1bd901d71759.

Original comment by orbeckst on 8 Jun 2012 at 1:52