fasta2select doesn't find ClustalW

[GoogleCodeExporter]

import MDAnalysis.analysis.align
dict1=MDAnalysis.analysis.align.fasta2select("test.fasta")

I obtain the following error 

Traceback (most recent call last):
  File "./allin.py", line 3, in <module>
    dict1=MDAnalysis.analysis.align.fasta2select("test.fasta")
  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 577, in fasta2select
    import Bio.Clustalw
ImportError: No module named Clustalw

I am using MDAnalysis-0.7.5.1, python 2.7, biopython 1.59 (automatically 
installed by MDAnalysis), clustalw-2.1 on Debian.

Original issue reported on code.google.com by francesc...@gmail.com on 5 Jun 2012 at 5:40

Attachments:

• test.fasta

[GoogleCodeExporter]

According to https://github.com/biopython/biopython/blob/master/DEPRECATED , 
Biopython removed Bio.Clustalw in 1.58 (see below).

If we support the new Bio.AlignIO then we probably need to require at least 
1.51 (see below) and figure out how to change the MDAnalysis code...

==========
DEPRECATED
==========

Bio.Clustalw
============

Declared obsolete in Release 1.52, deprecated in Release 1.55 final, and
removed in Release 1.58. Replaced with Bio.AlignIO for parsing and writing
clustal format alignments (since Release 1.46), and Bio.Align.Applications
for calling the ClustalW command line tool (since Release 1.51). See the
Tutorial for examples.

Original comment by orbeckst on 8 Jun 2012 at 12:17

• Changed state: Accepted
• Added labels: Priority-Low
• Removed labels: Priority-Medium

[GoogleCodeExporter]

This issue was closed by revision 6a764636f624.

Original comment by orbeckst on 18 Jun 2012 at 4:12

• Changed state: Fixed
• Added labels: ****
• Removed labels: ****