You can run clustalw as a command passing it -INFILE , -PROFILE1 , PROFILE2 etc params without getting into user input mode. Make sure clustalw executable is in your PATH variable [HTML][HTML]here are the options[HTML] http://www.sacs.ucsf.edu/Documentation/seqsoftware/ClustalW1.7/help9.html

I had a big headache when solving this problem 6 months back when I didn't knew anything. But anyway now I can write you in detail how to do it silently through script.

import subprocess
from Bio.Align.Applications import ClustalwCommandline
cline = ClustalwCommandline("clustalw2", infile="opuntia.fasta", seqnos="ON", gapopen=2, gapext=0.5)
child = subprocess.call(str(cline), shell=(sys.platform!="win32"))

• Importing clustalw command line wrapper
• Subprocess - The subprocess module allows you to spawn new processes, connect to their input/output/error pipes, and obtain their return codes

Other parameters available

• Gap open penalty: -gapopen
• Gap extension penalty: -gapext
• no end gap(yes, no): -endgaps
• gap distance: -gapdist
• weight matrix(blosum, pam etc): -matrix ["BLOSUM", "PAM", "GONNET", "ID"]
• type (DNA,protein): -type

It's easy to check the availabe parameters/options after wrapper have been created. Suppose from the above given example:

>>> cline = ClustalwCommandline(type='dna')
>>> dir(cline)
['__class__', '__delattr__', '__dict__', '__doc__', '__getattribute__', '__hash__', 
'__init__', '__module__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', 
'__setattr__', '__str__', '__weakref__', '_check_value', '_clear_parameter', 
'_get_parameter', '_validate', 'align', 'bootlabels', 'bootstrap', 'case', 'check', 
'clustering', 'convert', 'dnamatrix', 'endgaps', 'fullhelp', 'gapdist', 'gapext', 
'gapopen', 'helixendin', 'helixendout', 'helixgap', 'help', 'hgapresidues', 'infile',  
'iteration', 'kimura', 'ktuple', 'loopgap', 'matrix', 'maxdiv', 'maxseqlen',
'negative', 'newtree', 'newtree1', 'newtree2', 'nohgap', 'nopgap', 'nosecstr1',
'nosecstr2', 'noweights', 'numiter', 
'options', 'outfile', 'outorder', 'output', 'outputtree', 'pairgap', 'parameters', 
'profile', 'profile1', 'profile2', 'program_name', 'pwdnamatrix', 'pwgapext', 
'pwgapopen', 'pwmatrix', 'quicktree', 'quiet', 'range', 'score', 'secstrout', 'seed', 
'seqno_range', 'seqnos', 'sequences', 'set_parameter', 'stats', 'strandendin',  
'strandendout', 'strandgap', 
'terminalgap', 'topdiags', 'tossgaps', 'transweight', 'tree', 'type', 'usetree',  
'usetree1', 'usetree2', 'window']

>>> print cline
clustalw2 -infile=opuntia.fasta -seqnos=ON -gapopen=2 -gapext=0.5

Before writing script you can first try by importing clustalwcommandline wrapper object play by passing parameters through shell/command line.

More information and Links

• http://www.daimi.au.dk/~mailund/scripting2005/lecture-notes/clustalw-ex.html
• http://www.sacs.ucsf.edu/Documentation/seqsoftware/ClustalW1.7/help9.html
• http://blog.sina.com.cn/s/blog_679a18eb0100ittq.html (Clear example on how to do it)
• My similar post in Biostar

Note- If you are using under windows then its important to put the clustalw on the system variable path

Hope it helps :)