Passing Alignment Parameters Through Clustalwcommandline

Question

[Thaman]

As i am trying to do more work in Multiple sequence alignment using clustalw wrapper in biopython, i am wondering how can i pass parameters through clustalcommandline which i fail to do repeatedly.

Parameters in details like :

• Gap open penalty, Gap extension penalty, no end gap(yes, no), gap distance, weight matrix(blosum, pam etc), type (DNA,protein) and other optional parameters.

Right now i am working on default alignment settings provided by clustalw. As default settings are not fulfilling my interest, i am more keen in adding parameters in given below lines.

 import sys, subprocess
 from Bio import AlignIO
 from Bio.Align.Applications import ClustalwCommandline
 cline = ClustalwCommandline("clustalw",
      infile="opuntia.fasta")
 child = subprocess.call(str(cline),
      shell=(sys.platform!="win32"))

Moreover, i will be more pleased if you guys will explain how can i know the inputted fasta file is of nucleotide,DNA or protein.

Thanks for your interest

Answer 1

[Giovanni M Dall'Olio]

I didn't test this, but it all gets a lot clearer if you look at the source of Bio/Align/Applications/_Clustalw.py

• 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

note: if you use ipython, you can look at the code of a function easily, just type ClustalwCommandline??

In any case, notice that you can access all these options after having created a wrapper for the clustalw command line. For example:

>>> c = ClustalwCommandline(type='dna')
>>> dir(c)
['__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']
>>> c.gapopen = -2
>>> print c
clustalw -type=dna -gapopen=-2

[Peter]

Also try typing help(c) at the python prompt to find out more about the command line wrapper object you've just created.

[Thaman]

Ok let me try and see whether my understanding will work or not. If not then i will again click you. Thanks

[Giovanni M Dall'Olio]

you are welcome... I don't want to be silly, but please consider voting up the answers that you find useful, even if you don't want to accept them :-)

[Thaman]

Can you answer my below query about inputted fasta file.

[Giovanni M Dall'Olio]

I think you should ask that as a separate question. In principle, neither clustalw nor Bio.Align.Applications from Biopython have tools to determine whether a sequence is protein or dna.

[Thaman]

Okei i will do that.