[BioPython] Error generated by Clustalw example in Tutorial

[Y Tu]

I tested both commands under window prompt, initially both generated error because window don't know clustalw. Once I give the correct path of the clustalw, both generated alignment results without any error. BTW, I used the one inside BioEdit, I did not find clustalw coming with Biopython. It looks like python use online program at ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/. Am I right?

Then I replace the old _ini_with the new one, but there is a new error message similar to the old one:

>>> alignment = Clustalw.do_alignment(cline)
Traceback (most recent call last):
  File "<interactive input>", line 1, in <module>
  File "C:\Python25\Lib\site-packages\Bio\Clustalw\__init__.py", line 117, in do_alignment
    # check if the outfile exists before parsing
IOError: Output .aln file result1.aln not produced, commandline: clustalw opuntia.fasta -OUTFILE=result1.aln

Also I tested the example on OS X, the same error was generated:

>>> alignment = Clustalw.do_alignment(cline)
sh: line 1: clustalw: command not found
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Bio/Clustalw/__init__.py", line 117, in do_alignment
    % (out_file, command_line))
IOError: Output .aln file result1.aln not produced, commandline: clustalw ./opuntia.fasta -OUTFILE=result1.aln

It seems like the problem is not linked to OS. What other things could be wrong? Thanks.








> Date: Fri, 5 Oct 2007 10:26:06 +0100
> From: biopython at maubp.freeserve.co.uk
> To: ytu888 at hotmail.com
> CC: biopython at lists.open-bio.org
> Subject: Re: [BioPython] Error generated by Clustalw example in Tutorial
> 
> Y Tu wrote:
> > Hi,
> > 
> > I'm reading the Biopython tutorial and running the example of clustalw. But it generate the following error. What's wrong? Thanks.
> > 
> >>>> from Bio import Clustalw
> >>>> cline = Clustalw.MultipleAlignCL(os.path.join(os.curdir, "opuntia.fasta"))
> >>>> cline.set_output("result.aln")
> >>>> print cline
> > clustalw .\opuntia.fasta -OUTFILE=result.aln
> 
> The Windows version of ClustalW is very fussy.  To experiment try 
> running this by hand at the windows command prompt - note that I'm not 
> at my Windows machine so I haven't double checked this:
> 
> clustalw .\opuntia.fasta -OUTFILE=result.aln
> 
> or,
> 
> clustalw opuntia.fasta -OUTFILE=result.aln
> 
> Any error messages would be helpful.
> 
> I suggest you try this in Biopython:
> 
> from Bio import Clustalw
> cline = Clustalw.MultipleAlignCL("opuntia.fasta")
> cline.set_output("result.aln")
> print cline
> 
> Also, we have made a few tweaks to this code since Biopython 1.43 was 
> released (see emails with Emanuel Hey in July 2007).  If you like, you 
> can try updating this module to the CVS version.  Simply backup the 
> existing C:\Python25\Lib\site-packages\Bio\Clustalw\__init__.py and 
> replace it with the latest code from here:
> 
> http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/biopython/Bio/Clustalw/__init__.py?rev=HEAD&cvsroot=biopython&content-type=text/x-python
> 
> Peter
> 

_________________________________________________________________
Peek-a-boo FREE Tricks & Treats for You!
http://www.reallivemoms.com?ocid=TXT_TAGHM&loc=us