[BioPython] error about do_alignment function in Clustalw module

[biter bilen]

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hi everybody,

i wanted to test clustal_run.py at 

http://bioweb.pasteur.fr/docs/doc-gensoft/biopython/Doc/examples/clustal_run.py

this uses do_alignment function and i see an error as:

raise ValueError("Bad command line option in the command: %s"
ValueError: Bad command line option in the command: clustalw .\opuntia.fasta -OUTFILE=test.aln

i downloaded clustalx 1.81 (sorry for the previous message) as said in the help documentation. 

can the error happen due to not seeing the path of clustalw? i realised that no clustalw executable file exists in the said (clustalx 1.81) package. can anyone help me about it? 

special thanks

biter



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<P>hi everybody,</P>
<P>i wanted to test clustal_run.py at </P>
<P>http://bioweb.pasteur.fr/docs/doc-gensoft/biopython/Doc/examples/clustal_run.py</P>
<P>this uses do_alignment function and i see an error as:</P>
<P>raise ValueError("Bad command line option in the command: %s"<BR>ValueError: Bad command line option in the command: clustalw .\opuntia.fasta -OUTFILE=test.aln</P>
<P>i downloaded clustalx 1.81 (sorry for the previous message)&nbsp;as said in the help documentation. </P>
<P>can&nbsp;the error&nbsp;happen due to not seeing the path of clustalw? i realised that no clustalw executable file exists in the said (clustalx 1.81) package. can&nbsp;anyone help me about it? <IMG src="http://us.i1.yimg.com/us.yimg.com/i/mesg/tsmileys/2.gif"></P>
<P>special thanks</P>
<P>biter</P><p><br><hr size=1><b>Do You Yahoo!?</b><br>
<a href="http://health.yahoo.com/">Yahoo! Health</a> - Feel better, live better
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