[BioPython] clustaw

[biter bilen]

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hi everybody,

i am to write a program that makes gapless multiple alignments with 17 sequences. i attempted to use clustalw within biopyhon. but even the example program at

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

gave errors as:

Traceback (most recent call last):
  File "<pyshell#2>", line 1, in ?
    execfile('clustal_run.py')
  File "clustal_run.py", line 24, in ?
    alignment = Clustalw.do_alignment(cline)
  File "C:\Python22\Lib\site-packages\Bio\Clustalw\__init__.py", line 86, in do_alignment
    raise ValueError("Bad command line option in the command: %s"
ValueError: Bad command line option in the command: clustalw .\opuntia.fasta -OUTFILE=test.aln

it is not mentioned in the cookbook that i should download a software for running clustalw. i think the problem is not the files(opuntia.fasta or test.aln) but clustalw since i dowloaded opuntia.fasta. 

has anyone got idea about the problem?

thanks 

biter



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<P>hi everybody,</P>
<P>i am to write a program that makes gapless multiple alignments with&nbsp;17 sequences.&nbsp;i attempted to use clustalw within&nbsp;biopyhon. but even the example program at</P>
<P>&nbsp;<A href="http://bioweb.pasteur.fr/docs/doc-gensoft/biopython/Doc/examples/clustal_run.py">http://bioweb.pasteur.fr/docs/doc-gensoft/biopython/Doc/examples/clustal_run.py</A></P>
<P>gave errors as:</P>
<P>Traceback (most recent call last):<BR>&nbsp; File "&lt;pyshell#2&gt;", line 1, in ?<BR>&nbsp;&nbsp;&nbsp; execfile('clustal_run.py')<BR>&nbsp; File "clustal_run.py", line 24, in ?<BR>&nbsp;&nbsp;&nbsp; alignment = Clustalw.do_alignment(cline)<BR>&nbsp; File "C:\Python22\Lib\site-packages\Bio\Clustalw\__init__.py", line 86, in do_alignment<BR>&nbsp;&nbsp;&nbsp; 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>it is not mentioned in the cookbook that i should download a software for running clustalw. i think the problem is not the files(opuntia.fasta&nbsp;or test.aln) but clustalw since i dowloaded opuntia.fasta. </P>
<P>has anyone got idea about the problem?</P>
<P>thanks </P>
<P>biter</P><p><br><hr size=1><b>Do You Yahoo!?</b><br>
<a href="http://rd.yahoo.com/finance/mailsig/new/*http://finance.yahoo.com">Yahoo! Finance</a> - Get real-time stock quotes
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