[Biopython] Subprocess:Clustalw

[Christian Schäfer]

On 01/19/2010 12:45 PM, Alvaro F Pena Perea wrote:
> but he point is that I would like to choose my "infile" from argv. I mean,
> something like this:
>
> archive = open(sys.argv[1])
> cline = ClustalwCommandline("clustalw2",infile=archive)

I'm not sure I understand the significance of your approach. If this is 
about reading the path to the fasta file from commandline, why don't you 
do just the following:

"""
Assuming, sys.argv[1] holds the path to the fasta file
"""
archive = sys.argv[1]	#Instead of archive = open(sys.argv[1])
cline = ClustalwCommandline("clustalw2",infile=archive)


Chris