Peter Rice peter.rice at
Tue Nov 26 13:53:50 UTC 2002

Vilanova,David,LAUSANNE,NRC/BS wrote:
> Dear all,
> I was wondering if matcher program accepts a sequence via stdin.
> the following exemple doesn't work for me.
> matcher -sequencea 'ATGCGA' -sequenceb 'ATCTAGATATGCGA'
>>cannot open ATGCGA file for read.
> Is there anyway to submit a sequence via stdin ???

You don't mean stdin (that can only read one sequence anyway) ... you mean 
"can I specify a sequence on the command line?"

Yes!!!! You need the "asis" special format.

matcher -sequencea 'asis::ATGCGA' -sequenceb 'asis::ATCTAGATATGCGA'

(assuming your shell allows the command line to be long enough for your 
sequences :-)

Hope this helps


Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at +44 1223 224723

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