-sbegin -send blues

Guy Bottu gbottu at ben.vub.ac.be
Tue Sep 17 07:50:05 UTC 2002

from : BEN

	Dear colleagues,
I just installed Staden and its EMBOSS interface. I noted a few problems and 
sent a bug report, with among other things the following :

Why is it that sometimes you can make a program operate only on a range of 
the sequence by filling in the "Start position" "End position" boxes, but 
sometimes not. An example of a program that operates on the complete sequence no 
matter what you do is octanol.

I received as reply :

All EMBOSS programs that take a -sequence option should also accept -sbegin
and -send options for indicating the range, but it appears some do not. I view 
this as an EMBOSS bug (in Octanol). There doesn't appear to be any component
of the ACD file to indicate whether sbegin and send are valid options, and
indeed octanol on the command line is happy to accept (and ignore) them.

What a surprise ! I had not thought of testing at the command line. Does someone 
know why it is that some EMBOSS programs behave in this nonstandard way ?

	Guy Bottu

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