-sbegin -send blues
gbottu at ben.vub.ac.be
Tue Sep 17 07:50:05 UTC 2002
from : BEN
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 ?
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