[EMBOSS] Nthseq issue

Scott Hazelhurst scott at cs.wits.ac.za
Mon Jan 19 13:23:49 UTC 2009

I don't know whether this is a bug or a feature, but I discovered  that
nthseq skips empty sequences in its counting. So if you have 10 sequences
and the  fifth is empty, then nthseq -number 6 actually returns the 7th
sequence. It does print out a warning that the sequence is empty but not
that its skipping (and also if you are putting this in a pipeline you
wouldn't see it). I couldn't see any documentation on this.

I found this problem in a data set from some collaborators, we ran dust and
then used biosed to remove Ns. Obviously this makes some sequences not
usable. While it is understandable why nthseq behaves in the way it does,
the problem is that in an automated set up it may be difficult do the



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