[EMBOSS] Nthseq issue

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
adjustment.

Regards

Scott

<html><p><font face = "verdana" size = "0.8" color = "navy">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary.</font></p></html>