[EMBOSS] iep/gifasta

Bernd Web bernd.web at gmail.com
Mon Dec 17 20:01:32 UTC 2007


I'd like to run iep on a sequence and use either pir or osformat gifasta.
The following gives an error (using emboss 5.0.0 on Debian):

iep -filter -osformat gifasta -sequence seq.txt
This returns "Died: Unknown qualifier -osformat"

iep -filter -sformat pir seq.txt or iep -sformat pir -sequence seq.txt
also give an error:
"Died: iep terminated: Bad value for '-sequence' with -auto defined"
(with or without the sequence flag)

However, iep -sformat fasta seq.txt works. What am I doing wrong?

I'd like output to contain the accession number. I thought -osformat
gifasta was for this purpose.
My FastA definition line is e.g.
The IEP report would me more useful if it contains the ENSG number
instead of "protein coding or the entire definition line.

How to do this?

Kind regards,

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