[EMBOSS] Unknown output format 'refseqp' and 'genpept'

Peter biopython at maubp.freeserve.co.uk
Mon Dec 7 19:36:30 UTC 2009


Hi,

I have a protein IntelliGenetics file used in the Biopython test suite:
http://biopython.org/SRC/biopython/Tests/IntelliGenetics/VIF_mase-pro.txt

I am using EMBOSS 6.1.0 (patch level 2 I think), and I am trying
to turn this into a "GenBank Protein File", or GenPept file, using
EMBOSS seqret.

EMBOSS can read the file fine, this works:
$ seqret -auto -sformat=ig -osformat=fasta VIF_mase-pro.txt temp.txt

Giving FASTA output with 16 gapped protein sequences, which is
good - although the ID of the first record is a bit odd.

Using "genbank" as the output format in EMBOSS seems to
mean nucleotide and not protein:

$ seqret -auto -sformat=ig -osformat=genbank VIF_mase-pro.txt temp.txt
Error: Sequence format 'genbank' not supported for protein sequences
Error: Sequence format 'genbank' not supported for protein sequences
...
Error: Sequence format 'genbank' not supported for protein sequences

Referring to the documentation,
http://emboss.sourceforge.net/docs/themes/SequenceFormats.html
I then tried "genpept" and "refseqp":

$ seqret -auto -sformat=ig -osformat=genpept VIF_mase-pro.txt temp.txt
Error: Unknown output format 'genpept'
Error: Unknown output format 'genpept'
...
Error: unknown output format 'genpept'

$ seqret -auto -sformat=ig -osformat=refseqp VIF_mase-pro.txt temp.txt
Error: Unknown output format 'refseqp'
Error: Unknown output format 'refseqp'
...
Error: unknown output format 'refseqp'

Doesn't EMBOSS seqret support genpept/refseqp as an output format?

Thanks,

Peter C.



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