[maker-devel] maker_functional_gff

[Carson Holt]

maker_functional_gff works with UniProt/Swiss-Prot.  The uniref-50 headers
are different.  The script looks for the OS= GN= and PE= tags. You might be
able to coerce it into working on the UniRef header by changing Tax= to OS=,
RepID= to GN= and then adding a PE= to the end of the header as just a
placeholder.

--Carson


From:  "Mack, Brian" <Brian.Mack at ARS.USDA.GOV>
Date:  Monday, April 7, 2014 at 6:55 AM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] maker_functional_gff

Hi, I am trying to use the maker_functional_gff program to add functional
annotations to my maker gff file. I used blastp with the tabular “-outfmt 6”
option against the uniprot uniref-50. I put these results in the
maker_functional_gff program using “maker_functional_gff  uniref-50
blastp-output  maker.gff” but I get the following errors and no updating of
the names in my maker gff file:
 
Use of uninitialized value $id in hash element at
/home/b/maker/bin/maker_functional_gff line 142, <$IN> line 16924097.
Use of uninitialized value $id in hash element at
/home/b/maker/bin/maker_functional_gff line 144, <$IN> line 16924097.
Can't parse details from FASTA header: >UniRef50_K1R9E3 Uncharacterized
protein n=1 Tax=Crassostrea gigas RepID=K1R9E3_CRAGI
 
Use of uninitialized value $id in hash element at
/home/b/maker/bin/maker_functional_gff line 142, <$IN> line 16924128.
Use of uninitialized value $id in hash element at
/home/b/maker/bin/maker_functional_gff line 144, <$IN> line 16924128.
Can't parse details from FASTA header: >UniRef50_K1R9E4 Transporter n=2
Tax=Mollusca RepID=K1R9E4_CRAGI
 
Any ideas of what I’m doing wrong?
 
Brian




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