[EMBOSS] featreport / featcopy outputting to genbank
Scott.Geib at ARS.USDA.GOV
Thu Apr 4 02:40:37 UTC 2013
I am trying to output a gff3 file to genbank format using featreprot or featcopy.
I have many molecules in my gff3 file (contigs from assembly), I was wondering how to designate them as different locus so that the flat file generates a new locus for each and then displays features associated with that locus. Right now it is all written to a single locus in the outputted genbank file.
Just as example, I am wrtting my gff files as follows:
Contig1 . databank_entry 1 1000 . . . organism="X";strain="Y"
Contig1 . gene 171 497 . + . gene="sod"
Contig1 . mRNA 171 497 . + . .
Contig1 . exon 171 497 . + . .
Contig1 . CDS 171 497 . + . gene="sod"
Contig2 . databank_entry 1 1000 . . . organism="X";strain="Y"
Contig2 . gene 3 323 . + . gene="ba"
Contig2 . mRNA 3 323 . + . .
Contig2 . exon 3 323 . + . .
Contig2 . CDS 3 323 . + . gene="ba"
And this is getting returned to me as a single locus
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