extract predicted gene sequences from gilmmer output
1 answer
You can use http://dawgpaws.sourceforge.net/man/cnv_genemark2gff.html (this is for GeneMark)
For glimmer:
grep ^orf output.glimmer | awk '{OFS="\t"}{strang = "+"}{if($4 < 0) strang="-"}{gsub(/[+-]/," ")}{print "FASTA_HEADER", "GLIMMER", "gene" , $2 , $3, $5, strang , $4, "ID="$1"; NOTE:GLIMMER ORF prediction;"}'
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