This is pretty old but the problem might still persist.
I took the final result file with the structure:
Code:
GLIMMER (ver. 3.02; iterated) predictions:
orfID start end frame score
-------- ----- ----- -- -----
>FASTA_HEADER
orf00003 560 63 -3 3.04
orf00004 865 752 -2 5.42
orf00010 2199 4055 +3 3.14
orf00027 4028 9019 +2 3.06
I believe that might do it:
Code:
grep ^orf output.glimmer.raw | 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;"}'
Result:
Code:
FASTA_HEADER GLIMMER gene 560 63 3.04 - 3 ID=orf00003; NOTE:GLIMMER ORF prediction;
FASTA_HEADER GLIMMER gene 865 752 5.42 - 2 ID=orf00004; NOTE:GLIMMER ORF prediction;
FASTA_HEADER GLIMMER gene 2199 4055 3.14 + 3 ID=orf00010; NOTE:GLIMMER ORF prediction;
FASTA_HEADER GLIMMER gene 4028 9019 3.06 + 2 ID=orf00027; NOTE:GLIMMER ORF prediction;
This has to be adapted especially if you have many Chromosomes/Contigs. I did have only one circular genome.