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  • Annotation: Glimmer to GFF

    Hi,

    We tried to work with Glimmer for prokaryotes annotation, but we need a GFF format to load in Artemis.
    anybody can tell me
    How can I convert the glimmer out to GFF3 format, please?

    Thanks.

  • #2
    A one liner for a simple genome

    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.

    Comment

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