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-   -   Annotation: Glimmer to GFF (http://seqanswers.com/forums/showthread.php?t=20663)

Daniel Fernandez 06-07-2012 01:16 PM

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.

ebioman 08-08-2014 01:00 AM

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.


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