Gff Converter For Use With Mummer/Promer (Microbial Genome)

Question

[Mat]

Hi,

Does anyone of a script to convert a gff3 file into a format that PROmer's mapview can accept for a bacterial genome? mapview's expectation is for eukaryotic genomes, and so it's looking for a gff file like this

D_melanogaster_2Rslice    Dpseudo    initial-exon    16918    16938    .    +    .    2R_CG14752.1
D_melanogaster_2Rslice    Dpseudo    internal-exon    17371    17432    .    +    .    2R_CG14752.1
D_melanogaster_2Rslice    Dpseudo    last-exon    17913    18168    .    +    .    2R_CG14752.1

My gff3 looks like this, which mapview is understandably not accepting.

BX571856.1    EMBL    gene    36132    36371    .    +    .    locus_tag=SAR0026
BX571856.1    EMBL    CDS    36132    36368    .    +    0    locus_tag=SAR0026;note=No significant database matches. Doubtful CDS;transl_table=11;product=hypothetical protein;protein_id=CAG39054.1;db_xref=GI:49240408;db_xref=UniProtKB%2FTrEMBL:Q6GKR9;exon_number=1
BX571856.1    EMBL    start_codon    36132    36134    .    +    0    locus_tag=SAR0026;note=No significant database matches. Doubtful CDS;transl_table=11;product=hypothetical protein;protein_id=CAG39054.1;db_xref=GI:49240408;db_xref=UniProtKB%2FTrEMBL:Q6GKR9;exon_number=1
BX571856.1    EMBL    stop_codon    36369    36371    .    +    0    locus_tag=SAR0026;note=No significant database matches. Doubtful CDS;transl_table=11;product=hypothetical protein;protein_id=CAG39054.1;db_xref=GI:49240408;db_xref=UniProtKB%2FTrEMBL:Q6GKR9;exon_number=1

I could extract all the lines like the first, but what I don't know how to do is persuade mapview to accept something that doesn't have the initial-exon, internal-exon,last-exon structure (incidentally, how are single-exon genes represented in this scheme?)

I guess I'm not the first to try use mummer/promer/mapview etc for bacterial work so there must be a solution out there somewhere? Sure hope so - I'm kindof new to this so would be happy to hear suggestions for how to go about this. Thanks M

Answer 1

[farpostv]

I am having a similar problem. I do not have a script to convert gff3 for use in mummer. But I did replace "gene" with "single-exon" and that seems to do the trick. However, you cannot see the gene direction. Interestingly, if I leave the "CDS" lines in, I get the "genes" and the "CDS" mapped on separate rows in the resulting mapview, but I cannot map just the CDS lines alone. Also I just repeat the same gff file for use as the "utr" file and the "cds" file for the mapview command (mapview -f pdf -p testmapview promer.coords test.gff test.gff)

Does anyone else have a better solution than this?

So some lines like this:

NC_009615.1 annotation remark 1 4811379 . . . gi=150006674

NC_009615.1 feature source 1 4811379 . + . strain=ATCC%208503;mol_type=genomic%20DNA

NC_009615.1 feature gene 1 1398 . + . db_xref=GeneID%3A5305156;locus_tag=BDI_0001;gene=dnaA

NC_009615.1 feature CDS 1 1398 . + 0 gene=dnaA;protein_id=YP_001301418.1

NC_009615.1 feature gene 1656 4196 . + . db_xref=GeneID%3A5305157;locus_tag=BDI_0002

NC_009615.1 feature CDS 1656 4196 . + 0 codon_start=1;product=ribonucleoside%20reductase;transl_table=11

NC_009615.1 feature gene 4220 6907 . + . db_xref=GeneID%3A5305158;locus_tag=BDI_0003

NC_009615.1 feature CDS 4220 6907 . + 0 codon_start=1;product=4-alpha-glucanotransferase;transl_table=11

NC_009615.1 feature gene 6947 7318 . - . db_xref=GeneID%3A5305352;locus_tag=BDI_0004

NC_009615.1 feature CDS 6947 7318 . - 0 codon_start=1;product=hypothetical%20protein;transl_table=11

NC_009615.1 feature gene 7410 7778 . + . db_xref=GeneID%3A5305353;locus_tag=BDI_0005

NC_009615.1 feature CDS 7410 7778 . + 0 codon_start=1;product=dihydroneopterin%20aldolase;transl_table=11

Becomes (just find and replace "gene" with "single-exon"):

NC_009615.1 annotation remark 1 4811379 . . . gi=150006674

NC_009615.1 feature source 1 4811379 . + . strain=ATCC%208503;mol_type=genomic%20DNA;

NC_009615.1 feature single-exon 1 1398 . + . db_xref=GeneID%3A5305156;locus_tag=BDI_0001;single-exon=dnaA

NC_009615.1 feature CDS 1 1398 . + 0 single-exon=dnaA;protein_id=YP_001301418.1

NC_009615.1 feature single-exon 1656 4196 . + . db_xref=GeneID%3A5305157;locus_tag=BDI_0002

NC_009615.1 feature CDS 1656 4196 . + 0 codon_start=1;product=ribonucleoside%20reductase;transl_table=11

NC_009615.1 feature single-exon 4220 6907 . + . db_xref=GeneID%3A5305158;locus_tag=BDI_0003

NC_009615.1 feature CDS 4220 6907 . + 0 codon_start=1;product=4-alpha-glucanotransferase;transl_table=11

NC_009615.1 feature single-exon 6947 7318 . - . db_xref=GeneID%3A5305352;locus_tag=BDI_0004

NC_009615.1 feature CDS 6947 7318 . - 0 codon_start=1;product=hypothetical%20protein;transl_table=11

NC_009615.1 feature single-exon 7410 7778 . + . db_xref=GeneID%3A5305353;locus_tag=BDI_0005

NC_009615.1 feature CDS 7410 7778 . + 0 codon_start=1;product=dihydroneopterin%20aldolase;transl_table=11