[maker-devel] GFF no longer valid after renaming genes

[Andrew Farmer]

Hi Glenna-
this may be totally off-base but I have a vague memory that some 
validators will complain about the
semicolon after the last attribute in the column nine attribute list; 
it's not clear to me from the specification
that this is truly illegal, but can imagine why a parser might not like 
to deal with it. In any case,
you might try just removing that terminal semicolon character and see if 
that solves the validation complaint.

but apologies in advance if my dim recollection has misled me into 
wasting your time...

Andrew Farmer

On 3/20/17 7:37 PM, Glenna Kramer wrote:
> Hi there,
>
> I am hoping that you can give me some assistance with finishing up my 
> maker annotated genome for submission.  I have been able to rename the 
> genes for GenBank submission - using Support Protocol 2 in the paper 
> by Campbell et. al "Genome Annotation and Curation Using MAKER and 
> MAKER-P" Curr Protoc Bioinformatics. 2014; 48: 4.11.1–4.11.39. 
> <https://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&retmode=ref&cmd=prlinks&id=25501943>(PMC4286374).  
> I have also been able to use the Support Protocol 3 from that same 
> paper to assign a putative gene function.  However, I am running into 
> problems when I am trying to convert the GFF file to the tbl format 
> for submission.  I have tried to use scripts from GAG (Genome 
> Annotation Generator) and maker (gff32table).  Both of these scripts 
> work wonderfully on the gff originally output from maker, but do not 
> work once I rename the genes for GenBank submission.  When I feed my 
> file into a gff validator it turns out that my gff is valid prior to 
> renaming, but after I rename the gff is no longer valid.  I have been 
> trying to troubleshoot what is happening to my gff when I rename as in 
> Support Protocol 2, but am stumped.  Has anyone else out there had a 
> similar issue?  I would be very thankful for any insight that you can 
> provide!
>
> Best,
> Glenna
>
> Not sure if this will be helpful, but here is an example gene from 
> prior to renaming:
>
> ##gff-version 3
> ChromoV|quiver|quiver    maker    gene    62081    62650    . +    . 
> ID=augustus_masked-ChromoV|quiver|quiver-processed-gene-0.9;Name=augustus_masked-ChromoV|quiver|quiver-processed-gene-0.9
> ChromoV|quiver|quiver    maker    mRNA    62081    62650    . +    . 
> ID=augustus_masked-ChromoV|quiver|quiver-processed-gene-0.9-mRNA-1;Parent=augustus_masked-ChromoV|quiver|quiver-processed-gene-0.9;Name=augustus_masked-ChromoV|quiver|quiver-processed-gene-0.9-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|189
> ChromoV|quiver|quiver    maker    exon    62081    62650    . +    . 
> ID=augustus_masked-ChromoV|quiver|quiver-processed-gene-0.9-mRNA-1:exon:11978;Parent=augustus_masked-ChromoV|quiver|quiver-processed-gene-0.9-mRNA-1
> ChromoV|quiver|quiver    maker    CDS    62081    62650    . +    0 
> ID=augustus_masked-ChromoV|quiver|quiver-processed-gene-0.9-mRNA-1:cds;Parent=augustus_masked-ChromoV|quiver|quiver-processed-gene-0.9-mRNA-1
>
> And after renaming:
>
> ##gff-version 3
> ChromoV|quiver|quiver    maker    gene    62081    62650    . +    . 
> ID=A9K44_2555|quiver|quiver-processed-gene-0.9;Name=A9K55_2555|quiver|quiver-processed-gene-0.9;Alias=augustus_masked-ChromoV|quiver|quiver-processed-gene-0.9;
> ChromoV|quiver|quiver    maker    mRNA    62081    62650    . +    . 
> ID=A9K44_2555|A9K55_2555-RA|quiver-processed-gene-0.9-mRNA-1;Parent=A9K55_2555|A9K55_2555-RA|quiver-processed-gene-0.9;Name=A9K55_2555|A9K55_2555-RA|quiver-processed-gene-0.9-mRNA-1;Alias=augustus_masked-ChromoV|quiver|quiver-processed-gene-0.9-mRNA-1;_AED=0.00;_QI=0|-1|0|1|-1|1|1|0|189;_eAED=0.00;
> ChromoV|quiver|quiver    maker    exon    62081    62650    . +    . 
> ID=A9K44_2555-RA|quiver|quiver-processed-gene-0.9-mRNA-1:exon:11978;Parent=A9K55_2555-RA|quiver|quiver-processed-gene-0.9-mRNA-1;
> ChromoV|quiver|quiver    maker    CDS    62081    62650    . +    0 
> ID=A9K44_2555-RA|quiver|quiver-processed-gene-0.9-mRNA-1:cds;Parent=A9K55_2555-RA|quiver|quiver-processed-gene-0.9-mRNA-1;
>
> The commands I used were:
>
> % maker_map_ids --prefix_A9K44_ --justify 4 myfilename.gff>myfilename.map
>
> %map_gff_ids myfilename.map myfilename.gff
>
>
>
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-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

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