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Hi Glenna-<br>
this may be totally off-base but I have a vague memory that some
validators will complain about the<br>
semicolon after the last attribute in the column nine attribute
list; it's not clear to me from the specification<br>
that this is truly illegal, but can imagine why a parser might not
like to deal with it. In any case,<br>
you might try just removing that terminal semicolon character and
see if that solves the validation complaint.<br>
<br>
but apologies in advance if my dim recollection has misled me into
wasting your time...<br>
<br>
Andrew Farmer<br>
<br>
<div class="moz-cite-prefix">On 3/20/17 7:37 PM, Glenna Kramer
wrote:<br>
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<div style="direction: ltr;font-family: Tahoma;color:
#000000;font-size: 10pt;">Hi there,<br>
<br>
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" <a moz-do-not-send="true"
href="https://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&retmode=ref&cmd=prlinks&id=25501943"
target="pmc_ext">
<span class="cit">Curr Protoc Bioinformatics. 2014; 48:
4.11.1–4.11.39. </span></a>(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the gff is no longer valid.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!
<br>
<br>
Best,<br>
Glenna <br>
<br>
Not sure if this will be helpful, but here is an example gene
from prior to renaming:<br>
<br>
##gff-version 3<br>
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<br>
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<br>
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<br>
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<br>
<br>
And after renaming:<br>
<br>
##gff-version 3<br>
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;<br>
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;<br>
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;<br>
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;<br>
<br>
The commands I used were:<br>
<br>
% maker_map_ids --prefix_A9K44_ --justify 4
myfilename.gff>myfilename.map<br>
<br>
%map_gff_ids myfilename.map myfilename.gff<br>
<br>
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<br>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.
Friedrich Nietzsche</pre>
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