[maker-devel] GFF3 file format not accepted by pred_gff options

[Gowthaman Ramasamy]

Thats a very nice catch. I will adjust parent to Parent and try. 

Its nice idea to run maker first with prok. mode. I will keep that in mind.

Thanks,
Gowtham

_____________________________
From: Carson Holt [Carson.Holt at oicr.on.ca]
Sent: Thursday, June 07, 2012 6:28 AM
To: Gowthaman Ramasamy; maker-devel at yandell-lab.org
Subject: Re: GFF3 file format not accepted by pred_gff options

You have parent= instead of Parent=.  In GFF3, attribute tags are case
sensitive.  Those starting with uppercase letters represent reserved
words, and all others represent ad hoc tags.
The modencode validator would not check parent= for validity because it
sees it as an ad hoc tag (thus not producing an error).

Try changing parent= to some invalid value and compare with what you get
when Parent= is set to an invalid value in the modencode validator, and
you will see what I mean.


The fixed version is attached.


Also the genemark_gtf2gff script was made for converting the GeneMark-ES
output, so I'm not surprised it didn't work on the prokaryote version, but
you should
be fine just by fixing the parent= tag on the conversion you made.  You
could also have run MAKER once in prokaryote mode with the prokaryotic
parameter file to get it to produce a GFF3 for you.

Thanks,
Carson




On 12-06-06 9:53 PM, "Gowthaman Ramasamy"
<gowthaman.ramasamy at seattlebiomed.org> wrote:

>Hi Carson,
>As I wrote to you earlier, I was able to successfully create a gff3 file
>from our predictor to be used in pred_gff option. But, now, I am trying
>to add another abinitio prediction (GeneMark-prokaryotic).  For some
>weird reasons,  I would like to run GeneMark-prokaryote and
>Augustus-eukaryotes. So, i am not able to run both inside maker.
>
>But, that gff3 was not used by pred_gff. I tried to make it as similar to
>the working gffs as possible. Still in vein. Would you mind having look
>at the attached gff file. I even run it by gff validator at
>modencode(http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online). All
>passed.
>
>In the maker produced gff i just see one pair of match-matchpart that
>corresponds to entire supercontig from GeneMark. Not corresponding to
>genes.
>
>I really appreciate your time and help.
>
>Gowthaman