[maker-devel] Maker: accessory scripts

[Carson Holt]

All maker gene annotations will be of the format  gene/mRNA/exon/CDS.
Anything in the format match/match_part is an evidence alignment or rejected
model and is there for reference purposes.  If you want to upgrade all of
the rejected loci to gene annotations, set keep_preds=1 in the control
files.  If you want to upgrade a subset of rejected models to a full
annotation, create a list of IDs (one per line) then give them to the
attached script.  gff3_preds2models was previously deprecated and no longer
part of the maker distribution, but the attached script is an updated
version with the same functionality.

--Carson



From:  Innocent Onsongo <onson001 at umn.edu>
Date:  Wednesday, 5 June, 2013 12:35 PM
To:  Carson Holt <carson.holt at oicr.on.ca>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>, Barry
Moore <barry.utah at gmail.com>
Subject:  [maker-devel]  Maker: accessory scripts

I was able to successfully ran Maker and now want to converts the gene
prediction match/match_part format to annotation gene/mRNA/exon/CDS format.
I looked at the tutorial and the script gff3_preds2models
is supposed to do this conversion. How do I access this script. It is not in
/maker/2.28-beta/bin/

Also, in running gff3_preds2models <gff3 file> <pred list>  is <pred list>
the file I used for pred_gff=?

Long story short, how do I transform the GFF output from Maker to the more
traditional annotation of exon/intron?

Thanks,  
Getiria
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