[maker-devel] gff3_preds2models usage question

[Carson Holt]

Sorry for the slow response.  The gff3_preds2models script has been
deprecated for some time now (isn't even in the release code anymore), and
the old one won't work with the new library.

I've attached a made from scratch drop-in replacement that you can use to do
what the old script would have done.  In the current release of MAKER,
instead of the gff3_preds2models script users can just give MAKER  a set of
predictions in GFF3 format (pred_gff option) and set keep_preds=1 (then
leave all other options blank).  The predictions given will the be converted
into gene models.

Thanks,
Carson



From:  Walter Eckalbar <weckalba at asu.edu>
Date:  Tuesday, 3 April, 2012 7:28 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] gff3_preds2models usage question

Hello maker developers and users,

I am attempting to use the gff3_preds2models scripts, but running into a few
issues.

Initially, I hit errors that seemed to be fixed by installing CGI and its
dependancies.  However, that during that installation a few tests did fail.
I can provide error logs if that would be helpful, however, I went on to
install and attempt gff3_preds2models anyway.

What I am currently doing is running gff3_merge first, to gather the maker
outputs.  I am doing so with both the -n option on and off.  When providing
the gff3 file with the sequence I get the following error from
gff3_preds2models:

Undefined subroutine &maker::auto_annotator::annotate called at
/Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
<GEN16> line 992291.

This seemed to be the same error as that of what someone else saw on these
boards, but I did not see a later email resolving the issue.

I also tried giving it just the gff3 without the sequences at the bottom of
the file and then I get this error:

ERROR: There was a problem in the writing the fasta entry
Either no sequence was given, or there was an error in writing

This leads me to believe I should be using the one with the sequence, but I
am not certain of that.

I see it might be possible to go from maker outputs to chado database then
to gene->mRNA->exon gff3s, but I have not set up my machine for XML or chado
yet, and it does not appear trivial.

Thanks for the help,

Walter
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