[maker-devel] gff3_preds2models usage question

[Walter Eckalbar]

Hi Carson,

Thanks for the response, even a late one, and thanks for the script.  I'll
certainly be giving that a try.

Walter

On 1 May 2012 15:07, Carson Holt <carsonhh at gmail.com> wrote:

> 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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