[maker-devel] Fwd: iprscan2gff3

[Rebecca Harris]

Hey,

Thanks for the reply. The problem was that I didn't upgrade the matches to
gene/mRNA features before running the ipr_upgrade_gff3 script.

R


On Thu, Jun 19, 2014 at 1:47 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Also make sure there are gene/mRNA features in your GFF3 for your iprscan
> results.  If you used the ab initio calls (which will be match/match_part
> features in the GFF3) as your input to iprscan, then you will need to
> upgrade them to gene/mRNA features before the script will add domains to
> them.
>
> --Carson
>
>
> From: Daniel Ence <dence at genetics.utah.edu>
> Date: Thursday, June 19, 2014 at 2:44 PM
> To: Rebecca Harris <rbharris at uw.edu>
> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] Fwd: iprscan2gff3
>
> Hi Rebecca, I at the conversation you linked to and it seems that Carson
> resolved the those parsing issues in an update to maker. What version of
> maker are you using?
>
> Also, in that same conversation Carson said that those errors wouldn't
> affect the output (because the script was parsing the mRNA features fine,
> but giving errors on the gene features). Does the output that you get from
> iprscan2gff3 seem complete?
>
> ~Daniel
>
>
> Daniel Ence
> Graduate Student
> dence at genetics.utah.edu
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
>
> On Jun 19, 2014, at 1:07 PM, Rebecca Harris <rbharris at uw.edu>
>  wrote:
>
> Hi,
>
> I'm trying to use the iprscan2gff3 script to update my final gff3 file
> with annotations from Interproscan 5. I'm getting a bunch of errors similar
> to another user but do not see how their issue was resolved:
>
> https://groups.google.com/forum/#!searchin/maker-devel/iprscan2gff3/maker-devel/MykTxL2Da64/5yrO3e6WBHUJ
>
> I ran Interproscan on my ab initio predictions, then converted the xml to
> raw format. When I run iprscan2gff3 I get the errors:
>
> Use of uninitialized value $name in hash element at
> /gscratch/leache/rbharris/maker/bin/ipr_update_gff line 107, <$IN> line
> 1090.
> Thanks,
> Rebecca
>
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