[maker-devel] Fwd: iprscan2gff3

[Carson Holt]

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-deve
> l/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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