[maker-devel] Fwd: iprscan2gff3

[Rebecca Harris]

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

[Daniel Ence]

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

de...@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 <rbha...@uw.edu>

 wrote:

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[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

[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