[maker-devel] quality_filter.pl script -question for Mike Campbell

[Michael Campbell]

Hi Jason,

It could be a couple of things. If you have a cut down version of your gff3 that I can use to recreate the error I can debug it. The quality_filter.pl script is still a pretty young accessory script, so you may have something in your file that It wasn’t tested against.

Thanks,
Mike

 

> On Nov 3, 2015, at 2:48 PM, Jason Gallant <jgallant at msu.edu> wrote:
> 
> Hi Mike (list copied for future reference),
> 
> I found your very nice protocols paper on using Maker from 2014.  I’ve been following it to the letter as I’m wrapping up my annotation project.
> 
> I’ve located your quality_filter.pl <http://quality_filter.pl/> script and am using it on my GFF files to create maker standard and maker default data sets from my maker-max GFF file.  I’m noticing that perl complains a lot while this is running about “use of uninitialized value”.  This occurs on two separate passes as far as I can tell.  When generating the “maker standard” file, it occurs for many lines in my GFF file as:
> 
> Use of uninitialized value $array[2] in pattern match (m//) at /mnt/home/jgallant/quality_filter.pl <http://quality_filter.pl/> line 50, <GEN0> line Y.
> 
> And then later it complains again with a similar message
> 
> Use of uninitialized value $array[2] in string eq at /mnt/home/jgallant/quality_filter.pl <http://quality_filter.pl/> line 92, <GEN1> line X.
> Use of uninitialized value $array[2] in string eq at /mnt/home/jgallant/quality_filter.pl <http://quality_filter.pl/> line 96, <GEN1> line X.
> Use of uninitialized value $array[2] in string eq at /mnt/home/jgallant/quality_filter.pl <http://quality_filter.pl/> line 100, <GEN1> line X
> 
> Any insights as to what causes this?  I seem to get a fully formed GFF3 file out the other side, but the command line fills with these messages and makes me nervous that something isn’t right.
> 
> I’d appreciate any thoughts!
> 
> Best,
> Jason Gallant
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20151103/856c4acf/attachment-0003.html>