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

[Jason Gallant]

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 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 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 line 92, <GEN1> line X.
Use of uninitialized value $array[2] in string eq at /mnt/home/jgallant/
quality_filter.pl line 96, <GEN1> line X.
Use of uninitialized value $array[2] in string eq at /mnt/home/jgallant/
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20151103/9a53ff45/attachment-0002.html>