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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
GNU General Public License v3.0
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Parsing creates empty file #179

Closed rsalz closed 3 years ago

rsalz commented 3 years ago

Hi,

I have 3 gff3 files created by Transdecoder. These files were all generated with the same script. Visually, I see no difference in format between the 3. For some reason, AGAT can only parse 2 out of the 3 gff files. The one that doesn't work actually does run to completion (in 1 second). agat_convert_sp_gxf2gxf.pl produces an empty file. Pretty bizarre. What could be going on?

Screenshot 2021-09-21 at 4 44 11 PM

TIA

Juke34 commented 3 years ago

What version of AGAT are you using? Could you show few lines of your gff/gtf file?

Maybe you are in this case: https://agat.readthedocs.io/en/latest/troubleshooting.html#agat-throws-features-out-because-child-features-are-not-provided

rsalz commented 3 years ago

Just updated my installation to the newest version and it doesn't seem to fix the problem. Here is what my GFF looks like:

Screenshot 2021-09-21 at 5 34 52 PM

again, it seems to be identical in format to the other 2 GFF files where parsing did work properly. What would you suggest I do?

Juke34 commented 3 years ago

Check tabulation, you must have 9 columns separated by tabulations. Check if you have windows carriage return (do a dos2unix to your file)

You can run agat_convert_sp_gxf2gxf.pl with verbosity to get more information: -v 3

rsalz commented 3 years ago

I work exclusively on Linux. To make 100% sure I had 9 columns with tabs, I imported my gff into a pandas DataFrame and simply printed out to a file again. That seemed to have fixed my problem. Weird. Anyways, thanks for your quick responses! I'll close the issue.