Turning off the GFF3 parser

[sanyalab]

Hi Jacques,

This is not a feature request but a question.

Is there a way to turn off the checking of GFF3 files in AGAT. I have a situation where I have already checked the accuracy of the GFF3 format, and I will be using another AGAT tool to compare the GFF3 files. For the comparison step, I do not wish to use the GFF3 parser to check the files again. Can this be turned off? What is the process?

Thanks Abhijit

[Juke34]

Run agat config --exopse The parser checks that can be disable are packed in that paragraph

# ----------------------------- Checks made by the parser ----------------------
# in order of appearance wihtin the parser
check_sequential: true
check_l2_linked_to_l3: true
check_l1_linked_to_l2: true
remove_orphan_l1: true
check_all_level3_locations: true
check_cds: true
check_exons: true
check_utrs: true
check_all_level2_locations: true
check_all_level1_locations: true
check_identical_isoforms: true

Set everything to false. But if the file has already been corrected, the computation time required for passing through the test again is probably negligible.

If you use scripts with sp prefix AGAT will anyway take the time needed to put everything in memory in a specific shape, with or without tests.

[sanyalab]

Hi Jacques,

Thank you for the reply. The GFF3 files are actually alignment files and pretty large in size ~5G. Therefore, I think making the changes to the config might help. I'll let you know.

Thanks Abhijit