Describe the bug
When attempting to filter out non-protein_coding entries using the agat_sp_filter_feature_by_attribute_value.pl script with the --attribute biotype --value protein_coding -t "!" parameters, an error is returned stating that the test to apply is wrong. The error message suggests that valid tests are <, >, <=, >=, !, or =.
General:
AGAT version: v1.4.0
AGAT installation/use: Conda, miniconda3
OS: Linux
To Reproduce
Steps to reproduce the behavior:
Execute the following command:
agat_sp_filter_feature_by_attribute_value.pl --gff GCF_963259705.1_mMyoDau2.1_genomic.gff --attribute biotype --value protein_coding -t "!"
The error message returned is:
The input file is [GCF_963259705.1_mMyoDau2.1_genomic.gff](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/963/259/705/GCF_963259705.1_mMyoDau2.1/GCF_963259705.1_mMyoDau2.1_genomic.gff.gz).
Expected behavior
I expected the script to filter out all entries that are not protein_coding and retain only those that are protein_coding.
Describe the bug When attempting to filter out non-protein_coding entries using the
agat_sp_filter_feature_by_attribute_value.plscript with the--attribute biotype --value protein_coding -t "!"parameters, an error is returned stating that the test to apply is wrong. The error message suggests that valid tests are<, >, <=, >=, !, or =.General:
To Reproduce Steps to reproduce the behavior:
Execute the following command:
agat_sp_filter_feature_by_attribute_value.pl --gff GCF_963259705.1_mMyoDau2.1_genomic.gff --attribute biotype --value protein_coding -t "!"The error message returned is:
The input file is
[GCF_963259705.1_mMyoDau2.1_genomic.gff](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/963/259/705/GCF_963259705.1_mMyoDau2.1/GCF_963259705.1_mMyoDau2.1_genomic.gff.gz).Expected behavior I expected the script to filter out all entries that are not
protein_codingand retain only those that areprotein_coding.