The script reads a gff annotation file, and create two output files, one contains the gene models with ORF passing the test, the other contains the rest. By default the test is "> 100" that means all gene models that have ORF longer than 100 Amino acids, will pass the test.
agat_sp_filter_by_ORF_size.pl --gff infile.gff [ -o outfile ] agat_sp_filter_by_ORF_size.pl -h
-g or --gff
Input GTF/GFF file.
-s or --size
ORF size to apply the test. Default 100.
-t or --test Test to apply (> < = >= <=). If you us one of these two character >, <, please don't forget to quote you parameter liket that "<=". Else your terminal will complain. By default it will be ">"
Verbose. Useful for debugging purpose. Bolean
-o or --out or --output or --outfile
Output GFF file. If no output file is specified, the output will be written to STDOUT.
-h or --help
Display this helpful text.