agat_sp_filter_gene_by_intron_numbers.pl
DESCRIPTION
The script aims to filter genes by intron numbers. It will create two files. one with the genes passing the intron number filter, the other one with the remaining genes.
Some examples: Select intronless genes: agat_sp_filter_gene_by_intron_numbers.pl --gff infile.gff -o result.gff Select genes with more or equal 10 introns: agat_sp_filter_gene_by_intron_numbers.pl --gff infile.gff --test ">=" --nb 10 [ --output outfile ]
SYNOPSIS
agat_sp_filter_gene_by_intron_numbers.pl --gff infile.gff --test ">=" --nb 10 [ --output outfile ]
agat_sp_filter_gene_by_intron_numbers.pl --help
OPTIONS
-f, --reffile, --gff or -ref
Input GFF3 file that will be read
-n, --nb or --number
Integer - Number of introns [Default 0]
-t or --test Test to apply (>, <, =, >= or <=). If you use one of these two characters >, <, please do not forget to quote your parameter like that "<=". Else your terminal will complain. [Default "="]
-o or --output
Output GFF file. If no output file is specified, the output will be written to STDOUT.
-v
Verbose option for debugging purpose.
-h or --help
Display this helpful text.