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.

  • -c or --config

    String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).

  • -h or --help

    Display this helpful text.