agat_sq_split.pl#

DESCRIPTION#

split gff3 file into several files. By default we create files containing 1000 genes and all sub-features associated. GFF3 input file must be sequential.

SYNOPSIS#

agat_sq_split.pl --input <input file> -o <output file>
agat_sq_split.pl --help

OPTIONS#

• --gff, --file or --input

  STRING: Input GTF/GFF file.

• -i or --interval Integer. Number of group of feature to include in each file. 1000 by default.

• --ft or --feature_type The top feature of the feature group. By default "gene".

• -o or --output

  STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format.

• -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).

• --help or -h

  Display this helpful text.