agat_sq_mask.pl

DESCRIPTION

The script masks (hard or soft) GFF-denoted segments out of a FASTA format file. It needs 3 input parameters: a gff3 file, a fasta file, and a Mask method. The result is written to the specified output file, or to STDOUT.

SYNOPSIS

agat_sq_mask.pl -g infile.gff -f infile.fasta  (-hm or -sm) [ -o outfile ]
agat_sq_mask.pl --help

OPTIONS

• -g, --gff or -ref

  Input GTF/GFF file.

• -f or --fasta

  Input fasta file that will be masked

• -sm

  SoftMask option =>Sequences masked will be in lowercase

• -hm

  HardMask option => Sequences masked will be replaced by a character. By default the character used is 'n'. But you are allowed to speceify any character of your choice. To use 'z' instead of 'n' type: -hm z

• -o or --output

  Output GFF file. If no output file is specified, the output will be written to STDOUT.

• -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.