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.