agat_sq_reverse_complement.pl

DESCRIPTION

This script will reverse complement the annotation of all annotation from the gff that are hold by sequences described in the fasta file. The match between sequence name in the fasta file and the 1st column of the gff3 file is case sensitive.

SYNOPSIS

agat_sq_reverse_complement.pl --gff <gff_file.gff> --fasta <fasta_file.fa> [-o <output file>]
agat_sq_reverse_complement.pl --help

OPTIONS

• --gff, --file or --input

  STRING: Input GTF/GFF file.

• -f, --fasta

  STRING: fasta file.

• -v, --verbose

  BOOLEAN: For verbosity.

• -o or --output

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

• --help or -h

  BOOLEAN: Display this helpful text.