agat_sq_keep_annotation_from_fastaSeq.pl¶
DESCRIPTION¶
This script is a kind of annotation filter by sequence name. It goes through the gff annotation features and remove those that are not linked to a sequence from the fasta file provided. The match between sequence name in the fasta file and the 1st column of the gff3 file is case sensitive.
SYNOPSIS¶
agat_sq_keep_annotation_from_fastaSeq.pl --gff <gff_file.gff> --fasta <fasta_file.fa> [-o <output file>]
agat_sq_keep_annotation_from_fastaSeq.pl --help
OPTIONS¶
--gff, --file or --input
STRING: Input GTF/GFF file.
-f or --fasta
STRING: fasta file.
-v or --verbose
For verbosity
-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.
--help or -h
Display this helpful text.