agat_sq_filter_feature_from_fasta.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_filter_feature_from_fasta.pl --gff <gff_file.gff> --fasta <fasta_file.fa> [-o <output file>]
agat_sq_filter_feature_from_fasta.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.

• -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.