4.7. jsa.seq.gff2fasta: Extract gene sequences

jsa.seq.gff2fasta extract the functional sequences (genes, CDS, etc) from a gff file and a sequence file.

4.7.1. Synopsis

jsa.seq.gff2fasta: Extract sequences from a gff annotation

4.7.2. Usage

jsa.seq.gff2fasta [options]

4.7.3. Options

--sequence=s The sequence (whole chromosome) (REQUIRED)
--gff=s Annotation file in gff format (REQUIRED)
--type=s types of features to be extracted (all, gene, CDS etc) (default=’gene’)
--flank=i Size of flanking regions (default=‘0’)
--output=s Name of the output file, - for standard output (REQUIRED)
--help Display this usage and exit (default=’false’)