Retrieve summary statistics for a coding sequence (CDS) file

A summary statistics of specific CDS features is returned.

Usage

summary_cds(file, organism)

Arguments

file

file path to a CDS file in fasta format.

organism

character string specifying the organism at hand.

Details

The summary statistics include:

• total_seqs:

• nnn_abs: The total number of NNN's (over all chromosomes/scaffolds/contigs) in all coding sequences combined

• nnn_perc: The percentage (relative frequency) of NNN's (over all chromosomes/scaffolds/contigs) compared to the total number of nucleotides of all coding sequences

See also

getCollection, getCDS, read_cds, summary_genome

Author

Hajk-Georg Drost