AGCT_count_V2.pl

Script counts the number of G, C, A and T present in all fasta entries of each genome fasta file present in the running folder. Additionally, the program calculates the fraction of nucleotides that correspond to each nucleotide type and the fraction of nucleotides that correspond to either G or C. The script is designed to select all fasta files with the text “_genomic.fna” in order to select full genomes and not annotated features such as RNAs or CDS. If you prefer to determine these parameters considering only CDS, please comment variables $pat, $notpat and $notpat2 in lines 15 to 17 of the script and uncomment the corresponding variables in lines 20 to 22 or change variables according to the text in the file names you are are analyzing.

Usage: perl AGCT_count_V2.pl