Examples (8)
Count observed frequencies of words in a FASTA file, providing parameter values with interactive prompt
compseq path/to/file.fastaCount observed frequencies of amino acid pairs from a FASTA file, save output to a text file
compseq path/to/input_protein.fasta -word 2 path/to/output_file.compCount observed frequencies of hexanucleotides from a FASTA file, save output to a text file and ignore zero counts
compseq path/to/input_dna.fasta -word 6 path/to/output_file.comp -nozeroCount observed frequencies of codons in a particular reading frame; ignoring any overlapping counts (i.e. move window across by word-length 3)
compseq -sequence path/to/input_rna.fasta -word 3 path/to/output_file.comp -nozero -frame 1Count observed frequencies of codons frame-shifted by 3 positions; ignoring any overlapping counts (should report all codons except the first one)
compseq -sequence path/to/input_rna.fasta -word 3 path/to/output_file.comp -nozero -frame 3Count amino acid triplets in a FASTA file and compare to a previous run of `compseq` to calculate expected and normalized frequency values
compseq -sequence path/to/human_proteome.fasta -word 3 path/to/output_file1.comp -nozero -infile path/to/output_file2.compApproximate the above command without a previously prepared file, by calculating expected frequencies using the single base/residue frequencies in the supplied input sequence(s)
compseq -sequence path/to/human_proteome.fasta -word 3 path/to/output_file.comp -nozero -calcfreqDisplay help (use `-help -verbose` for more information on associated and general qualifiers)
compseq -help