Calculates different variations of tetra-nucleotide frequencies of different input data. Most of the fuctions can be accesed by including this repository as package, as well as, using this application as a command line utility.
countTetraNucleotide(sequence: string):CountTable[string]
Counts 4-mer amount of a given string. If a 4-mer does not not occur in the string, it will not occur in Table, to get a Table in which not occuring 4-mers have a value of 0 in the table use countTetraNucleotideAll
Parameter 1: String of which to count the mount of 4-mers.
Return: Table in which keys are the 4-mers and the corresponding values are the amounts of it.
countTetraNucleotideAll(sequence: string):CountTable[string]
Counts 4-mer amount of a given string. If a 4-mer does not not occur in the string, it will still occur in the table with a value of zero.
Parameter 1: String of which to count the mount of 4-mers.
Return: Table in which keys are the 4-mers and the corresponding values are the amounts of it. Not occuring 4-mers have a value of zero.
countTetraNucleotideReversed*(sequence: string):OrderedTable[string, int]
Counts 4-mer amount of a given string. it further collapses 4-mers and their reverse complement into single dictionary entries i.e. if a sequence contains AAAA and TTTT one time only AAAA will appear with a value of 2.
Parameter 1: String of which to count the mount of 4-mers.
Return: Table in which keys are the 4-mers and the corresponding values are the amounts of it. Not occuring 4-mers have a value of zero.
countAllFreqs(sequences: seq[Sequence], normalized:bool=false): OrderedTable[string, string]
Counts the amount of 4-mers of a given array of sequences, this funtction is normally used with a FASTA file and will output the tetra-nucleotide amount for each contig.
Parameter 1: String of which to count the mount of 4-mers.
Parameter 2: If normalization is enabled the tetranucleotide-frequency will be normalized by the contig length.
Return: Table in which keys are the 4-mers and the corresponding values are the amounts of it. Not occuring 4-mers have a value of zero.
countSliding(whole_file: string, reversed=false): OrderedTable[string, string]
Counts the tetranucleotide frequency of 3000bp windows of a given string.
Parameter 1: String of which to count the mount of 4-mers.
Parameter 2: If reverse is true, coontAllFreqsRev will be used to generate the output table, i.e. 4-mers and their corresponding reverse complement we be collapsed in the output.
Return: Table in which keys are the 4-mers and the corresponding values are the amounts of it. Not occuring 4-mers have a value of zero.