package phylogenetics

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package phylogenetics
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Module Phylogenetics.DnaSource

Strings that represent valid DNA sequences

Sourcetype t = private string
Sourceval of_string_unsafe : string -> t

of_string_unsafe s creates a DNA sequence from a string without validation.

  let dna_sequence = of_string_unsafe "ACGT" in
  (* dna_sequence is now "ACGT". If an unexpected character is encountered, the result is undefined. *)
Sourceval of_string_exn : string -> t

of_string_exn s creates a DNA sequence from a string, raising an exception if an unexpected character is encountered. Raises Invalid_argument if an unexpected character is found.

Example:

  let dna_sequence = of_string_exn "ACGT" in
  (* dna_sequence is now "ACGT" *)

of_codons codons creates a DNA sequence from an array of codons.

Example:

  let codons = [|Codon.Universal_genetic_code.NS.Adenine; Codon.Universal_genetic_code.NS.Cytosine; Codon.Universal_genetic_code.NS.Guanine; Codon.Universal_genetic_code.NS.Thymine|] in
  let dna_sequence = of_codons codons in
  (* dna_sequence is now "ACGT" *)
Sourceval gc_contents : t -> float

gc_contents s calculates the GC (Guanine/Cytosine) contents of a DNA sequence, that is it counts the occurrences of 'C' and 'G' in s and returns the ratio of GC bases to the total length of the sequence.

Example:

  let dna_sequence = of_string_exn "ACGT" in
  let gc_content = gc_contents dna_sequence in
  (* gc_content is approximately 0.5 *)