Parsing for the PHYLIP format
This module provides functionality for working with the Phylip file format, which is commonly used in phylogenetic analysis and sequence alignment. The Phylip format is a plain text format that represents multiple biological sequences along with their associated metadata. The original format is described there. This implementation also allows a somewhat more relaxed syntax:
<nb sequences> <nb cols> <id> TAB <sequence> <id> TAB <sequence> ...
which is specified with the option ~strict:false.
Example usage of the functions:
let items = [
{ name = "Seq1"; sequence = "ACGT" };
{ name = "Seq2"; sequence = "CGTA" };
] in
let data = make_exn items in
write data "output.txt";
let parsed_data = read "output.txt" in
match parsed_data with
| Ok parsed -> Printf.printf "Number of sequences: %d\n" parsed.number_of_sequences
| Error (`Msg msg) -> Printf.printf "Parsing error: %s\n" msgmake_exn items creates a new t value from a list of items. It validates the input by checking that the list is not empty and that all sequences have the same length. Raises Invalid_argument if the list of items is empty or if the sequences have different lengths.
val read : ?strict:bool -> string -> (t, [> `Msg of string ]) Stdlib.resultread ?strict fn reads the contents of the specified file fn and returns a t value representing the data. The strict parameter specifies whether to use strict parsing or relaxed parsing. If strict is set to true, the function expects the file to follow the strict format. If strict is set to false, the function allows a more relaxed syntax.
Returns:
Ok t if the file is successfully parsed and the t value is created.Error (`Msg msg) if an error occurs during parsing, with msg describing the error.val read_exn : ?strict:bool -> string -> tread_exn ?strict fn is similar to read, but raises an exception with the error message if the parsing fails.
val write : ?strict:bool -> t -> string -> unitwrite ?strict t fn writes the data from the t value to the specified file fn. The strict parameter specifies whether to use strict writing or relaxed writing. If strict is set to true, the function writes the data in strict format. If strict is set to false, the function writes the data in a more relaxed format.