Module Biocaml_chr (.ml)

Chromosome names. A chromosome name, as defined by this module, consists of two parts. An optional prefix "chr" (case-insensitive), followed by a suffix identifying the chromosome. The possible suffixes (case-insensitive) are:

"X" representing the maternal chromosome
"Y" representing the paternal chromosome
"M", "Mt", or "MtDNA" representing mitochondrial DNA
"N" where N is a positive number in either arabic or roman numeral form

Some suffixes have ambiguous interpretations, e.g. "X" could be a Roman numeral or the maternal chromosome. Preference is given to the non-numeric interpretation. Thus "chrX" is treated as the maternal chromosome, not chromosome 10. Strings not in the above form are left unaltered by the functions of this module.

Functions for converting to an Arabic or Roman format are provided. The benefit is that these functions convert to a canonical form, and thus the resulting strings can be compared reliably. For example, to_arabic "Chr4" and to_arabic "IV" both return "4". The Arabic format is recommended over the Roman form because the Roman form is incomplete; e.g. it cannot represent chromosome number 10 because there would be an ambiguity with the maternal chromosome "chrX".

module Biocaml_chr:

sig

module Error:

sig

type t = [ `chromosome_ambiguous_in_roman_form of string ]

Possible errors:

`chromosome_ambiguous_in_roman_form chr - chr's Roman representation is ambiguous, e.g. "chr10" and "chrX" both lead to "X"

end

exception Error of Error.t

val to_arabic : string -> string

to_arabic s returns the canonical Arabic representation of s.

val to_roman : string -> (string, Error.t) Core.Std.Result.t

to_roman s returns the canonical Roman representation of s.

val to_roman_exn : string -> string

end