Module Biocaml_fasta

module Biocaml_fasta: sig .. end

FASTA files.

FASTA files are in the format:

    # comment
    # comment
    ...
    >header
    content
    >header
    content
    ...

where the content may span multiple lines.

Header lines begin with the '>' character. It is often considered that all characters until the first whitespace define the name of the content, and any characters beyond that define additional information in a format specific to the file provider.

The content section is most often a sequence of characters denoting nucleotides, but also somtimes ASCII encoded quality scores, e.g. as supported by the PhredScore module. Sometimes, the quality scores are provided as space separated integers.

Thus, the FASTA format is really a family of formats with a fairly loose specification of the header and content formats. The only consistently followed meaning of the format is:

the file can begin with comment lines that begin with the '#' character and/or all white-space lines

the header lines begins with the '>' character, is followed optionally by whitespace, and then contains some string

each header line is followed by a content section, often just one line but allowed to span multiple lines

and this alternating pair of header/content lines can occur repeatedly.

This module supports the full set of possibilities by providing two record types.

exception Error of string

type record = string * string

Header and content. Multiline content is concatenated into a single string. All characters other than newline are retained.

type recordi = string * int list

Header and integers. Content is assumed to be space-separated integers, possibly spanning multiple lines.

val enum_input : Batteries.IO.input ->
       Biocaml_comments.t * record Batteries.Enum.t

Returns comments and enumeration of fasta records in given input.

val enum_of_file : string -> Biocaml_comments.t * record Batteries.Enum.t

Returns comments and enumeration of fasta records in given path.

val enum_inputi : Batteries.IO.input ->
       Biocaml_comments.t * recordi Batteries.Enum.t