Module Biocaml_fasta (.ml)

module Biocaml_fasta: sig .. end

FASTA files. The FASTA family of file formats has different incompatible descriptions (1, 2, 3, etc.). Roughly FASTA files are in the format:

    # comment
    # comment
    ...
    >header
    sequence
    >header
    sequence
    ...
   

where the sequence may span multiple lines, and a ';' may be used instead of '#' to start comments.

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.

Sequence are most often a sequence of characters denoting nucleotides or amino acids. However, sometimes FASTA files provide quality scores, either as ASCII encoded, e.g. as supported by modules Biocaml_phred_score and Biocaml_solexa_score, or 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 a '#' or ';' 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 sequence of characters or space-separated integers, often just one line but allowed to span multiple lines

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

Names used throughout this module use sequence to generically mean either kind of data found in the sequence lines, char_seq to mean specifically a sequence of characters, and int_seq to mean specifically a sequence of integers.

Parsing functions throughout this module take the following optional arguments:

• filename - used only for error messages when the data source is not the file.

• pedantic - if true, which is the default, report more errors: Biocaml_transform.no_error lines, non standard characters.

• sharp_comments and semicolon_comments - if true, allow comments beginning with a '#' or ';' character, respectively. Setting both to true is okay, although it is not recommended to have such files. Setting both to false implies that comments are disallowed.

type char_seq = string 

type int_seq = int list 

type 'a item = {

module Error: sig .. end

Errors.

exception Error of Error.t

val in_channel_to_char_seq_item_stream : ?buffer_size:int ->
       ?filename:string ->
       ?pedantic:bool ->
       ?sharp_comments:bool ->
       ?semicolon_comments:bool ->
       Pervasives.in_channel -> char_seq item Stream.t

Returns a stream of char_seq items. Initial comments are discarded.
Raises Error in case of any errors.

val in_channel_to_int_seq_item_stream : ?buffer_size:int ->
       ?filename:string ->
       ?pedantic:bool ->
       ?sharp_comments:bool ->
       ?semicolon_comments:bool ->
       Pervasives.in_channel -> int_seq item Stream.t

Returns a stream of int_seq items. Initial comments are discarded.
Raises Error in case of any errors.

module Result: sig .. end

module Transform: sig .. end

Low-level transforms.

val sexp_of_char_seq : char_seq -> Sexplib.Sexp.t

val char_seq_of_sexp : Sexplib.Sexp.t -> char_seq

val sexp_of_int_seq : int_seq -> Sexplib.Sexp.t

val int_seq_of_sexp : Sexplib.Sexp.t -> int_seq

val sexp_of_item : ('a -> Sexplib.Sexp.t) -> 'a item -> Sexplib.Sexp.t

val item_of_sexp : (Sexplib.Sexp.t -> 'a) -> Sexplib.Sexp.t -> 'a item