Module Biocaml_fasta.Transform (.ml)

module Transform: sig .. end

Low-level transforms.

type 'a raw_item = [ `comment of string | `header of string | `partial_sequence of 'a ]

Lowest level items parsed by this module:

`comment _ - a single comment line without the final newline.

`header _ - a single header line without the initial '>', whitespace following this, nor final newline.

`partial_sequence _ - either a sequence of characters, represented as a string, or a sequence of space separated integers, represented by an int list. The value does not necessarily carry the complete content associated with a header. It may be only part of the sequence, which can be useful for files with large sequences (e.g. genomic sequence files).

char_seq parsers

val string_to_char_seq_raw_item : ?filename:string ->
       ?pedantic:bool ->
       ?sharp_comments:bool ->
       ?semicolon_comments:bool ->
       unit ->
       (string,
        (Biocaml_fasta.char_seq raw_item,
         Biocaml_fasta.Error.t)
        Core.Result.t)
       Biocaml_transform.t

Parse a stream of strings as a char_seq FASTA file.

val char_seq_raw_item_to_item : unit ->
       (Biocaml_fasta.char_seq raw_item,
        (Biocaml_fasta.char_seq Biocaml_fasta.item,
         [ `unnamed_char_seq of Biocaml_fasta.char_seq ])
        Core.Result.t)
       Biocaml_transform.t

Aggregate a stream of FASTA char_seq raw_items into

char_seq
          item

s. Comments are discared.

char_seq unparsers

val char_seq_item_to_raw_item : ?items_per_line:int ->
       unit ->
       (Biocaml_fasta.char_seq Biocaml_fasta.item,
        Biocaml_fasta.char_seq raw_item)
       Biocaml_transform.t

Cut a stream of char_seq items into a stream of

char_seq
          raw_item

s, where lines are cut at items_per_line characters (default 80).

val char_seq_raw_item_to_string : ?comment_char:char ->
       unit ->
       (Biocaml_fasta.char_seq raw_item, string)
       Biocaml_transform.t

Print char_seq items. Comments will be ignored if comment_char is omitted.

int_seq parsers

val string_to_int_seq_raw_item : ?filename:string ->
       ?pedantic:bool ->
       ?sharp_comments:bool ->
       ?semicolon_comments:bool ->
       unit ->
       (string,
        (Biocaml_fasta.int_seq raw_item,
         Biocaml_fasta.Error.t)
        Core.Result.t)
       Biocaml_transform.t

Parse a stream of strings as an int_seq FASTA file.

val int_seq_raw_item_to_item : unit ->
       (Biocaml_fasta.int_seq raw_item,
        (Biocaml_fasta.int_seq Biocaml_fasta.item,
         [ `unnamed_int_seq of Biocaml_fasta.int_seq ])
        Core.Result.t)
       Biocaml_transform.t

Aggregate a stream of FASTA int_seq raw_items into

int_seq
          item

s. Comments are discared.

int_seq unparsers

val int_seq_item_to_raw_item : ?items_per_line:int ->
       unit ->
       (Biocaml_fasta.int_seq Biocaml_fasta.item,
        Biocaml_fasta.int_seq raw_item)
       Biocaml_transform.t

Cut a stream of int_seq items into a stream of

int_seq
          raw_item

s, where lines are cut at items_per_line integers (default 27).

val int_seq_raw_item_to_string : ?comment_char:char ->
       unit ->
       (Biocaml_fasta.int_seq raw_item, string)
       Biocaml_transform.t

Print int_seq items. Comments will be ignored if comment_char is omitted.

S-expressions

val sexp_of_raw_item : ('a -> Sexplib.Sexp.t) ->
       'a raw_item -> Sexplib.Sexp.t

val raw_item_of_sexp : (Sexplib.Sexp.t -> 'a) ->
       Sexplib.Sexp.t -> 'a raw_item

val raw_item_of_sexp__ : (Sexplib.Sexp.t -> 'a) ->
       Sexplib.Sexp.t -> 'a raw_item