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Module Biocaml_fasta.Transform (.ml)

module Transform:
sig

Low-level transforms, c.f. Biocaml_transform.

Parsers For char_seq Items


val string_to_char_seq_raw_item : ?filename:string ->
       ?tags:Biocaml_fasta.Tags.t ->
       unit ->
       (string,
        (Biocaml_fasta.char_seq Biocaml_fasta.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 Biocaml_fasta.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 items. Comments are discared.

Printers For char_seq Items


val char_seq_item_to_raw_item : ?tags:Biocaml_fasta.Tags.t ->
       unit ->
       (Biocaml_fasta.char_seq Biocaml_fasta.item,
        Biocaml_fasta.char_seq Biocaml_fasta.raw_item)
       Biocaml_transform.t
Cut a stream of char_seq items into a stream of char_seq raw_items, where lines are cut at items_per_line characters (where items_per_line is defined with the `max_items_per_line _ tag, if not specified the default is 80).
val char_seq_raw_item_to_string : ?tags:Biocaml_fasta.Tags.t ->
       unit ->
       (Biocaml_fasta.char_seq Biocaml_fasta.raw_item, string) Biocaml_transform.t
Print char_seq items. Comments will be ignored if neither of the tags `sharp_comments or `semicolon_comments is provided.

Parsers For int_seq Items


val string_to_int_seq_raw_item : ?filename:string ->
       ?tags:Biocaml_fasta.Tags.t ->
       unit ->
       (string,
        (Biocaml_fasta.int_seq Biocaml_fasta.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 Biocaml_fasta.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 items. Comments are discared.

Printers For int_seq Items


val int_seq_item_to_raw_item : ?tags:Biocaml_fasta.Tags.t ->
       unit ->
       (Biocaml_fasta.int_seq Biocaml_fasta.item,
        Biocaml_fasta.int_seq Biocaml_fasta.raw_item)
       Biocaml_transform.t
Cut a stream of int_seq items into a stream of int_seq raw_items, the default line-cutting threshold is 27 (c.f. Biocaml_fasta.Tags.t).
val int_seq_raw_item_to_string : ?tags:Biocaml_fasta.Tags.t ->
       unit ->
       (Biocaml_fasta.int_seq Biocaml_fasta.raw_item, string) Biocaml_transform.t
Print int_seq items. Comments will be ignored if no *_comments tag is provided.
end