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Module Biocaml_tags (.ml)

Meta-information about files and their formats.

module Biocaml_tags:
sig
type file_format = [ `bam
       | `bed
       | `fasta of Biocaml_fasta.Tags.t
       | `fastq
       | `gff of Biocaml_gff.Tags.t
       | `gzip of file_format
       | `raw_zip of file_format
       | `sam
       | `table of Biocaml_table.Row.Tags.t
       | `wig of Biocaml_wig.Tags.t ]
Description of file formats.
type t = [ `bam
       | `bed
       | `fasta of Biocaml_fasta.Tags.t
       | `fastq
       | `gff of Biocaml_gff.Tags.t
       | `gzip of file_format
       | `list of t list
       | `raw_zip of file_format
       | `sam
       | `table of Biocaml_table.Row.Tags.t
       | `wig of Biocaml_wig.Tags.t ]
Description of multiple file formats.
val to_tag : file_format -> t
Do a practical coercion.
val default_extension : file_format -> string
Get a filename extension for a given format. E.g. default_extension (`gzip (`fasta `char)) will be "fasta.gz".
val default_extensions : t -> string list
Do like default_extension but for potentially multiple file-formats.
val add_extensions : t ->
       string list ->
       (string list * string list, [> `tags of [> `not_enough_filenames ] ])
       Core.Result.t
For a given tags value and a list of file-base-names add extensions to the files, and return also the base-names not touched. If t involves n file-formats, add_extensions t fl will add extensions to the first n files of fl and return also the untouched base-names: (files_with_extensions, remaingin_base_names). If there are not enough base-names, the result is the error `tags `not_enough_filenames.
val guess_from_filename : string ->
       (file_format,
        [> `extension_absent | `extension_unknown of string ])
       Core.Result.t
Get a tag as precise as possible for a given filename.
val of_string : string -> (t, [> `parse_tags of exn ]) Core.Result.t
Parse a tag specification (the format is, for now, based on S-Expressions, but this will change).
val to_string : t -> string
Convert a tag to its string specification.

Transforms From Tags 


module Output_transform:
sig
type output_error = [ `bam of Biocaml_bam.Error.item_to_raw
       | `fastq of [ `cannot_convert_ascii_phred_score of string ]
       | `sam of Biocaml_sam.Error.item_to_raw ]
Union possible output errors of the transforms leading to Biocaml_sam.item values. (the other output transforms are error-free).
type tags = Biocaml_tags.t
Alias to Tags.t for this module.
type t = [ `bed_to_file of (Biocaml_bed.item, string) Biocaml_transform.t
       | `char_fasta_to_file of
           (Biocaml_fasta.char_seq Biocaml_fasta.raw_item, string)
           Biocaml_transform.t
       | `fastq_to_file of (Biocaml_fastq.item, string) Biocaml_transform.t
       | `fastq_to_two_files of
           (Biocaml_fastq.item,
            (string * string, output_error)
            Core.Result.t)
           Biocaml_transform.t
       | `gff_to_file of (Biocaml_gff.item, string) Biocaml_transform.t
       | `int_fasta_to_file of
           (Biocaml_fasta.int_seq Biocaml_fasta.raw_item, string)
           Biocaml_transform.t
       | `sam_item_to_file of
           (Biocaml_sam.item,
            (string, output_error) Core.Result.t)
           Biocaml_transform.t
       | `table_to_file of (Biocaml_table.Row.t, string) Biocaml_transform.t
       | `wig_to_file of (Biocaml_wig.item, string) Biocaml_transform.t ]
Generic union of possible output transforms.
val name : t -> string
Get a string naming the transform (for debug/error messages).
val from_tags : ?zip_level:int ->
       ?zlib_buffer_size:int ->
       tags ->
       (t, [> `not_implemented of string ])
       Biocaml_internal_pervasives.Result.t
Guess the Output_transform.t from file tags.
val sexp_of_output_error : output_error -> Sexplib.Sexp.t
end

module Input_transform:
sig
type input_error = [ `bam of Biocaml_bam.Error.raw_bam
       | `bam_to_item of Biocaml_bam.Error.raw_to_item
       | `bed of Biocaml_bed.Error.parsing
       | `fasta of Biocaml_fasta.Error.t
       | `fasta_lengths_mismatch
       | `fastq of Biocaml_fastq.Error.t
       | `gff of Biocaml_gff.Error.parsing
       | `sam of Biocaml_sam.Error.string_to_raw
       | `sam_to_item of Biocaml_sam.Error.raw_to_item
       | `table_row of Biocaml_table.Row.Error.t
       | `unzip of Biocaml_zip.Error.unzip
       | `wig of Biocaml_wig.Error.parsing ]
An union of all possible input errors.
type tags = Biocaml_tags.t
An alias of the type Tags.t.
type t = [ `file_to_bed of
           (string,
            (Biocaml_bed.item, input_error)
            Core.Result.t)
           Biocaml_transform.t
       | `file_to_char_fasta of
           (string,
            (Biocaml_fasta.char_seq Biocaml_fasta.raw_item,
             input_error)
            Core.Result.t)
           Biocaml_transform.t
       | `file_to_fastq of
           (string,
            (Biocaml_fastq.item, input_error)
            Core.Result.t)
           Biocaml_transform.t
       | `file_to_gff of
           (string,
            (Biocaml_gff.item, input_error)
            Core.Result.t)
           Biocaml_transform.t
       | `file_to_int_fasta of
           (string,
            (Biocaml_fasta.int_seq Biocaml_fasta.raw_item,
             input_error)
            Core.Result.t)
           Biocaml_transform.t
       | `file_to_sam_item of
           (string,
            (Biocaml_sam.item, input_error)
            Core.Result.t)
           Biocaml_transform.t
       | `file_to_table of
           (string,
            (Biocaml_table.Row.t, input_error)
            Core.Result.t)
           Biocaml_transform.t
       | `file_to_wig of
           (string,
            (Biocaml_wig.item, input_error)
            Core.Result.t)
           Biocaml_transform.t
       | `two_files_to_fastq of
           (string * string,
            (Biocaml_fastq.item, input_error)
            Core.Result.t)
           Biocaml_transform.t ]
The general input transformation.
val name : t -> string
Get a string describing and input transform (for debug/display purposes).
val from_tags : ?zlib_buffer_size:int ->
       tags ->
       (t, [> `not_implemented of string ])
       Core.Result.t
Create an Input_transform.t from tags describing the format.
val sexp_of_input_error : input_error -> Sexplib.Sexp.t
end

S-Expression Conversions


val file_format_of_sexp : Sexplib.Sexp.t -> file_format
val sexp_of_file_format : file_format -> Sexplib.Sexp.t
include Core.Sexpable.S
end