package bio_io

You can search for identifiers within the package.

in-package search v0.2.0

package bio_io

bio_io
- Bio_io
  - Btab
    
    In_channel
    
    Record
    
    Parsed
    
    Fields
    
    Direct
  - Btab_queries
    
    In_channel
    
    T
    
    Record
  - Cigar
  - Fasta
    
    In_channel
    
    Record
  - Fastq
    
    In_channel
    
    Record
  - Private
    
    In_channel
    
    Peekable_in_channel
  - Record_in_channel
    
    In_channel_input_record
    
    Make
    
    M
    
    S
  - Utils

Legend:
Library
Module
Module type
Parameter
Class
Class type

In_channel for Btab records.

For more general info, see the Bio_io.Record_in_channel module mli file.

For some examples, see Bio_io.Fasta.In_channel. Those are for the FASTA files, but the API is the same..

include Record_in_channel.S with type record := Record.t

API

type t

val stdin : t

create file_name opens an t on the standard input channel.

val create : Base.string -> t

create file_name opens an input channel on the file specified by file_name. You may want to use Base.Exn.protectx with this.

val close : t -> Base.unit

close t Close the t.

val with_file : Base.string -> f:(t -> 'a) -> 'a

with_file file_name ~f executes ~f on the channel created from file_name and ensures it is closed properly.

val equal : t -> t -> Base.bool

equal t1 t2 compares t1 and t2 for equality.

val input_record : t -> Record.t Base.option

input_record t returns Some record if there is a record to return. If there are no more records, None is returned. Raises exceptions on bad input (e.g., bad file format).

Folding over records

val fold_records : t -> init:'a -> f:('a -> Record.t -> 'a) -> 'a

fold_records t ~init ~f reduces all records from a t down to a single value of type 'a.

val foldi_records : t -> init:'a -> f:(Base.int -> 'a -> Record.t -> 'a) -> 'a

fold'_records t ~init ~f is like fold_records except that f is provided the 0-based record index as its first argument.

Folding with file name

val with_file_fold_records : 
  Base.string ->
  init:'a ->
  f:('a -> Record.t -> 'a) ->
  'a

with_file_fold_records file_name ~init ~f is like fold_records t ~init ~f except that it is passed a file name, and it manages t automatically. See with_file.

val with_file_foldi_records : 
  Base.string ->
  init:'a ->
  f:(Base.int -> 'a -> Record.t -> 'a) ->
  'a

with_file_foldi_records file_name ~init ~f is like foldi_records t ~init ~f except that it is passed a file name, and it manages t automatically. See with_file.

Iterating over records

The iter functions are like the fold functions except they do not take an init value and the f function returns unit insead of some other value 'a, and thus return unit rather than a value 'a.

Use them for side-effects.

val iter_records : t -> f:(Record.t -> Base.unit) -> Base.unit

iter_records t ~f calls f on each record in t. As f returns unit this is generally used for side effects.

val iteri_records : t -> f:(Base.int -> Record.t -> Base.unit) -> Base.unit

iteri_records t ~f is like iteri_records t ~f except that f is passed in the 0-indexed record index as its first argument.

Iterating with file name

val with_file_iter_records : 
  Base.string ->
  f:(Record.t -> Base.unit) ->
  Base.unit

with_file_iter_records file_name ~init ~f is like iter_records t ~init ~f except that it is passed a file name, and it manages t automatically. See with_file.

val with_file_iteri_records : 
  Base.string ->
  f:(Base.int -> Record.t -> Base.unit) ->
  Base.unit

with_file_iteri_records file_name ~init ~f is like iteri_records t ~init ~f except that it is passed a file name, and it manages t automatically. See with_file.

Getting records as a list

These functions return record lists.

val records : t -> Record.t Base.list

With file name

val with_file_records : Base.string -> Record.t Base.list

Getting records as a sequence

These are a bit different:

* There are no with_file versions as you would have to do some fiddly things to keep the channel open, making them not so nice to use.

* If an exception is raised sometime during the pipeline, it will blow up, but any successful processing that happended, will have happened. So be careful if you are doing side-effecting things.

val record_sequence : t -> Record.t Base.Sequence.t

record_sequence t returns a Sequence.t of record.