package bio_io

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Overview
Example

package bio_io

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

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Module type
Parameter
Class
Class type

In_channel for Btab files where each query in the file is a single record.

Overview

WARNING: This module assumes that queries are sorted. One case in which this assumption does not hold is with mmseqs when using more than one iteration. E.g., mmseqs easy-search --num-iterations 3. This behavior will likely change in the future.

You should consider this module experimental.

Example

Here is a short example program. It reads a btab file and prints out the records.

open! Base
open! Bio_io.Btab_queries

let parse_argv () =
  match Sys.get_argv () with
  | [| _; file_name |] -> file_name
  | _ -> failwith "missing file_name"

let () =
  let file_name = parse_argv () in
  In_channel.with_file_iter_records_exn file_name ~f:(fun r ->
      Stdio.print_endline "===";
      Stdio.print_endline @@ Record.query r;
      let hits = List.map ~f:Bio_io.Btab.Record.parse @@ Record.hits r in
      Stdio.print_s @@ [%sexp_of: Bio_io.Btab.Record.Parsed.t list] hits)

The output will be somthing like.

===
Q 1
(((query "Q 1") (target q1t1) (pident 0.1) (alnlen 2) (mismatch 3)
  (gapopen 4) (qstart 5) (qend 6) (tstart 7) (tend 8) (evalue 9.99E-05)
  (bits 10) (qlen ()) (tlen ()))
 ((query "Q 1") (target q1t2) (pident 0.11) (alnlen 12) (mismatch 13)
  (gapopen 14) (qstart 15) (qend 16) (tstart 17) (tend 18) (evalue 1.9E-05)
  (bits 20) (qlen ()) (tlen ())))
===
Q_2
(((query Q_2) (target q2t1) (pident 0.21) (alnlen 22) (mismatch 23)
  (gapopen 24) (qstart 25) (qend 26) (tstart 27) (tend 28) (evalue 2.9E-05)
  (bits 30) (qlen ()) (tlen ())))

module T : sig ... end

include module type of struct include T end

include module type of struct include Private.Peekable_in_channel end

A wrapper of Jane Street's Stdio.In_channel. Add's peek_char and peek_line functions that work on fifos as well as regular files.

Used internally for bio input channels so that you can pipe directly from gzip even in channels that need peeking.

Differences from Stdio.In_channel

No binary mode

Some functions are not implemented.

input
really_input
really_input_exn
input_char
input_byte
input_binary_int
unsafe_input_value
input_buffer
seek
pos
length
set_binary_mode_out

type t = Private.Peekable_in_channel.t

include Ppx_compare_lib.Equal.S with type t := t

val input_all : t -> Base.string

val input_line : ?fix_win_eol:Base.bool -> t -> Base.string Base.option

val input_line_exn : ?fix_win_eol:Base.bool -> t -> Base.string

val fold_lines : 
  ?fix_win_eol:Base.bool ->
  t ->
  init:'a ->
  f:('a -> Base.string -> 'a) ->
  'a

val input_lines : ?fix_win_eol:Base.bool -> t -> Base.string Base.list

val iter_lines : 
  ?fix_win_eol:Base.bool ->
  t ->
  f:(Base.string -> Base.unit) ->
  Base.unit

val read_lines : ?fix_win_eol:Base.bool -> Base.string -> Base.string Base.list

val read_all : Base.string -> Base.string

Both peek functions are safe to call in the context of one of the iterator functions.

val peek_char : ?fix_win_eol:Base.bool -> t -> Base.char Base.option

val peek_line : ?fix_win_eol:Base.bool -> t -> Base.string Base.option

type record = Record.t

include sig ... end

val stdin : T.t

val create_exn : Base.string -> T.t

val create : Base.string -> T.t Base.Or_error.t

val close_exn : T.t -> Base.unit

val close : T.t -> Base.unit Base.Or_error.t

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

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

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

val input_record_exn : T.t -> T.record Base.option

val input_record : T.t -> T.record Base.option Base.Or_error.t

val fold_records_exn : T.t -> init:'a -> f:('a -> T.record -> 'a) -> 'a

val fold_records : 
  T.t ->
  init:'a ->
  f:('a -> T.record -> 'a) ->
  'a Base.Or_error.t

val foldi_records_exn : 
  T.t ->
  init:'a ->
  f:(Base.int -> 'a -> T.record -> 'a) ->
  'a

val foldi_records : 
  T.t ->
  init:'a ->
  f:(Base.int -> 'a -> T.record -> 'a) ->
  'a Base.Or_error.t

val with_file_fold_records_exn : 
  Base.string ->
  init:'a ->
  f:('a -> T.record -> 'a) ->
  'a

val with_file_fold_records : 
  Base.string ->
  init:'a ->
  f:('a -> T.record -> 'a) ->
  'a Base.Or_error.t

val with_file_foldi_records_exn : 
  Base.string ->
  init:'a ->
  f:(Base.int -> 'a -> T.record -> 'a) ->
  'a

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

val iter_records_exn : T.t -> f:(T.record -> Base.unit) -> Base.unit

val iter_records : 
  T.t ->
  f:(T.record -> Base.unit) ->
  Base.unit Base.Or_error.t

val iteri_records_exn : 
  T.t ->
  f:(Base.int -> T.record -> Base.unit) ->
  Base.unit

val iteri_records : 
  T.t ->
  f:(Base.int -> T.record -> Base.unit) ->
  Base.unit Base.Or_error.t

val with_file_iter_records_exn : 
  Base.string ->
  f:(T.record -> Base.unit) ->
  Base.unit

val with_file_iter_records : 
  Base.string ->
  f:(T.record -> Base.unit) ->
  Base.unit Base.Or_error.t

val with_file_iteri_records_exn : 
  Base.string ->
  f:(Base.int -> T.record -> Base.unit) ->
  Base.unit

val with_file_iteri_records : 
  Base.string ->
  f:(Base.int -> T.record -> Base.unit) ->
  Base.unit Base.Or_error.t

val records_exn : T.t -> T.record Base.List.t

val records : T.t -> T.record Base.List.t Base.Or_error.t

val with_file_records_exn : Base.string -> T.record Base.List.t

val with_file_records : Base.string -> T.record Base.List.t Base.Or_error.t

val record_sequence_exn : T.t -> T.record Base.Sequence.t

val record_sequence : T.t -> T.record Base.Or_error.t Base.Sequence.t