package bio_io

In_channel for FASTA records. For more general info, see the Record_in_channel module mli file.

Examples

Return all records in a list

Simplest way. May raise exceptions.

let records = Fasta.In_channel.with_file_records_exn fname 

A bit more involved, but you won't get exceptions. Instead, you have to handle the Or_error.t.

let records =
  match Fasta.In_channel.with_file_records name with
  | Error err ->
      eprintf "Problem reading records: %s\n" (Error.to_string_hum err);
      exit 1
  | Ok records -> records

Iterating over records

Use the iter functions when you need to go over each record and perform some side-effects with them.

Print sequence IDs and sequence lengths

let () =
  Fasta.In_channel.with_file_iter_records_exn "sequences.fasta"
    ~f:(fun record ->
      let open Fasta.Record in
      printf "%s => %d\n" (id record) (seq_length record))

Print sequence index, IDs, and sequence lengths.

This is like the last example except that we also want to print the index. The first record is 0, the 2nd is 1, etc.

let () =
  Fasta.In_channel.with_file_iteri_records_exn "sequences.fasta"
    ~f:(fun index record ->
      let open Fasta.Record in
      printf "%d: %s => %d\n" (index + 1) (id record)
        (seq_length record)

Folding over records

If you need to reduce all the records down to a single value, use the fold functions.

Get total length of all sequences in the file.

Watch out as this may raise exceptions...see the _exn suffix.

let total_length =
  Fasta.In_channel.with_file_fold_records_exn "sequences.fasta" ~init:0
    ~f:(fun length record -> length + Fasta.Record.seq_length record)

Same thing, but this won't raise exceptions. You do have to handle Or_error.t to get the final value. Note that within the fold function, you get Fasta.Record.t and not Fasta.Record.t Or_error.t.

let total_length =
  match
    Fasta.In_channel.with_file_fold_records name ~init:0
      ~f:(fun length record -> length + Fasta.Record.seq_length record)
  with
  | Error err ->
      eprintf "Problem reading records: %s\n" (Error.to_string_hum err);
      exit 1
  | Ok total_length -> total_length

Pipelines with records

Sometimes you have a "pipeline" of computations that you need to do one after the other on records. In that case, you could the sequence functions. Here's a silly example.

let () =
  Fasta.In_channel.with_file_exn name ~f:(fun chan ->
      Fasta.In_channel.record_sequence_exn chan
      (* Add sequence index to record description *)
      |> Sequence.mapi ~f:(fun i record ->
             let new_desc =
               match Fasta.Record.desc record with
               | None -> Some (sprintf "sequence %d" i)
               | Some old_desc ->
                   Some (sprintf "%s -- sequence %d" old_desc i)
             in
             Fasta.Record.with_desc new_desc record)
      (* Convert all sequence chars to lowercase *)
      |> Sequence.map ~f:(fun record ->
             let new_seq = String.lowercase (Fasta.Record.seq record) in
             Fasta.Record.with_seq new_seq record)
      (* Print sequences *)
      |> Sequence.iter ~f:(fun record ->
             print_endline @@ Fasta.Record.serialize record))

One thing to watch out for though...if you get an exception half way through and you are running side-effecting code like we are here then part of your side effects will have occured and part of them will not have occured.

There are also Or_error.t flavors of the sequence functions. Just watch out because these you actually do have to deal with Or_error.t for each Fasta.Record.t in the sequence.

As an alternative, you could use the record_sequence_exn function, but wrap that in the with_file function. That way you don't have to deal with the Or_error.t inside your pipeline. Instead you deal with it at the end.

let total_length =
  match
    Fasta.In_channel.with_file name ~f:(fun chan ->
        Fasta.In_channel.record_sequence_exn chan
        (* Blow up pipeline on second sequence. *)
        |> Sequence.mapi ~f:(fun i record ->
               if i = 1 then assert false;
               record)
        |> Sequence.fold ~init:0 ~f:(fun length record ->
               length + String.length (Fasta.Record.seq record)))
  with
  | Error err ->
      eprintf "Problem in parsing pipeline: %s\n"
        (Error.to_string_hum err);
      exit 1
  | Ok total_length -> total_length

As you can see, if that fasta file has more than one sequence it will hit the assert false and blow up.