bio_io

A library for reading and writing common file formats used in bioinformatics like FASTA files
README

Bio_io is an OCaml library that provides programmatic access to
common file formats used in bioinformatics like FASTA files.

Quick Start

Install

opam install bio_io

Example

Read a FASTA file and print the ID and sequence length for each record.

open! Base

let fasta_file = "sequences.fasta"

let () =
  (* This open gives you [In_channel] and [Record]. *)
  let open Bio_io.Fasta in
  In_channel.with_file_iter_records_exn fasta_file ~f:(fun record ->
      (* Print the ID and the length of the sequence. *)
      Stdio.printf "%s => %d\n" (Record.id record) (Record.seq_length record))

Docs

For more examples, API, and other usage info, see the docs.

License

Licensed under the Apache License, Version 2.0 or the MIT license, at
your option. This program may not be copied, modified, or distributed
except according to those terms.

Install
Published
14 Jul 2022
Maintainers
Sources
0.5.1.tar.gz
md5=6cc64d38a9cba13754cae52db1ade85d
sha512=5008a30225ec306378e282dab2c00d545949be0e778e4b352c5e29012e08f88acef4ed75cf03a55276b657a057355399be3a55ea77d58231a03efc66a03a8b13
Dependencies
odoc
with-doc
re
>= "1.10" & with-test
ppx_inline_test
>= "v0.15" & with-test
ppx_expect
>= "v0.15" & with-test
base_quickcheck
>= "v0.15" & with-test
ppx_assert
>= "v0.15" & with-test
stdio
>= "v0.15"
ppx_sexp_conv
>= "v0.15"
ppx_compare
>= "v0.15"
ocaml
>= "4.10"
base
>= "v0.15"
dune
>= "3.2"
Reverse Dependencies