package bio_io

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  1. Overview
  2. Docs
A library for reading and writing common file formats used in bioinformatics like FASTA files

Install 

dune-project
 Dependency

github.com Readme Changelog Edit opam file Versions (8)

Authors

  1. R
    Ryan M. Moore

Maintainers

  1. R
    Ryan M. Moore

Sources

0.7.0.tar.gz
md5=f1c5c5d9436a9572340b313043f3f96b
sha512=70f204e5b4bf7e3418efca8e6ca6d0bb446b0c1623be8410b014fc559901a7d333b22770c8a5344b5fd1c5d058ca9678d90e0b32fafdc429a7932209df81c5a2

Description

Added to opam-repository:

README

Bio_io

Build and test Coverage Status

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 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

license MIT or Apache 2.0

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.

Dependencies (7)

  1. stdio >= "v0.16"
  2. ppx_sexp_conv >= "v0.16"
  3. ppx_fields_conv >= "v0.16"
  4. ppx_compare >= "v0.16"
  5. ocaml >= "4.14"
  6. base >= "v0.16"
  7. dune >= "3.2"

Dev Dependencies (6)

  1. odoc with-doc
  2. re >= "1.10" & with-test
  3. ppx_inline_test >= "v0.16" & with-test
  4. ppx_expect >= "v0.16" & with-test
  5. base_quickcheck >= "v0.16" & with-test
  6. ppx_assert >= "v0.16" & with-test

Optional Dependencies

None

Used by

None

Conflicts

None

Build status

Results of building bio_io with each compiler on check.ci.ocaml.org, run of against opam-repository 7cdc698. All results for this package.

Each result links to its build log. To keep crawlers from overloading the site, build logs require a GitHub sign-in (see ocurrent/opam-health-check). On your first log, GitHub asks you to “Authorize opam-health-check”, the OCurrent app that runs these checks; it sees only your public profile, not your repositories. The sign-in lasts 30 days.

Version OCaml 4.11 OCaml 4.14 OCaml 5.2 OCaml 5.4 OCaml 5.5
0.7.0 (this version) n/a good good good good
0.6.0 good good good n/a n/a
  • good Package successfully built
  • partial One of the dependencies failed to build
  • bad Package failed to build
  • n/a Package is not available in this environment
  • internal Internal failure