bio_elixir v0.2.0

View Source Bio.IO.Fasta (bio_elixir v0.2.0)

Allow the input/output of FASTA formatted files. Reads and writes fasta data to and from a number of formats.

The FASTA file format is composed of pairs of lines where the pair is demarcated by the ">" character. All data proceeding the ">" character represents the 'header' of the pair, while the next line after a newline represents sequence data.

The FASTA file format does not specify the type of the data in the sequence. That means that you can reasonably store RNA, DNA, amino acid, or realistically any other polymer sequence using the format. In general, the expectation is that the data is ASCII encoded.

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Types

fasta_data()
header()
read_opts()
sequence()

Functions

read(filename, opts \\ [])

Read a FASTA formatted file

read!(filename, opts \\ [])

Read a FASTA formatted file

write(filename, data, modes \\ [])

Write a FASTA file using sequence data.

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fasta_data()

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@type fasta_data() ::
  [String.t()]
  | [struct()]
  | [{header(), sequence()}]
  | %{headers: [header()], sequences: [sequence()]}
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header()

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@type header() :: String.t()
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read_opts()

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@type read_opts() :: {:type, any()} | {:parse_header, (String.t() -> String.t())}
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sequence()

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@type sequence() :: String.t()

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read(filename, opts \\ [])

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@spec read(filename :: Path.t(), opts :: [read_opts()]) ::
  {:ok, any()} | {:error, File.posix()}

Read a FASTA formatted file

The read/2 function returns an error tuple of the content or error code from File.read. You can use :file.format_error/1 to get a descriptive string of the error.

You can specify the return type of the contents by using a module which matches the Bio.Behaviours.Sequence. Specifically the type must have a new/2 method that matches the spec of the behaviour.

options

 Options

  • :type - The module for the type of struct you wish to have returned. This should minimally implement a new/2 function equivalent to the Bio.Behaviours.Sequence behaviour.
  • :parse_header - A callable for parsing the header values of the FASTA file.
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read!(filename, opts \\ [])

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@spec read!(filename :: Path.t(), opts :: [read_opts()]) :: any() | no_return()

Read a FASTA formatted file

The same as read/2, but will raise a File.Error on failure.

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write(filename, data, modes \\ [])

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@spec write(filename :: Path.t(), data :: fasta_data(), [File.mode()]) ::
  :ok | {:error, File.posix()}

Write a FASTA file using sequence data.

The data type that this function accepts is varied. Help with whatever your workflow requires, the List types are:

List:

  [{header(), sequence()}, ...]
  [header(), sequence(), header(), sequence(), ...]
  [%Bio.Sequence._{}, ...]

Where %Bio.Sequence._{} indicates any struct of the Bio.Sequence module or child modules implementing the Bio.Behaviours.Sequence behaviour.

It also supports data in a Map format:

%{
  headers: [header(), ...],
  sequences: [sequence(), ...]
}

examples

 Examples 

iex> Fasta.write("/tmp/test_file.fasta", ["header", "sequence", "header2", "sequence2"])
:ok

Will return error types in common with File.write/3