skbio.io.util.open

skbio.io.util.open(file, mode='r', encoding=None, errors=None, newline=None, compression='auto', compresslevel=9)

Convert input into a filehandle.

State: Stable as of 0.4.0.

Supported inputs:

type	can read	can write	source type
file path	True	True	Binary
URL	True	False	Binary
["lines list\n"]	True	True	Text
io.StringIO	True	True	Text
io.BytesIO	True	True	Binary
io.TextIOWrapper	True	True	Text
io.BufferedReader	True	False	Binary
io.BufferedWriter	False	True	Binary
io.BufferedRandom	True	True	Binary
tempfile.TemporaryFile()	True	True	Binary
tempfile.NamedTemporaryFile()	True	True	Binary

Note

When reading a list of unicode (str) lines, the input for newline is used to determine the number of lines in the resulting file handle, not the number of elements in the list. This is to allow composition with file.readlines().

Parameters

• file (filepath, url, filehandle, list) – The input to convert to a filehandle.

• mode ({'r', 'w'}, optional) – Whether to return a readable or writable file. Conversely, this does not imply that the returned file will be unwritable or unreadable. To get a binary filehandle set encoding to binary.

• encoding (str, optional) – The encoding scheme to use for the file. If set to ‘binary’, no bytes will be translated. Otherwise this matches the behavior of io.open().

• errors (str, optional) – Specifies how encoding and decoding errors are to be handled. This has no effect when encoding is binary (as there can be no errors). Otherwise this matches the behavior of io.open().

• newline ({None, "", '\n', '\r\n', '\r'}, optional) – Matches the behavior of io.open().

• compression ({'auto', 'gzip', 'bz2', None}, optional) – Will compress or decompress file depending on mode. If ‘auto’ then determining the compression of the file will be attempted and the result will be transparently decompressed. ‘auto’ will do nothing when writing. Other legal values will use their respective compression schemes. compression cannot be used with a text source.

• compresslevel (int (0-9 inclusive), optional) – The level of compression to use, will be passed to the appropriate compression handler. This is only used when writing.

Returns

filehandle – When encoding=’binary’ an io.BufferedReader or io.BufferedWriter will be returned depending on mode. Otherwise an implementation of io.TextIOBase will be returned.

Note

Any underlying resources needed to create filehandle are managed transparently. If file was closeable, garbage collection of filehandle will not close file. Calling close on filehandle will close file. Conversely calling close on file will cause filehandle to reflect a closed state. This does not mean that a `flush` has occured for `filehandle`, there may still have been data in its buffer! Additionally, resources may not have been cleaned up properly, so ALWAYS call `close` on `filehandle` and NOT on `file`.

Return type

io.TextIOBase or io.BufferedReader/Writer