skbio.alignment.TabularMSA.read¶

classmethod TabularMSA.read(file, format=None, **kwargs)[source]¶

Create a new TabularMSA instance from a file.

This is a convenience method for skbio.io.registry.read(). For more information about the I/O system in scikit-bio, please see skbio.io.

Supported file formats include:

'clustal' (skbio.io.format.clustal)
'fasta' (skbio.io.format.fasta)
'fastq' (skbio.io.format.fastq)
'phylip' (skbio.io.format.phylip)
'stockholm' (skbio.io.format.stockholm)

Parameters:

Parameters:	file : openable (filepath, URL, filehandle, etc.) The location to read the given format. Something that is understood by `skbio.io.util.open()`. Filehandles are not automatically closed, it is the responsibility of the caller. format : str, optional The format must be a format name with a reader for `TabularMSA`. If a format is not provided or is None, it will attempt to guess the format. kwargs : dict, optional Keyword arguments passed to `skbio.io.registry.read()` and the file format reader for `TabularMSA`.
Returns:	TabularMSA A new instance.

file : openable (filepath, URL, filehandle, etc.)

The location to read the given format. Something that is understood by skbio.io.util.open(). Filehandles are not automatically closed, it is the responsibility of the caller.

format : str, optional

The format must be a format name with a reader for TabularMSA. If a format is not provided or is None, it will attempt to guess the format.

kwargs : dict, optional

Keyword arguments passed to skbio.io.registry.read() and the file format reader for TabularMSA.

Returns:

TabularMSA

A new instance.