skbio.alignment.TabularMSA.read

classmethod TabularMSA.read(file, format=None, **kwargs)

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:

fileopenable (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.

formatstr, 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.

kwargsdict, optional

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

Returns:

TabularMSA

A new instance.

See also

write

skbio.io.registry.read

skbio.io.util.open

skbio.io.format.clustal

skbio.io.format.fasta

skbio.io.format.fastq

skbio.io.format.phylip

skbio.io.format.stockholm