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:

• 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:

A new instance.

Return type:

TabularMSA

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