skbio.alignment.TabularMSA.write¶

TabularMSA.write(file, format='fasta', **kwargs)[source]¶

Write an instance of TabularMSA to a file.

This is a convenience method for skbio.io.registry.write(). 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 write the given format into. Something that is understood by skbio.io.util.open(). Filehandles are not automatically closed, it is the responsibility of the caller.

• format (str) – The format must be a registered format name with a writer for TabularMSA. Default is ‘fasta’.

• kwargs (dict, optional) – Keyword arguments passed to skbio.io.registry.write() and the file format writer.

See also

read(), skbio.io.registry.write(), skbio.io.util.open(), skbio.io.format.clustal(), skbio.io.format.fasta(), skbio.io.format.fastq(), skbio.io.format.phylip(), skbio.io.format.stockholm()