skbio.alignment.TabularMSA.write

TabularMSA.write(file, format='fasta', **kwargs)

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:

fileopenable (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.

formatstr

The format must be a registered format name with a writer for TabularMSA. Default is ‘fasta’.

kwargsdict, 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