skbio.sequence.GrammaredSequence.write

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

Write an instance of Sequence 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:

• 'embl' (skbio.io.format.embl)

• 'fasta' (skbio.io.format.fasta)

• 'fastq' (skbio.io.format.fastq)

• 'genbank' (skbio.io.format.genbank)

• 'gff3' (skbio.io.format.gff3)

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 Sequence. 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.embl, skbio.io.format.fasta, skbio.io.format.fastq, skbio.io.format.genbank, skbio.io.format.gff3