skbio.alignment.TabularMSA.read

TabularMSA.read(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 into. 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 of the file. The format must be a format name with a reader for TabularMSA. If None, the format will be inferred.

constructortype, required

The type of sequence to read each alignment entry into. Must be a subclass of GrammaredSequence (e.g., DNA, RNA, Protein). Required by most formats that read into a TabularMSA.

kwargsdict, optional

Additional arguments passed to skbio.io.registry.read and the 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