skbio.sequence.GrammaredSequence.read¶

classmethod GrammaredSequence.read(file, format=None, **kwargs)[source]¶

Create a new Sequence 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:

• 'embl' (skbio.io.format.embl)

• 'fasta' (skbio.io.format.fasta)

• 'fastq' (skbio.io.format.fastq)

• 'qseq' (skbio.io.format.qseq)

• 'genbank' (skbio.io.format.genbank)

• 'gff3' (skbio.io.format.gff3)

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 Sequence. 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 Sequence.

Returns

A new instance.

Return type

Sequence

See also

write(), skbio.io.registry.read(), skbio.io.util.open(), skbio.io.format.embl(), skbio.io.format.fasta(), skbio.io.format.fastq(), skbio.io.format.qseq(), skbio.io.format.genbank(), skbio.io.format.gff3()