load_seq#
- load_seq(filename: PathLike, annotation_path: PathLike | None = None, format: str | None = None, moltype: str | None = None, label_to_name: Callable | None = None, parser_kw: dict | None = None, info: dict | None = None, new_type: bool = False, annotation_offset: int = 0, **kw: dict) Sequence#
loads unaligned sequences from file
- Parameters:
- filename
path to sequence file
- annotation_path
path to annotation file, ignored if format is genbank
- format
sequence file format, if not specified tries to guess from the path suffix
- moltype
the moltype, eg DNA, PROTEIN, ‘dna’, ‘protein’
- label_to_name
function for converting original name into another name.
- parser_kw
optional arguments for the parser
- info
a dict from which to make an info object
- new_type
if True, returns a new type Sequence (cogent3.core.new_sequence.Sequence) The default will be changed to True in 2024.12. Support for the old style will be removed as of 2025.6.
- annotation_offset
integer indicating start position relative to annotations
- **kw
other keyword arguments passed to sequence loader
- Returns:
Sequence
Notes
Returns one sequence from a file. Use load_aligned_seqs or load_unaligned_seqs to get a collection.