core.seqview.SeqDataView
core.seqview.SeqDataView(
parent,
alphabet,
parent_len,
seqid=None,
slice_record=None,
offset=0,
)A view class for SeqsData, providing methods for different representations of a single sequence.
Notes
str_value / array_value are not complemented, but can be reversed. The latter is done by the Sequence object which has a moltype.
Attributes
| Name | Description |
|---|---|
| array_value | returns the sequence as a numpy array |
| bytes_value | returns the sequence as bytes |
| offset | the annotation offset of this view |
| parent_len | length of the parent sequence |
| parent_offset | returns the offset from the true parent |
| seqid | name of the sequence |
| slice_record | the slice state of this view |
| str_value | returns the sequence as a string |
Methods
| Name | Description |
|---|---|
| copy | returns copy |
| parent_coords | returns coordinates on parent |
| to_rich_dict | returns a json serialisable dict. |
| with_offset | returns new instance with annotation offset set |
copy
core.seqview.SeqDataView.copy(sliced=False)returns copy
parent_coords
core.seqview.SeqDataView.parent_coords(apply_offset=False, **kwargs)returns coordinates on parent
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
| apply_offset | bool | if True adds annotation offset from parent | False |
Returns
| Name | Type | Description |
|---|---|---|
| parent seqid, start, stop, strand |
to_rich_dict
core.seqview.SeqDataView.to_rich_dict()returns a json serialisable dict.
Notes
This method will slice the underlying sequence to the start and stop values
Warnings
This method is not intended to provide serialisation of this object, instead, it is intended for usage by an enclosing class.
with_offset
core.seqview.SeqDataView.with_offset(offset)returns new instance with annotation offset set