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- builtins.object
-
- Heap
- ReadsAccessor
- collections.abc.Mapping(collections.abc.Collection)
-
- Read
class Heap(builtins.object) |
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Methods defined here:
- __init__(self)
- Initialize self. See help(type(self)) for accurate signature.
- empty(self)
- pop(self)
- Remove and return the lowest priority task. Raise KeyError if empty.
- push(self, task, priority=0)
- Add a new task or update the priority of an existing task
- remove(self, task)
- Mark an existing task as REMOVED. Raise KeyError if not found.
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
Data and other attributes defined here:
- REMOVED = '<removed-task>'
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class Read(collections.abc.Mapping) |
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Read(position=None, values=None, sequence=None, image=None, channels=None, **kwargs)
A sequencing read found in an image. Can be constructed with
a position and the image or with a position and the values
from that position.
A Read has three main components, each of which can be None, depending
on what is known about the read and in what step of the sequencing process
it is. These attributes are:
position (ndarray of shape (2,)): The position of the read. This is relevant for all
reads detected from the sequencing images, and holds the position at which they were found, in pixels.
Reads without a position would be library barcodes that need to be compared to sequencing reads,
or cell consensus reads that don't have a single position.
values (ndarray of shape (n_cycles, n_channels)): The values extracted from the sequencing
images for this read. As such, this is only present for reads that came from sequencing
images, for example barcodes from the library don't have any raw sequencing values related to them.
sequence (string of len n_cycles): The sequence of the read.
The sequence of the read is always present and will not be None, however if a sequence
is not specified when creating the Read it is inferred from the values, by taking
the maximum channel for each cycle.
Additional attributes can be added when creating the Read as keyword arguments, and can be accessed as if
the read is a dictionary
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- Method resolution order:
- Read
- collections.abc.Mapping
- collections.abc.Collection
- collections.abc.Sized
- collections.abc.Iterable
- collections.abc.Container
- builtins.object
Methods defined here:
- __getitem__(self, name)
- __init__(self, position=None, values=None, sequence=None, image=None, channels=None, **kwargs)
- __iter__(self)
- __len__(self)
- __repr__(self)
- Return repr(self).
- __setitem__(self, name)
- __str__(self)
- Return str(self).
Static methods defined here:
- asread(obj)
Readonly properties defined here:
- qualities
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
- sequence
- sequence_array
Data and other attributes defined here:
- DEFAULT_CHANNELS = ('G', 'T', 'A', 'C')
- __abstractmethods__ = frozenset()
Methods inherited from collections.abc.Mapping:
- __contains__(self, key)
- __eq__(self, other)
- Return self==value.
- get(self, key, default=None)
- D.get(k[,d]) -> D[k] if k in D, else d. d defaults to None.
- items(self)
- D.items() -> a set-like object providing a view on D's items
- keys(self)
- D.keys() -> a set-like object providing a view on D's keys
- values(self)
- D.values() -> an object providing a view on D's values
Data and other attributes inherited from collections.abc.Mapping:
- __hash__ = None
- __reversed__ = None
Class methods inherited from collections.abc.Collection:
- __subclasshook__(C) from abc.ABCMeta
- Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__().
It should return True, False or NotImplemented. If it returns
NotImplemented, the normal algorithm is used. Otherwise, it
overrides the normal algorithm (and the outcome is cached).
Class methods inherited from collections.abc.Iterable:
- __class_getitem__ = GenericAlias(...) from abc.ABCMeta
- Represent a PEP 585 generic type
E.g. for t = list[int], t.__origin__ is list and t.__args__ is (int,).
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class ReadsAccessor(builtins.object) |
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ReadsAccessor(table)
Accessor object to provide attributes and functions for
dataframes containing in situ sequencing reads
A dataframe with the columns below can use the accessor:
(optional) 'position_x', 'position_y': The pixel location of the sequencing read
'values_cycle00_G', 'values_cycle00_T' ... 'values_cycle11_A', 'values_cycle11_C':
The sequencing values of the read, from the filtered sequencing images.
Values from every cycle and each channel are stored.
(optional) 'sequence': The sequences of the read
The accessor provides custom properties listed below:
'positions': a numpy array of shape (num_reads, 2). The positions of the reads,
'values': a numpy array of shape (num_reads, num_cycles, num_channels).
The sequencing values for all reads
'sequences': a numpy array of strings of shape (num_reads,). If there is a column
called 'sequence' in the dataframe this is just the contents of that column.
Otherwise, the sequences are generated from the sequencing values, by selecting
the maximum channel in each cycle to build up a sequence.
Changes to positions and values will both propagate back to the underlying dataframe, so
you can do something like:
table.reads.positions *= 2
table.reads.values /= np.linalg.norm(table.reads.values, axis=2)[:,:,None]
Full reference documentation is available at <https://fowlerlab.github.io/starcall-docs/starcall.html>
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Methods defined here:
- __getitem__(self, index)
- __init__(self, table)
- Initialize self. See help(type(self)) for accurate signature.
- __iter__(self)
- __len__(self)
- aggfuncs(self, position=None, values=None, **kwargs)
- normalize(self, method='full')
- Normalizes the values of this read set, based on the method specified
Possible methods are:
'full' (default): values are normalized across the channel axis, so that for each
cycle the norm of the vector of all channels is 1
- to_cell_table(self, cell_column='cell', include_attrs=['count'], cell_index=None)
Readonly properties defined here:
- positions
- sequences
- sequences_array
- values
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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