Parser¶

This module provides elements for parsing data manually, i.e. getting a handful list of samples and extract specific structures (colony, lineage, cell) from such samples.

Parser: handles how to parse an experiment with a given filterset

class tunacell.base.parser.Parser(exp=None, filter_set=None)¶

Defines how user wants to parse data.

Parameters:	exp (`Experiment` instance) – filter_set (`FilterSet` instance) – this is the set of filters used to read/build data, used for for iterators (usually, only .cell_filter and .container_filter are used)

add_sample(*args)¶

Add sample to sample list.

Parameters: args (list) – list of items such as: integer, strings, couple, and/or dict An integer denotes the number of sample_ids to be chosen randomly (if many integers are given, only the first is used) A string will result in loading the corresponding Container, with a cell identifier randomly chosen. A couple (str, cellID) denotes (container_label, cell_identifier) A dictionary should provide ‘container’ key, and ‘cellID’ key

clear_samples()¶: Erase all samples.

get_cell(sample_id)¶

Get Cell instance corresponding to sample_id.

Parameters:	sample_id (dict) – element of self.samples
Returns:	cell – corresponding to sample_id
Return type:	`Cell` instance

get_colony(sample_id)¶

Get Colony instance corresponding to sample_id.

Parameters:	sample_id (dict) – element of self.samples
Returns:	colony – corresponding to sample_id
Return type:	`Colony` instance

get_container(sample_id)¶

Get Container instance corresponding to sample_id.

Parameters:	sample_id (dict) – element of self.samples
Returns:	container
Return type:	`Container` instance

get_lineage(sample_id)¶

Get Lineage instance corresponding to sample_id.

Parameters:	sample_id (dict) – element of self.samples
Returns:	lineage – corresponding to sample_id
Return type:	:class:` Lineage` instance

get_sample(index, level='cell')¶

Return sample corresponding to index.

Parameters:	index (int) – index of sample id in self.samples level (str {'cell'\|'lineage'\|'colony'}) –
Returns:	structure level corresponding to sample id
Return type:	out

info_samples()¶: Table output showing stored samples.

iter_cells(mode='samples', size=None)¶

Iterate through valid cells.

Parameters:	mode (str {'samples'} (default 'samples')) – whether to iterate over all cells (up to number limitation), or over registered samples size (int (default None)) – limit the number of lineages to size. Works only in mode=’all’
Yields:	cell (`Cell` instance) – filtering removed outlier cells, containers, colonies, and lineages

iter_colonies(mode='samples', size=None)¶

Iterate through valid colonies.

Parameters:	mode (str {'samples'} (default 'samples')) – whether to iterate over all colonies (up to number limitation), or over registered samples size (int (default None)) – limit the number of colonies to size.
Yields:	colony (`Colony` instance) – filtering removed outlier cells, containers, and colonies

iter_containers(mode='samples', size=None)¶

Iterate through valid containers.

Parameters:	mode (str {'samples'} (default 'samples')) – iterates over containers pointed by parser.samples size (int (default None)) – number of containers to be parsed
Yields:	container (`tunacell.core.Container` instance) – filtering removed outlier cells, containers

iter_lineages(mode='samples', size=None)¶

Iterate through valid lineages.

Parameters:	mode (str {''samples'} (default 'samples')) – whether to iterate over all lineages (up to number limitation), or over registered samples size (int (default None)) – limit the number of lineages to size.
Yields:	lineage (`Lineage` instance) – filtering removed outlier cells, containers, colonies, and lineages

load_experiment(path, filetype='text')¶

Loads an experiment from path to file.

Parameters:	path (str) – path to root directory (‘text’), or to datafile (‘h5’) filetype (str {'text', 'h5}) –

remove_sample(index, verbose=True)¶: Remove sample of index in sample list.

set_filter(fset)¶

Set build filter.

Parameters:	fset (`FilterSet` instance) –