Source code for synbiopython.lab_automation.containers.Plate

# pylint: disable=C0330,C0103,E1101,R0913,E0102,R1705,E0401
"""This module implements the Base class for all plates.

See synbiopython.lab_automation.containers for more specific plate subclasses, with
set number of wells, well format, etc.
from collections import OrderedDict
import pandas
from synbiopython.lab_automation.containers.Well import Well
from synbiopython.lab_automation.containers.helper_functions import (
from import replace_nans_in_dict

[docs]class NoUniqueWell(Exception): """NoUniqueWell exception class."""
[docs]class Plate: """Base class for all plates. See the builtin_containers for usage classes, such as generic microplate classes (Plate96, Plate384, etc). :param name: Name or ID of the Plate as it will appear in strings and reports :param wells_data: A dict {"A1": {data}, "A2": ...}. The format of the data is left free :param plate_data: plate data """ well_class = Well def __init__(self, name=None, wells_data=None, plate_data=None): = name = plate_data or {} self.wells_data = wells_data or {} self.num_wells = self.num_rows * self.num_columns self.wells = {} self.columns = {column: [] for column in range(1, self.num_columns + 1)} self.rows = {number_to_rowname(row): [] for row in range(1, self.num_rows + 1)} for row in range(1, self.num_rows + 1): for column in range(1, self.num_columns + 1): wellname = coordinates_to_wellname((row, column)) data = self.wells_data.get(wellname, {}) well = self.well_class( plate=self, row=row, column=column, name=wellname, data=data, ) self.wells[wellname] = well self.columns[column] += [wellname] self.rows[number_to_rowname(row)] += [wellname] def __getitem__(self, k): """Return e.g. well A1's dict when calling `myplate['A1']`.""" return self.wells[k]
[docs] def find_unique_well_by_condition(self, condition): """Return the unique well of the plate satisfying the condition. The ``condition`` method should have a signature of Well=>True/False. Raises a NoUniqueWell error if 0 or several wells satisfy the condition. """ wells = [well for name, well in self.wells.items() if condition(well)] if len(wells) > 1: raise NoUniqueWell("Query returned several wells: %s" % wells) if len(wells) == 0: raise NoUniqueWell("No wells found matching the condition") return wells[0]
[docs] def find_unique_well_containing(self, query): """Return the unique well whose content contains the query.""" def condition(well): return query in well.content.quantities.keys() return self.find_unique_well_by_condition(condition)
[docs] def list_well_data_fields(self): """Return all fields used in well data in the plate.""" return sorted(list(set(field for well in self for field in
[docs] def return_column(self, column_number): """Return the list of all wells of the plate in the given column.""" return [self.wells[wellname] for wellname in self.columns[column_number]]
[docs] def list_wells_in_column(self, column_number): """Return the list of all wells of the plate in the given column. Examples: >>> for well in plate.list_wells_in_column(5): >>> print( """ return [well for well in self.iter_wells() if well.column == column_number]
[docs] def return_row(self, row): """Return the list of all wells of the plate in the given row. The `row` can be either a row number (1,2,3) or row letter(s) (A,B,C). """ if isinstance(row, int): row = number_to_rowname(row) return [self.wells[wellname] for wellname in self.rows[row]]
[docs] def list_wells_in_row(self, row): """Return the list of all wells of the plate in the given row. The `row` can be either a row number (1,2,3) or row letter(s) (A,B,C). Examples: >>> for well in plate.list_wells_in_row("H"): >>> print( """ if isinstance(row, str): row = rowname_to_number(row) return [well for well in self.iter_wells() if well.row == row]
[docs] def list_filtered_wells(self, well_filter): """List filtered wells. Examples: >>> def condition(well): >>> return well.volume > 50 >>> for well in myplate.list_filtered_wells(condition): >>> print( """ return list(filter(well_filter, self.wells.values()))
[docs] def wells_grouped_by( self, data_field=None, key=None, sort_keys=False, ignore_none=False, direction_of_occurence="row", ): """Return wells grouped by key.""" if key is None: def key(well): return, None) dct = OrderedDict() for well in self.iter_wells(direction=direction_of_occurence): well_key = key(well) if well_key not in dct: dct[well_key] = [well] else: dct[well_key].append(well) if ignore_none: dct.pop(None, None) keys = dct.keys() if sort_keys: keys = sorted(keys) return [(k, dct[k]) for k in keys]
[docs] def get_well_at_index(self, index, direction="row"): """Return the well at the corresponding index. Examples: >>> plate.get_well_at_index(1) # well A1 >>> plate.get_well_at_index(2) # well A2 >>> plate.get_well_at_index(2, direction="column") # well B1 """ return self[self.index_to_wellname(index, direction=direction)]
[docs] def index_to_wellname(self, index, direction="row"): """Return the name of the well at the corresponding index. Examples: >>> plate.index_to_wellname(1) # "A1" >>> plate.get_well_at_index(2) # "A2" >>> plate.get_well_at_index(2, direction="column") # "B1" """ return index_to_wellname(index, self.num_wells, direction=direction)
[docs] def wellname_to_index(self, wellname, direction="row"): """Return the index of the well in the plate. Examples: >>> plate.wellname_to_index("A1") # 1 >>> plate.wellname_to_index("A2") # 2 >>> plate.wellname_to_index("A1", direction="column") # 9 (8x12 plate) """ return wellname_to_index(wellname, self.num_wells, direction=direction)
[docs] def wells_sorted_by(self, sortkey): """Return wells sorted by sortkey""" return (e for e in sorted(self.wells.values(), key=sortkey))
[docs] def iter_wells(self, direction="row"): """Iter through the wells either by row or by column. Examples: >>> for well in plate.iter_wells(): >>> print ( """ if direction == "row": return self.wells_sorted_by(lambda w: (w.row, w.column)) else: return self.wells_sorted_by(lambda w: (w.column, w.row))
[docs] def to_dict(self, replace_nans_by="null"): """Convert plate to dict.""" dct = { "data":, "wells": { well.to_dict() for well in self.wells.values()}, } if replace_nans_by is not None: replace_nans_in_dict(dct, replace_by=replace_nans_by) return dct
[docs] def to_pandas_dataframe(self, fields=None, direction="row"): """Return a dataframe with the info on each well.""" dataframe = pandas.DataFrame.from_records(self.to_dict()["wells"]).T by = ["row", "column"] if direction == "row" else ["column", "row"] dataframe = dataframe.sort_values(by=by) if fields is not None: dataframe = dataframe[fields] return dataframe
def __repr__(self): return "%s(%s)" % (self.__class__.__name__,