synbiopython.lab_automation.containers

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.

exception synbiopython.lab_automation.containers.Plate.NoUniqueWell

Bases: Exception

NoUniqueWell exception class.

class synbiopython.lab_automation.containers.Plate.Plate(name=None, wells_data=None, plate_data=None)

Bases: object

Base class for all plates.

See the builtin_containers for usage classes, such as generic microplate classes (Plate96, Plate384, etc).

Parameters

• name – Name or ID of the Plate as it will appear in strings and reports

• wells_data – A dict {“A1”: {data}, “A2”: …}. The format of the data is left free

• plate_data – plate data

find_unique_well_by_condition(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.

find_unique_well_containing(query)

Return the unique well whose content contains the query.

get_well_at_index(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

index_to_wellname(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"

iter_wells(direction='row')

Iter through the wells either by row or by column.

Examples:

>>> for well in plate.iter_wells():
>>>     print (well.name)

list_filtered_wells(well_filter)

List filtered wells.

Examples:

>>> def condition(well):
>>>     return well.volume > 50
>>> for well in myplate.list_filtered_wells(condition):
>>>     print(well.name)

list_well_data_fields()

Return all fields used in well data in the plate.

list_wells_in_column(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(well.name)

list_wells_in_row(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(well.name)

return_column(column_number)

Return the list of all wells of the plate in the given column.

return_row(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).

to_dict(replace_nans_by='null')

Convert plate to dict.

to_pandas_dataframe(fields=None, direction='row')

Return a dataframe with the info on each well.

well_class

alias of synbiopython.lab_automation.containers.Well.Well

wellname_to_index(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)

wells_grouped_by(data_field=None, key=None, sort_keys=False, ignore_none=False, direction_of_occurence='row')

Return wells grouped by key.

wells_sorted_by(sortkey)

Return wells sorted by sortkey

This module contains a generic class for a well.

class synbiopython.lab_automation.containers.Well.Well(plate, row, column, name, data=None)

Bases: object

Generic class for a well.

Parameters

• plate – The plate on which the well is located

• row – The well’s row (a number, starting from 0)

• column – The well’s column (a number, starting from 0)

• name – The well’s name, for instance “A1”

• data – A dictionary storing data on the well, used in algorithms and reports.

add_content(components_quantities, volume=None, unit_volume='L')

Add content to well.

Parameters

• components_quantities – Dictionary of components and quantities (default: gram). Example {“Compound_1”: 5}.

• volume – Volume (default: liter).

• unit_volume – Unit of volume (default: liter). Options: liter (L), milliliter (mL), microliter (uL), nanoliter (nL).

capacity = None

property coordinates

Return (well.row, well.column).

dead_volume_per_transfer_class = None

empty_completely()

Empty the well.

index_in_plate(direction='row')

Return the index of the well in the plate.

is_after(other, direction='row')

Return whether this well is located strictly after the other well.

Example: iterate over all free wells after the last non-free well:

>>> direction = 'row'
>>> last_occupied_well = plate.last_nonempty_well(direction=direction)
>>> free_wells = (w for w in plate.iter_wells(direction=direction)
>>>               if w.is_after(last_occupied_well))
>>> for well in free_wells: ...

property is_empty

Return true if the well’s volume is 0.

iterate_sources_tree()

Iterate through the tree of sources.

pretty_summary()

Return a summary string of the well.

subtract_content(components_quantities, volume=0)

Subtract content from well.

to_dict()

Convert well to dict

property volume

Return volume.

This module contains a class to represent the volume and quantities of a well.

class synbiopython.lab_automation.containers.WellContent.WellContent(quantities=None, volume=0)

Bases: object

Class to represent the volume and quantities of a well.

Having the well content represented as a separate object makes it possible to have several wells share the same content, e.g. in throughs.

components_as_string(separator=' ')

Return a string representation of what’s in the well mix.

concentration(component=None, default=0)

Return concentration of component.

make_empty()

Empty the well.

to_dict()

Return a dict {volume: 0.0001, quantities: {…:…}}.