Cells

get_SIM_class(cell)

PROVISIONAL method to return whether a cell is Sensory/Interneuron/Motorneuron (or Other)

Parameters:

Name	Type	Description	Default
cell	str	which cell to assess	required

Returns:

Name	Type	Description
str		whether a cell is Sensory/Interneuron/Motorneuron (or Other)

Source code in cect/Cells.py

def get_SIM_class(cell: str):
    """
    PROVISIONAL method to return whether a cell is Sensory/Interneuron/Motorneuron (or Other)

    Parameters:
        cell: which cell to assess

    Returns:
        str: whether a cell is Sensory/Interneuron/Motorneuron (or Other)
    """

    pharyngeal_polymodal_to_class_motor = [
        "MI",
        "NSML",
        "NSMR",
        "MCL",
        "MCR",
    ]
    pharyngeal_polymodal_to_class_sensory = [
        "NSML",
        "NSMR",
    ]

    if cell in SENSORY_NEURONS_COOK + pharyngeal_polymodal_to_class_sensory:
        return "Sensory"
    elif cell in MOTORNEURONS_COOK + pharyngeal_polymodal_to_class_motor:
        return "Motorneuron"
    elif cell in INTERNEURONS_COOK:
        return "Interneuron"
    else:
        if len(cell) == 3:
            if get_SIM_class("%sL" % cell) == get_SIM_class("%sR" % cell):
                return get_SIM_class("%sL" % cell)
        return "Other"

get_cell_notes(cell)

Get a short description of the cell, mainly cell type

Parameters:

Name	Type	Description	Default
cell	str	Name of the cell	required

Returns:

Name	Type	Description
str		Description of the cell type

Source code in cect/Cells.py

def get_cell_notes(cell: str):
    """Get a short description of the cell, mainly cell type

    Args:
        cell (str): Name of the cell

    Returns:
        str: Description of the cell type
    """
    desc = cell_notes[cell] if cell in cell_notes else "???"
    desc = desc[0].upper() + desc[1:]
    return desc

get_contralateral_cell(cell)

Gets the contralateral cell for a given cell, based on Kim et al. 2024: https://doi.org/10.1101/2024.10.03.616419

Parameters:

Name	Type	Description	Default
cell	_type_	description	required

Raises:

Type	Description
Exception	description

Returns:

Name	Type	Description
_type_		description

Source code in cect/Cells.py

def get_contralateral_cell(cell: str):
    """Gets the contralateral cell for a given cell, based on Kim et al. 2024: https://doi.org/10.1101/2024.10.03.616419

    Args:
        cell (_type_): _description_

    Raises:
        Exception: _description_

    Returns:
        _type_: _description_
    """
    if not is_known_cell(cell):
        raise Exception(
            "Cannot determine contralateral cell for: %s (unknown cell)" % cell
        )
    if is_known_muscle(cell):
        if cell in ["MVR24", "MANAL"]:
            return cell
        if "L" in cell:
            return cell.replace("L", "R")
        if "R" in cell:
            return cell.replace("R", "L")
        return cell
    """elif not is_any_neuron(cell):
        raise Exception(
            "Determining contralateral cell is not yet implemented/tested for non neuronal cells, e.g. %s"
            % cell
        )"""
    if is_bilateral_left(cell):
        return cell[:-1] + "R"
    if is_bilateral_right(cell):
        return cell[:-1] + "L"
    else:
        return cell

get_primary_classification()

Get the primary classification of the cells, based on https://www.wormatlas.org/colorcode.htm

Returns:

Name	Type	Description
dict		Dict of cells vs classification/group from https://www.wormatlas.org/colorcode.htm

Source code in cect/Cells.py

def get_primary_classification():
    """Get the primary classification of the cells, based on https://www.wormatlas.org/colorcode.htm

    Returns:
        dict: Dict of cells vs classification/group from https://www.wormatlas.org/colorcode.htm
    """

    classification = {}

    for sex in WA_COLORS:
        for cell_class in WA_COLORS[sex]:
            for cell_type in WA_COLORS[sex][cell_class]:
                print_(" - %s/%s/%s" % (sex, cell_class, cell_type))

                if cell_type == "body wall muscle":
                    for cell in BODY_WALL_MUSCLE_NAMES + UNSPECIFIED_BODY_WALL_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "vulval muscle":
                    for cell in VULVAL_MUSCLE_NAMES:
                        classification[cell] = cell_type
                elif cell_type == "uterine muscle":
                    for cell in UTERINE_MUSCLE_NAMES:
                        classification[cell] = cell_type
                elif cell_type == "interneuron":
                    for cell in (
                        INTERNEURONS_COOK
                        + MALE_HEAD_INTERNEURONS
                        + MALE_NON_HEAD_INTERNEURONS
                    ):
                        classification[cell] = cell_type
                elif cell_type == "motor neuron":
                    for cell in MOTORNEURONS_COOK:
                        classification[cell] = cell_type
                elif cell_type == "sensory neuron":
                    for cell in (
                        SENSORY_NEURONS_COOK
                        + MALE_HEAD_SENSORY_NEURONS
                        + MALE_NON_HEAD_SENSORY_NEURONS
                    ):
                        classification[cell] = cell_type
                elif cell_type == "odd numbered pharyngeal muscle":
                    for cell in ODD_PHARYNGEAL_MUSCLE_NAMES:
                        classification[cell] = cell_type
                elif cell_type == "even numbered pharyngeal muscle":
                    for cell in EVEN_PHARYNGEAL_MUSCLE_NAMES:
                        classification[cell] = cell_type
                elif cell_type == "polymodal neuron":
                    for cell in PHARYNGEAL_POLYMODAL_NEURONS:
                        classification[cell] = cell_type
                elif cell_type == "marginal cells (mc) of the pharynx":
                    for cell in PHARYNGEAL_MARGINAL_CELLS:
                        classification[cell] = cell_type
                elif cell_type == "pharyngeal epithelium":
                    for cell in PHARYNGEAL_EPITHELIUM + PHARYNGEAL_GLIAL_CELL:
                        classification[cell] = cell_type  # TODO: check!
                elif cell_type == "basement membrane":
                    for cell in PHARYNGEAL_BASEMENT_MEMBRANE:
                        classification[cell] = cell_type  # TODO: check!
                elif cell_type == "neuron with unknown function":
                    for cell in UNKNOWN_FUNCTION_NEURONS:
                        classification[cell] = cell_type
                elif cell_type == "sheath cell other than amphid sheath and phasmid":
                    for cell in CEPSH_CELLS:
                        classification[cell] = cell_type
                elif cell_type == "excretory cell":
                    for cell in EXCRETORY_CELL:
                        classification[cell] = cell_type
                elif cell_type == "sphincter and anal depressor muscle":
                    for cell in ANAL_SPHINCTER_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "gland cell":
                    for cell in EXCRETORY_GLAND:
                        classification[cell] = cell_type
                elif cell_type == "head mesodermal cell":
                    for cell in HEAD_MESODERMAL_CELL:
                        classification[cell] = cell_type
                elif cell_type == "hypodermis":
                    for cell in HYPODERMIS:
                        classification[cell] = cell_type
                elif cell_type == "intestinal cells":
                    for cell in INTESTINE:
                        classification[cell] = cell_type
                elif cell_type == "intestinal muscle":
                    for cell in INTESTINAL_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "GLR cell":
                    for cell in GLR_CELLS:
                        classification[cell] = cell_type
                elif cell_type == "diagonal muscles":
                    for cell in MALE_DIAGONAL_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "posterior outer longitudinal muscles":
                    for cell in MALE_POSTERIOR_OUTER_LONGITUDINAL_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "anterior inner longitudinal muscles":
                    for cell in MALE_ANTERIOR_INNER_LONGITUDINAL_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "posterior inner longitudinal muscles":
                    for cell in MALE_POSTERIOR_INNER_LONGITUDINAL_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "caudal inner longitudinal muscles":
                    for cell in MALE_CAUDAL_LONGITUDINAL_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "spicule retractor muscles":
                    for cell in (
                        MALE_VENTRAL_SPICULE_RETRACTOR + MALE_DORSAL_SPICULE_RETRACTOR
                    ):
                        classification[cell] = cell_type
                elif cell_type == "spicule protractor muscles":
                    for cell in (
                        MALE_VENTRAL_SPICULE_PROTRACTOR + MALE_DORSAL_SPICULE_PROTRACTOR
                    ):
                        classification[cell] = cell_type
                elif cell_type == "gubernacular retractor muscles":
                    for cell in MALE_GUBERNACULAR_RETRACTOR_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "gubernacular erector muscles":
                    for cell in MALE_GUBERNACULAR_ERECTOR_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "anterior oblique muscles":
                    for cell in MALE_ANTERIOR_OBLIQUE_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "posterior oblique muscles":
                    for cell in MALE_POSTERIOR_OBLIQUE_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "vas deferens":
                    for cell in GONAD_CELL_MALE:
                        classification[cell] = cell_type
                elif cell_type == "proctodeum":
                    for cell in PROCTODEUM_CELL_MALE:
                        classification[cell] = cell_type
                elif cell_type == "diagonal muscles":
                    for cell in MALE_DIAGONAL_MUSCLES:
                        classification[cell] = cell_type
                elif cell_type == "ray structural cell":
                    for cell in MALE_RAY_STRUCTURAL_CELLS:
                        classification[cell] = cell_type
                elif cell_type in [
                    "General code for neuronal tissue if subtype is unspecified",
                    "vulval epithelium",
                    "germline",
                    "DTC and somatic gonad",
                    "embryo",
                    "uterus",
                    "spermatheca",
                    "spermatheca-uterine valve",
                    "excretory pore cell",
                    "duct cell",
                    "excretory duct",
                    "seam cell",
                    "socket cell, XXX cells",
                    "amphid sheath and phasmid sheath",
                    "pharyngeal-intestinal valve, intestinal rectal valve",
                    "arcade cell",
                    "rectal epithelium (U, F, K, K', Y, B)",
                    "rectal gland, pharyngeal glands",
                    "pseudocoelomic space",
                    "coeloemocyte",
                    "anterior outer longitudinal muscles",
                    "seminal vesicle",
                    "sheath cell (spicules, hook or post-cloacal sensilla)",
                    "socket cell (spicules, hook or post-cloacal sensilla)",
                ]:
                    print_(
                        "No synaptic connnections to cells of type %s..?" % cell_type
                    )
                else:
                    raise Exception("Cell type %s not handled" % cell_type)
    for cell in ALL_PREFERRED_CELL_NAMES:
        assert cell in classification

    return classification

is_known_cell(cell)

Is this string the name of one of the known cells?

Parameters:

Name	Type	Description	Default
cell	str	Cell name	required

Returns:

Name	Type	Description
bool		Whether this is a known cell name

Source code in cect/Cells.py

def is_known_cell(cell: str):
    """Is this string the name of one of the known cells?

    Args:
        cell (str): Cell name

    Returns:
        bool: Whether this is a known cell name
    """
    return cell in ALL_PREFERRED_CELL_NAMES

remove_leading_index_zero(cell)

Returns neuron name with an index without leading zero. E.g. VB01 -> VB1.

Source code in cect/Cells.py

def remove_leading_index_zero(cell: str):
    """
    Returns neuron name with an index without leading zero. E.g. VB01 -> VB1.
    """
    if cell[:2] in ["DA", "AS", "DD", "DB", "VA", "VB", "VC", "VD"] and cell[
        -2:
    ].startswith("0"):
        return "%s%s" % (cell[:-2], cell[-1:])
    return cell