예제 #1
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def _get_ahringer_384_parent(child_stock):
    """
    Get the 384-format LibraryStock corresponding to a 96-format child stock.

    Assumes standard Ahringer naming conventions.

    If the parent doesn't exist, creates it, assuming same parent
    as the child.
    """
    child_plate_parts = child_stock.plate.id.split('-')
    parent_plate_name = child_plate_parts[0] + '-' + child_plate_parts[1]
    parent_plate = get_library_plate(parent_plate_name)

    child_well = child_stock.well
    parent_well = get_384_parent_well(child_plate_parts[2], child_well)

    parent_pk = generate_library_stock_name(parent_plate_name, parent_well)

    try:
        parent_stock = LibraryStock.objects.get(pk=parent_pk)

    except ObjectDoesNotExist:
        parent_stock = LibraryStock(
            id=parent_pk,
            plate=parent_plate,
            well=parent_well,
            parent_stock=None,
            intended_clone=child_stock.intended_clone,
        )

        parent_stock.save()

    return parent_stock
예제 #2
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def _get_ahringer_384_parent(child_stock):
    """
    Get the 384-format LibraryStock corresponding to a 96-format child stock.

    Assumes standard Ahringer naming conventions.

    If the parent doesn't exist, creates it, assuming same parent
    as the child.
    """
    child_plate_parts = child_stock.plate.id.split('-')
    parent_plate_name = child_plate_parts[0] + '-' + child_plate_parts[1]
    parent_plate = get_library_plate(parent_plate_name)

    child_well = child_stock.well
    parent_well = get_384_parent_well(child_plate_parts[2], child_well)

    parent_pk = generate_library_stock_name(parent_plate_name, parent_well)

    try:
        parent_stock = LibraryStock.objects.get(pk=parent_pk)

    except ObjectDoesNotExist:
        parent_stock = LibraryStock(
            id=parent_pk,
            plate=parent_plate,
            well=parent_well,
            parent_stock=None,
            intended_clone=child_stock.intended_clone,
        )

        parent_stock.save()

    return parent_stock
예제 #3
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def get_library_stock(legacy_plate_name, well):
    """Get a library well from its legacy plate name and well."""
    library_stock_name = generate_library_stock_name(legacy_plate_name, well)

    try:
        return LibraryStock.objects.get(id=library_stock_name)

    except ObjectDoesNotExist:
        raise ObjectDoesNotExist(get_missing_object_message(
            'LibraryStock', id=library_stock_name))
예제 #4
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    def sync_secondary_L4440_row(legacy_row):
        plate_name = legacy_row[0]
        well = get_three_character_well(legacy_row[1])

        new_well = LibraryStock(
            id=generate_library_stock_name(plate_name, well),
            plate=get_library_plate(plate_name), well=well,
            parent_stock=None, intended_clone=get_clone('L4440'))

        return update_or_save_object(command, new_well, recorded_wells,
                                     fields_to_compare)
예제 #5
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    def handle(self, **options):
        require_db_write_acknowledgement()

        all_wells = get_well_set()

        # Get all wells, to determine which wells are missing.
        #
        # Skip 384-well plates, since the empty wells from these Ahringer
        # parent plates can be created in concert with their 96-well children.
        #
        # Also skip 'GHR-' style plates. Since we don't actually have these
        # plates in the lab, we only care about the small fraction of the
        # wells from these plates that were used to generated our Vidal
        # rearrays.
        library_stocks = (LibraryStock.objects.filter(
            plate__number_of_wells=96).exclude(plate__id__startswith='GHR-'))

        plate_wells = {}

        for library_stock in library_stocks:
            if library_stock.plate not in plate_wells:
                plate_wells[library_stock.plate] = set()

            plate_wells[library_stock.plate].add(library_stock.well)

        for library_plate in plate_wells:
            missing_wells = all_wells - plate_wells[library_plate]

            for missing_well in missing_wells:
                library_stock = LibraryStock(
                    id=generate_library_stock_name(library_plate.id,
                                                   missing_well),
                    plate=library_plate,
                    well=missing_well,
                    parent_stock=None,
                    intended_clone=None,
                )

                if library_plate.is_ahringer_96_plate():
                    parent_stock = _get_ahringer_384_parent(library_stock)

                    if parent_stock.intended_clone:
                        self.stderr.write(
                            '384 well {} has a non-null intended clone, '
                            'but its 96-well derivative {} is empty\n'.format(
                                parent_stock, library_stock))

                    library_stock.parent_stock = parent_stock

                library_stock.save()
예제 #6
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    def handle(self, **options):
        require_db_write_acknowledgement()

        all_wells = get_well_set()

        # Get all wells, to determine which wells are missing.
        #
        # Skip 384-well plates, since the empty wells from these Ahringer
        # parent plates can be created in concert with their 96-well children.
        #
        # Also skip 'GHR-' style plates. Since we don't actually have these
        # plates in the lab, we only care about the small fraction of the
        # wells from these plates that were used to generated our Vidal
        # rearrays.
        library_stocks = (LibraryStock.objects
                          .filter(plate__number_of_wells=96)
                          .exclude(plate__id__startswith='GHR-'))

        plate_wells = {}

        for library_stock in library_stocks:
            if library_stock.plate not in plate_wells:
                plate_wells[library_stock.plate] = set()

            plate_wells[library_stock.plate].add(library_stock.well)

        for library_plate in plate_wells:
            missing_wells = all_wells - plate_wells[library_plate]

            for missing_well in missing_wells:
                library_stock = LibraryStock(
                    id=generate_library_stock_name(library_plate.id,
                                                   missing_well),
                    plate=library_plate, well=missing_well,
                    parent_stock=None, intended_clone=None,
                )

                if library_plate.is_ahringer_96_plate():
                    parent_stock = _get_ahringer_384_parent(library_stock)

                    if parent_stock.intended_clone:
                        self.stderr.write(
                            '384 well {} has a non-null intended clone, '
                            'but its 96-well derivative {} is empty\n'
                            .format(parent_stock, library_stock))

                    library_stock.parent_stock = parent_stock

                library_stock.save()
예제 #7
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    def sync_primary_row(legacy_row):
        plate_name = legacy_row[0]
        well = get_three_character_well(legacy_row[1])
        clone_name = legacy_row[2]
        parent_plate_name = legacy_row[4]

        if re.match('sjj', clone_name):
            parent_chromosome = legacy_row[3]
            parent_plate_name = generate_ahringer_384_plate_name(
                parent_chromosome, parent_plate_name)
        parent_well_improper = legacy_row[5]
        if re.match('mv', clone_name):
            clone_name = generate_vidal_clone_name(parent_plate_name,
                                                   parent_well_improper)

        intended_clone = get_clone(clone_name)

        if re.match('L4440', clone_name):
            parent_stock = None

        else:
            parent_well_proper = get_three_character_well(parent_well_improper)
            parent_stock = get_library_stock(parent_plate_name,
                                             parent_well_proper)

            # Confirm that this intended clone matches parent's clone
            if parent_stock.intended_clone != intended_clone:
                raise CommandError('Clone {} does not match parent\n'
                                   .format(clone_name))

        new_well = LibraryStock(
            id=generate_library_stock_name(plate_name, well),
            plate=get_library_plate(plate_name), well=well,
            parent_stock=parent_stock,
            intended_clone=intended_clone)

        return update_or_save_object(command, new_well, recorded_wells,
                                     fields_to_compare)
예제 #8
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    def sync_source_row(legacy_row):
        plate_name = legacy_row[0]
        clone_name = legacy_row[3]

        if re.match('sjj', clone_name):
            chromosome = legacy_row[2]
            plate_name = generate_ahringer_384_plate_name(
                chromosome, plate_name)

        well_improper = legacy_row[1]
        well_proper = get_three_character_well(well_improper)

        if re.match('mv', clone_name):
            clone_name = generate_vidal_clone_name(plate_name,
                                                   well_improper)

        new_well = LibraryStock(
            id=generate_library_stock_name(plate_name, well_proper),
            plate=get_library_plate(plate_name), well=well_proper,
            parent_stock=None, intended_clone=get_clone(clone_name))

        return update_or_save_object(command, new_well, recorded_wells,
                                     fields_to_compare)
예제 #9
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    def sync_eliana_row(legacy_row):
        plate_name = legacy_row[0]
        well = get_three_character_well(legacy_row[1])

        if legacy_row[2]:
            try:
                parent_stock = get_library_stock(legacy_row[2], legacy_row[3])
                intended_clone = parent_stock.intended_clone
            except ObjectDoesNotExist:
                parent_stock = None
                intended_clone = None

        else:
            parent_stock = None
            intended_clone = None

        new_well = LibraryStock(
            id=generate_library_stock_name(plate_name, well),
            plate=get_library_plate(plate_name), well=well,
            parent_stock=parent_stock,
            intended_clone=intended_clone)

        return update_or_save_object(command, new_well, recorded_wells,
                                     fields_to_compare)
예제 #10
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    def sync_secondary_row(legacy_row):
        plate_name = legacy_row[0]
        well = get_three_character_well(legacy_row[1])
        clone_name = legacy_row[2]

        definite_parent_plate_name = legacy_row[3]
        definite_parent_well = legacy_row[4]
        if definite_parent_well:
            definite_parent_well = get_three_character_well(
                definite_parent_well)

        likely_parent_plate_name = legacy_row[5]
        likely_parent_well = legacy_row[6]
        if likely_parent_well:
            likely_parent_well = get_three_character_well(likely_parent_well)

        likely_parent_clone_name = legacy_row[7]

        if (definite_parent_plate_name and likely_parent_plate_name and
                definite_parent_plate_name != likely_parent_plate_name):
            raise CommandError(
                'ERROR: definite and likely parent plates disagree '
                'for {} {}\n'.format(plate_name, well))

        if (definite_parent_well and likely_parent_well and
                definite_parent_well != likely_parent_well):
            raise CommandError(
                'ERROR: definite and likely parent wells disagree '
                'for {} {}\n'.format(plate_name, well))

        try:
            if definite_parent_plate_name and definite_parent_well:
                parent_stock = get_library_stock(definite_parent_plate_name,
                                                 definite_parent_well)

            else:
                parent_stock = get_library_stock(likely_parent_plate_name,
                                                 likely_parent_well)

            intended_clone = parent_stock.intended_clone

        except ObjectDoesNotExist:
            command.stderr.write(
                'WARNING for LibraryStock {} {}: parent not '
                'found in LibraryStock\n'.format(plate_name, well))

            parent_stock = None
            intended_clone = None

        if clone_name and (clone_name != likely_parent_clone_name):
            command.stderr.write(
                'WARNING for LibraryStock {} {}: clone recorded '
                'in CherryPickRNAiPlate is inconsistent with '
                'CherryPickTemplate source/destination records\n'
                .format(plate_name, well))

        if re.match('sjj', clone_name):
            try:
                recorded_clone = get_clone(clone_name)
                if recorded_clone != intended_clone:
                    command.stderr.write(
                        'WARNING for LibraryStock {} {}: clone recorded '
                        'in CherryPickRNAiPlate does not match its '
                        'parent\'s clone\n'.format(plate_name, well))

            except ObjectDoesNotExist:
                command.stderr.write(
                    'WARNING for LibraryStock {} {}: clone recorded in '
                    'CherryPickRNAiPlate not found at all in RNAiPlate\n'
                    .format(plate_name, well))

        new_well = LibraryStock(
            id=generate_library_stock_name(plate_name, well),
            plate=get_library_plate(plate_name), well=well,
            parent_stock=parent_stock,
            intended_clone=intended_clone)

        return update_or_save_object(command, new_well, recorded_wells,
                                     fields_to_compare)