Implemented annotated local typing method without testing

src/autobigs/engine/structures/alignment.py

@@ -0,0 +1,17 @@
+from dataclasses import dataclass
+from numbers import Number
+
+@dataclass(frozen=True)
+class AlignmentStats:
+    percent_identity: float
+    mismatches: int
+    gaps: int
+    score: int
+
+@dataclass(frozen=True)
+class PairwiseAlignment:
+    reference: str
+    query: str
+    reference_indices: list[Number]
+    query_indices: list[Number]
+    alignment_stats: AlignmentStats

src/autobigs/engine/structures/genomics.py

@@ -0,0 +1,104 @@
+from dataclasses import dataclass
+from numbers import Number
+from typing import Mapping, Sequence, Set, Union
+
+
+@dataclass(frozen=True)
+class StringAnnotation:
+    type: str
+    start: int
+    end: int
+    feature_properties: Mapping[str, Set[str]]
+
+@dataclass(frozen=True)
+class NamedString:
+    name: str
+    sequence: str
+
+@dataclass(frozen=True)
+class AnnotatedString(NamedString):
+    annotations: Sequence[StringAnnotation]
+
+@dataclass(frozen=True)
+class SangerTraceData(NamedString):
+    seq_param_file_name: str
+    analysis_proto_settings_name: str
+    analysis_rpto_settings_ver: str
+    analysis_proto_xml_data: str
+    analysis_proto_xml_schema_ver: str
+    sample_comment: Union[None, str]
+    capillary_machine: bool
+    container_identifier: str
+    container_name: str
+    comment_title: str
+    channel_1: Sequence[Number]
+    channel_2: Sequence[Number]
+    channel_3: Sequence[Number]
+    channel_4: Sequence[Number]
+    measured_voltage_dv: Sequence[Number]
+    measured_current_ma: Sequence[Number]
+    measured_power_mw: Sequence[Number]
+    measured_temperature_celsius: Sequence[Number]
+    down_sample_factor: Number
+    dye_1: str
+    dye_2: str
+    dye_3: str
+    dye_4: str
+    dye_wavelength_1: str
+    dye_wavelength_2: str
+    dye_wavelength_3: str
+    dye_wavelength_4: str
+    dye_set_name: str
+    electrophoresis_voltage_setting_v: Number
+    start_run_event: str
+    stop_run_event: str
+    start_collection_event: str
+    stop_collection_event: str
+    base_order: Sequence[str]
+    gel_type_desc: str
+    injection_time_sec: Number
+    inection_voltage_v: Number
+    lane_or_capillary: Number
+    sample_tracking_id: str
+    length_to_detector_cm: Number
+    laser_power_mw: Number
+    instrument_name_and_serial: str
+    data_collection_module_file: str
+    model_number: str
+    pixels_avg_per_lane: Number
+    number_of_capillaries: Number
+    marked_off_scale_scans: Union[None, Sequence[Number]]
+    # Skipped Ovrl, OvrV
+    mobility_file: str
+    # Skipped PRJT, PROJ
+    pixel_bin_size: Number
+    # Skipped scan rate
+    results_group_comment: Union[None, str]
+    results_group_name: str
+    run_module_ver: str
+    run_module_xml: str
+    run_module_xml_ver: str
+    run_proto_name: str
+    run_proto_ver: str
+    run_start_date: str  # Date time object
+    run_stop_date: str  # Date time object
+    data_collection_start_date: str
+    data_collection_stop_date: str
+    run_name: str
+    run_start_time: str  # time object
+    run_stop_time: str  # time object
+    collection_start_time: str  # time object
+    collection_stop_time: str  # time object
+    saturated_data_points: Union[None, Sequence[Number]]
+    color_rescaling_divisor: Number
+    scan_count: Number
+    polymer_lot_expiration: str  # date time object
+    polymer_lot_number: Number
+    sample_name: str
+    # Skipped genescan data
+    # Skipped size standard file name
+    data_collection_software_ver: str
+    data_collection_firmware_ver: str
+    run_temperature_setting_celcius: Number
+    well_id: str
+    plate_user_name: str

src/autobigs/engine/structures/mlst.py

@@ -0,0 +1,33 @@
+from collections import defaultdict
+from dataclasses import dataclass
+from typing import Collection, Iterable, Mapping, Sequence, Union
+
+from autobigs.engine.structures.alignment import AlignmentStats
+
+@dataclass(frozen=True)
+class Allele:
+    allele_locus: str
+    allele_variant: str
+    partial_match_profile: Union[None, AlignmentStats]
+
+@dataclass(frozen=True)
+class MLSTProfile:
+    alleles: Collection[Allele]
+    sequence_type: str
+    clonal_complex: str
+
+@dataclass(frozen=True)
+class NamedMLSTProfile:
+    name: str
+    mlst_profile: Union[None, MLSTProfile]
+
+
+def alleles_to_mapping(alleles: Iterable[Allele]):
+    result = defaultdict(list)
+    for allele in alleles:
+        result[allele.allele_locus].append(allele.allele_variant)
+    result = dict(result)
+    for locus, variant in result.items():
+        if len(variant) == 1:
+            result[locus] = variant[0]
+    return result