Circular import fix attempt by merging files

Dockerfile

@@ -15,4 +15,4 @@ ENV PATH="${VENV}/bin:$PATH"
 
 # Install from PyPI
 RUN pip install --upgrade pip
-RUN pip install crispr-ambiguous-mapping==0.0.151
+RUN pip install crispr-ambiguous-mapping==0.0.152

crispr-ambiguous-mapping/crispr_ambiguous_mapping/models/__init__.py

@@ -1,3 +1,2 @@
 from .editing_models import *
-from .mapping_models import *
-from .types import *
+from .mapping_models import *

crispr-ambiguous-mapping/crispr_ambiguous_mapping/models/editing_models.py

@@ -1,7 +1,7 @@
 from dataclasses import dataclass
 from typing import Counter as CounterType
 from typing import Tuple, Optional, DefaultDict, Dict
-from .types import GeneralAlleleCountSeriesDict
+from .mapping_models import GeneralAlleleCountSeriesDict
 import pandas as pd
 
 @dataclass

crispr-ambiguous-mapping/crispr_ambiguous_mapping/models/mapping_models.py

@@ -7,7 +7,83 @@
 
 from .error_models import GuideCountError
 from .quality_control_models import QualityControlResult
-from .types import GeneralMappingInferenceDict
+
+from typing import Union, List, Mapping, Tuple, Optional, Any, DefaultDict, Dict
+from typing import Counter as CounterType
+import pandas as pd
+
+
+# Sequence Count Result Objects
+ProtospacerCounter = CounterType[str]
+ProtospacerSurrogateCounter = CounterType[Tuple[str, str]]
+ProtospacerBarcodeCounter = CounterType[Tuple[str, str]]
+ProtospacerSurrogateBarcodeCounter = CounterType[Tuple[str, str, str]]
+
+ProtospacerDictUMICounter = DefaultDict[str, CounterType[str]]
+ProtospacerSurrogateDictUMICounter = DefaultDict[Tuple[str, str], CounterType[str]]
+ProtospacerBarcodeDictUMICounter = DefaultDict[Tuple[str, str], CounterType[str]]
+ProtospacerSurrogateBarcodeDictUMICounter = DefaultDict[Tuple[str, str, str], CounterType[str]]
+
+GeneralGuideCountType = Union[ProtospacerCounter, 
+                       ProtospacerSurrogateCounter, 
+                       ProtospacerBarcodeCounter, 
+                       ProtospacerSurrogateBarcodeCounter,
+                       ProtospacerDictUMICounter,
+                       ProtospacerSurrogateDictUMICounter,
+                       ProtospacerBarcodeDictUMICounter, 
+                       ProtospacerSurrogateBarcodeDictUMICounter]
+
+# Mapping Count Dict Object
+
+ProtospacerSurrogateBarcodeMatchCountDict = DefaultDict[Tuple[str, str, str], Union[int, float]]
+ProtospacerSurrogateMatchCountDict = DefaultDict[Tuple[str, str], Union[int, float]]
+ProtospacerBarcodeMatchCountDict = DefaultDict[Tuple[str, str], Union[int, float]]
+ProtospacerMatchCountDict = DefaultDict[str, Union[int, float]]
+GeneralMatchCountDict = Union[ProtospacerSurrogateBarcodeMatchCountDict, 
+      ProtospacerSurrogateMatchCountDict, 
+      ProtospacerBarcodeMatchCountDict, 
+      ProtospacerMatchCountDict]
+
+ProtospacerSurrogateBarcodeMismatchCountDict = DefaultDict[Tuple[Tuple[str, str, str], Tuple[str, str, str]], Union[int, float]]
+ProtospacerSurrogateMismatchCountDict = DefaultDict[Tuple[Tuple[str, str], Tuple[str, str]], Union[int, float]]
+ProtospacerBarcodeMismatchCountDict = DefaultDict[Tuple[Tuple[str, str], Tuple[str, str]], Union[int, float]]
+ProtospacerMismatchCountDict = DefaultDict[Tuple[str, str], Union[int, float]]
+
+GeneralMismatchCountDict = Union[ProtospacerSurrogateBarcodeMismatchCountDict, 
+      ProtospacerSurrogateMismatchCountDict, 
+      ProtospacerBarcodeMismatchCountDict, 
+      ProtospacerMismatchCountDict]
+
+# Allele nested dict Object (Key of first dict is inferred, key of second dict is observed, value of second dict is count)
+ProtospacerSurrogateBarcodeAlleleDict = DefaultDict[Tuple[str, str, str], DefaultDict[Tuple[str, str, str], Union[int, float]]]
+ProtospacerSurrogateAlleleDict = DefaultDict[Tuple[str, str], DefaultDict[Tuple[str, str], Union[int, float]]]
+ProtospacerBarcodeAlleleDict = DefaultDict[Tuple[str, str], DefaultDict[Tuple[str, str], Union[int, float]]]
+ProtospacerAlleleDict = DefaultDict[str, DefaultDict[str, Union[int, float]]]
+
+GeneralAlleleDict = Union[ProtospacerSurrogateBarcodeAlleleDict,
+      ProtospacerSurrogateAlleleDict,
+      ProtospacerBarcodeAlleleDict,
+      ProtospacerAlleleDict]
+
+
+
+
+# Allele Count Series Dict
+ProtospacerSurrogateBarcodeAlleleCountSeriesDict = DefaultDict[Tuple[str, str, str], pd.Series]
+ProtospacerSurrogateAlleleCountSeriesDict = DefaultDict[Tuple[str, str], pd.Series]
+ProtospacerBarcodeAlleleCountSeriesDict = DefaultDict[Tuple[str, str], pd.Series]
+ProtospacerAlleleCountSeriesDict = DefaultDict[str, pd.Series]
+
+GeneralAlleleCountSeriesDict = Union[ProtospacerSurrogateBarcodeAlleleCountSeriesDict,
+                                     ProtospacerSurrogateAlleleCountSeriesDict,
+                                     ProtospacerBarcodeAlleleCountSeriesDict,
+                                     ProtospacerAlleleCountSeriesDict]
+
+
+
+
+
+
 
 @dataclass
 class SingleInferenceMatchResultValue:
@@ -52,6 +128,18 @@ class InferenceResult:
     inferred_value: CompleteInferenceMatchResult
 
 
+# Inference Result Object
+ProtospacerSurrogateBarcodeMappingInferenceDict = DefaultDict[Tuple[str,str,str], Dict[InferenceResult]]
+ProtospacerSurrogateMappingInferenceDict = DefaultDict[Tuple[str,str], Dict[InferenceResult]]
+ProtospacerBarcodeMappingInferenceDict = DefaultDict[Tuple[str,str], Dict[InferenceResult]]
+ProtospacerMappingInferenceDict = DefaultDict[str, Dict[InferenceResult]]
+
+GeneralMappingInferenceDict = Union[ProtospacerSurrogateBarcodeMappingInferenceDict,
+      ProtospacerSurrogateMappingInferenceDict,
+      ProtospacerBarcodeMappingInferenceDict,
+      ProtospacerMappingInferenceDict]
+
+
 @dataclass
 class MatchSetWhitelistReporterCounterSeriesResults:
     ambiguous_ignored_umi_noncollapsed_counterseries : Optional[pd.Series] = None
@@ -142,3 +230,11 @@ class WhitelistReporterCountsResult:
     observed_guide_reporter_umi_counts_inferred: GeneralMappingInferenceDict
     quality_control_result: QualityControlResult
     count_input: CountInput
+
+
+
+#
+# Types
+#
+
+

crispr-ambiguous-mapping/crispr_ambiguous_mapping/parsing/reporter_umitools_fastq_parsing.py

@@ -4,7 +4,7 @@
 from typeguard import typechecked
 from typing import Union, Optional, List, Tuple, DefaultDict
 from typing import Counter as CounterType
-from ..models.types import ProtospacerCounter, ProtospacerDictUMICounter, ProtospacerBarcodeCounter, ProtospacerBarcodeDictUMICounter, ProtospacerSurrogateCounter, ProtospacerSurrogateDictUMICounter, ProtospacerSurrogateBarcodeCounter, ProtospacerSurrogateBarcodeDictUMICounter
+from ..models.mapping_models import ProtospacerCounter, ProtospacerDictUMICounter, ProtospacerBarcodeCounter, ProtospacerBarcodeDictUMICounter, ProtospacerSurrogateCounter, ProtospacerSurrogateDictUMICounter, ProtospacerSurrogateBarcodeCounter, ProtospacerSurrogateBarcodeDictUMICounter
 from collections import Counter
 from typing import Callable
 from functools import partial

crispr-ambiguous-mapping/crispr_ambiguous_mapping/processing/crispr_count_processing.py

@@ -1,8 +1,7 @@
 from typeguard import typechecked
 from typing import Union, List, Mapping, Tuple, Optional, Any, DefaultDict
 from typing import Counter as CounterType
-from ..models.types import GeneralMappingInferenceDict, GeneralMatchCountDict, GeneralMismatchCountDict
-
+from ..models.mapping_models import GeneralMappingInferenceDict, GeneralMatchCountDict, GeneralMismatchCountDict
 
 from collections import Counter
 from collections import defaultdict

crispr-ambiguous-mapping/crispr_ambiguous_mapping/processing/crispr_editing_processing.py

@@ -3,7 +3,7 @@
 from typing import Optional, DefaultDict, Union, Tuple, List
 import pandas as pd
 from typing import Counter as CounterType
-from ..models.types import GeneralMappingInferenceDict, GeneralAlleleDict, GeneralAlleleCountSeriesDict
+from ..models.mapping_models import GeneralMappingInferenceDict, GeneralAlleleDict, GeneralAlleleCountSeriesDict
 from ..models.mapping_models import CompleteInferenceMatchResult, MatchSetSingleInferenceMatchResult, InferenceResult
 from ..models.editing_models import (MatchSetWhitelistReporterObservedSequenceCounterSeriesResults, 
                                      MatchSetWhitelistReporterObservedSequenceMutationProfiles, 

crispr-ambiguous-mapping/crispr_ambiguous_mapping/processing/crispr_guide_counting.py

@@ -25,7 +25,7 @@
 from . import crispr_guide_inference
 from .crispr_count_processing import get_counterseries_all_results
 from ..quality_control.crispr_mapping_quality_control import perform_counts_quality_control
-from ..models.types import GeneralGuideCountType, GeneralMappingInferenceDict
+from ..models.mapping_models import GeneralGuideCountType, GeneralMappingInferenceDict
 from ..models.mapping_models import WhitelistReporterCountsResult, InferenceResult, CountInput
 
 

crispr-ambiguous-mapping/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "crispr-ambiguous-mapping"
-version = "0.0.151"
+version = "0.0.152"
 description = ""
 authors = ["Basheer Becerra <[email protected]>"]
 readme = "README.md"