Merge pull request #36 from jodyphelan/dev

Dev

ntm_profiler/__init__.py

@@ -1,5 +1,5 @@
 from .utils import *
 from .output import *
 from .reformat import *
-from .db import *
-__version__="0.3.0"
+
+__version__="0.4.0"

ntm_profiler/models.py

@@ -0,0 +1,33 @@
+from pathogenprofiler import models, object_list2text
+from pathogenprofiler.models import Gene, Variant, BarcodeResult, DrGene, DrVariant, SpeciesPrediction, BamQC, FastaQC, VcfQC, FastqQC
+from pydantic import BaseModel
+from typing import List, Optional,  Union
+
+
+class Result(BaseModel):
+    id: str
+
+class SpeciesResult(Result):
+    result_type: str = 'Species'
+    species: SpeciesPrediction
+    qc: Union[FastqQC,FastaQC]
+
+class ProfileResult(SpeciesResult):
+    result_type: str = 'Profile'
+    notes: List[str] = []
+    resistance_db: dict = {}
+    barcode: Optional[List[BarcodeResult]] = []
+    dr_variants: List[DrVariant] = []
+    dr_genes: List[DrGene] = []
+    other_variants: List[Variant] = []
+    other_genes: List[Gene] = []
+    fail_variants: List[Variant] = []
+    qc: Union[BamQC, FastaQC, VcfQC]
+    result_type: str = 'Profile'
+
+    def get_qc(self):
+        if isinstance(self.qc, (BamQC, FastaQC)):
+            text = object_list2text(l = self.qc.target_qc)
+        else:
+            text = "Not available for VCF input"
+        return text