add more logic to compare_chrom_names

bedboss/refgenome_validator/refgenomevalidator.py

@@ -20,49 +20,9 @@ def __init__(self, genome_models):
             []
         )  # this will be a list of dictionary info with length of genome_models
 
-    def predict_parent(self):
-        """
-        Predicts from a mutually exclusive list of reference genomes
-
-        """
-
-        # For mutually exclusive items, we can quickly check, chrom sizes and chrom names and see if there are incompatible
-        # genome models and truncate the list at the very beginning
-
-        predicted_parents = []
-
-        for bed in self.bedfiles:
-            # We may be doing this somewhere else and should just pass this in...
-            bed_chrom_info = get_bed_chrom_info(bed)
-
-            for genome in self.genome_models:
-                exclude_result = self.compare_chrom_size(
-                    bed_chrom_info, genome.chrom_sizes
-                )
-                if not exclude_result:
-                    # keep the genome
-                    predicted_parents.append(genome.alias)
-                else:
-                    # Can we for sure exclude this? if so delete it
-                    # Do we need to deep copy this or will it cause issues?
-                    self.genome_models.remove(genome)
-
-        predicted_parent = "hg38"
-
-        return predicted_parent
-
-    def modify_compatibility_matrix(self):
-        """
-
-        modifys the data frame storing compatibility matrix of entries
-
-        """
-
-        pass
-
     def compare_chrom_names_lengths(
         self, bed_chrom_sizes: dict, genome_chrom_sizes: dict
-    ):
+    ) -> dict:
         """
         Given two dicts of chroms (key) and their sizes (values)
         determine overlap
@@ -73,32 +33,54 @@ def compare_chrom_names_lengths(
         return dict: returns a dictionary with information on Query vs Model, e.g. chrom names QueryvsModel
         """
 
-        # Check names
+        # Layer 1: Check names
         # Define Three separate counts
         # Q = Query, M = Model
         name_stats = {}
-        q_and_m = None
-        q_and_not_m = None
-        not_q_and_m = None
-
-        name_stats = {}
-
-        extra_chroms = False
-        chroms_beyond_range = False
-        exclude = False
+        q_and_m = 0
+        q_and_not_m = 0
+        not_q_and_m = 0
+        passed_chrom_names = True
 
         for key in list(bed_chrom_sizes.keys()):
             if key not in genome_chrom_sizes:
-                extra_chroms = True
-            elif key in genome_chrom_sizes:
-                if genome_chrom_sizes[key] < bed_chrom_sizes[key]:
-                    chroms_beyond_range = True
-
-        if extra_chroms or chroms_beyond_range:
-            exclude = True
-            return exclude
-
-        return exclude
+                q_and_not_m += 1
+            if key in genome_chrom_sizes:
+                q_and_m += 1
+        for key in list(genome_chrom_sizes.keys()):
+            if key not in bed_chrom_sizes:
+                not_q_and_m += 1
+
+        # What is our threshold for passing layer 1?
+        if q_and_not_m > 1:
+            passed_chrom_names = False
+
+        name_stats["q_and_m"] = q_and_m
+        name_stats["q_and_not_m"] = q_and_not_m
+        name_stats["not_q_and_m"] = not_q_and_m
+        name_stats["passed_chrom_names"] = passed_chrom_names
+
+        # Layer 2:  Check Lengths, but only if layer 1 is passing
+        if passed_chrom_names:
+            length_stats = {}
+
+            chroms_beyond_range = False
+            num_of_chrm_beyond = 0
+
+            for key in list(bed_chrom_sizes.keys()):
+                if key in genome_chrom_sizes:
+                    if bed_chrom_sizes[key] > genome_chrom_sizes[key]:
+                        num_of_chrm_beyond += 1
+                        chroms_beyond_range = True
+
+            length_stats["beyond_range"] = chroms_beyond_range
+            length_stats["num_of_chrm_beyond"] = num_of_chrm_beyond
+        else:
+            length_stats = {}
+            length_stats["beyond_range"] = None
+            length_stats["num_of_chrm_beyond"] = None
+
+        return {"chrom_name_stats": name_stats, "chrom_length_stats": length_stats}
 
     def determine_compatibility(
         self, bedfile: str, ref_filter: list[str]