define fix

cov-lineages · Aug 23, 2023 · 82b00de · 82b00de
1 parent 5d4db3a
commit 82b00de
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/scorpio/scripts/definitions.py b/scorpio/scripts/definitions.py
@@ -128,7 +128,7 @@ def __init__(self, variant=None, reference=None, ignore_fails=False):
         self.add_context(reference)
 
     def print(self):
-        print("{", self.name, self.space, self.type, self.ref_start, self.length, self.ref_allele, self.alt_allele, self.cds, self.aa_pos, self.before, self.after, self.fuzzy, "}")
+        print("{", self.name, self.space, self.type, self.ref_start, self.length, self.ref_allele, self.alt_allele, self.cds, self.aa_pos, self.before, self.after, self.fuzzy, self.count, self.frequency, "}")
 
     def equals(self, other, reference):
         if self.ref_start == other.ref_start or self.aa_pos == other.aa_pos:

diff --git a/scorpio/scripts/extract_definitions.py b/scorpio/scripts/extract_definitions.py
@@ -152,7 +152,8 @@ def parse_row_variants(list_variants, reference, include_protein, skip_translate
                 intermediate_list.append([var[0], int(var[1:-1]), var[-1]])
             except:
                 print("could not add var %s to intermediate list" % var)
-        merged_list.extend(merge_and_translate_nucs(intermediate_list, reference, include_protein, skip_translate))
+    merged_list.extend(merge_and_translate_nucs(intermediate_list, reference, include_protein, skip_translate))
+    assert len(merged_list) <= len(list_variants)
 
     return [Variant(v, reference) for v in merged_list]
 
@@ -180,7 +181,7 @@ def get_common_mutations(var_dict, min_occurance=3, threshold_common=0.98, thres
     common = []
     intermediate = []
     for var in var_dict:
-        #print("var", var, var_dict[var], min_occurance, var_dict["total"])
+        #print("var", var, var_dict[var], min_occurance, total)
         if var_dict[var].count == total:
             common.append(var_dict[var])
         elif var_dict[var].count >= min_occurance:
@@ -327,6 +328,8 @@ def extract_definitions(in_variants, in_groups, group_column, index_column, refe
             if index_column in row and var_column in row:
                 index = row[index_column]
                 variants = parse_row_variants(row[var_column].split("|"), reference, include_protein, skip_translate)
+                assert len(variants) <= len(row[var_column].split("|"))
+                #print(index, (index in group_dict), (index in outgroup_dict), (subset is None or group in subset), (index in group_dict and group_dict[index] in outgroup_dict))
                 if index in group_dict:
                     group = group_dict[index]
                     if subset is None or group in subset: