update tests inline

Author: rmcolq

scorpio/scripts/type_constellations.py

@@ -295,7 +295,7 @@ def parse_json_in(refseq, features_dict, variants_file, constellation_names=None
                 variant_list.append(record)
 
     if "rules" in json_dict:
-        if type(json_dict["rules"]) == dict:
+        if type(json_dict["rules"]) == dict and "default" in json_dict["rules"]:
             rules = json_dict["rules"]
         else:
             rules = {"default": json_dict["rules"]}
@@ -573,24 +573,24 @@ def var_follows_rules(call, rule):
     else:
         return call == rule_call
 
-def counts_follow_rules(counts, rules):
+def counts_follow_rules(counts, rules, key):
     # rules allowed include "max_ref", "min_alt", "min_snp_alt"
     is_rule_follower = True
     notes = []
-    for rule in rules:
+    for rule in rules[key]:
         if ":" in rule:
             continue
         elif str(rule).startswith("min") or str(rule).startswith("max"):
             rule_parts = rule.split("_")
             if len(rule_parts) <= 1:
                 continue
             elif len(rule_parts) == 2:
-                if rule_parts[0] == "min" and counts[rule_parts[1]] < rules[rule]:
+                if rule_parts[0] == "min" and counts[rule_parts[1]] < rules[key][rule]:
                     is_rule_follower = False
-                elif rule_parts[0] == "max" and counts[rule_parts[1]] > rules[rule]:
+                elif rule_parts[0] == "max" and counts[rule_parts[1]] > rules[key][rule]:
                     is_rule_follower = False
                 else:
-                    counts["rules"] += 1
+                    counts["rules"][key] += 1
             elif len(rule_parts) == 3:
                 part = None
                 if rule_parts[1] in ["substitution", "snp"]:
@@ -599,16 +599,16 @@ def counts_follow_rules(counts, rules):
                     part = "indel"
                 if not part:
                     is_rule_follower = False
-                elif rule_parts[0] == "min" and counts[part][rule_parts[2]] < rules[rule]:
+                elif rule_parts[0] == "min" and counts[part][rule_parts[2]] < rules[key][rule]:
                     is_rule_follower = False
-                    notes.append("%s_%s_count=%i is less than %i" % (part, rule_parts[2], counts[part][rule_parts[2]], rules[rule]))
-                elif rule_parts[0] == "max" and counts[part][rule_parts[2]] > rules[rule]:
+                    notes.append("%s_%s_count=%i is less than %i" % (part, rule_parts[2], counts[part][rule_parts[2]], rules[key][rule]))
+                elif rule_parts[0] == "max" and counts[part][rule_parts[2]] > rules[key][rule]:
                     is_rule_follower = False
-                    notes.append("%s_%s_count=%i is more than %i" % (part, rule_parts[2], counts[part][rule_parts[2]], rules[rule]))
+                    notes.append("%s_%s_count=%i is more than %i" % (part, rule_parts[2], counts[part][rule_parts[2]], rules[key][rule]))
                 else:
-                    counts["rules"] += 1
+                    counts["rules"][key] += 1
         else:
-            logging.warning("Warning: Ignoring rule %s:%s" % (rule, str(rules[rule])))
+            logging.warning("Warning: Ignoring rule %s:%s" % (rule, str(rules[key][rule])))
     return is_rule_follower, ";".join(notes)
 
 def count_and_classify(record_seq, variant_list, rules):
@@ -643,11 +643,13 @@ def count_and_classify(record_seq, variant_list, rules):
         if not is_rule_follower_dict[key]:
             continue
         else:
-            call, note = counts_follow_rules(counts, rules[key])
+            call, note = counts_follow_rules(counts, rules, key)
             if call:
                 counts["rules"] = counts["rules"][key]
                 call = key
                 return counts, call, note
+    counts["rules"] = counts["rules"]["default"]
+    return counts, False, ""
 
 
 def generate_barcode(record_seq, variant_list, ref_char=None, ins_char="?", oth_char="X",constellation_count_dict=None):

scorpio/tests/type_constellations_test.py

@@ -147,9 +147,9 @@ def test_parse_json_in():
     assert len([v for v in variant_list if v["type"] == "del"]) == 3
     assert len([v for v in variant_list if v["type"] == "aa"]) == 15
     assert name == "Lineage_X"
-    assert rules["min_alt"] == 4
-    assert rules["max_ref"] == 6
-    assert rules["s:E484K"] == "alt"
+    assert rules["default"]["min_alt"] == 4
+    assert rules["default"]["max_ref"] == 6
+    assert rules["default"]["s:E484K"] == "alt"
     assert mrca_lineage == "B.1.1.7"
     assert incompatible_lineages == "A|B.1.351"
 
@@ -162,7 +162,7 @@ def test_parse_csv_in():
     assert len([v for v in variant_list if v["type"] == "del"]) == 3
     assert len([v for v in variant_list if v["type"] == "aa"]) == 15
     assert name == "lineage_X"
-    assert rules["s:E484K"] == "alt"
+    assert rules["default"]["s:E484K"] == "alt"
 
 
 def test_parse_textfile_in():
@@ -178,8 +178,8 @@ def test_parse_textfile_in():
 def test_parse_variants_in():
     in_files = ["%s/lineage_X.json" % data_dir, "%s/lineage_X.csv" % data_dir, "%s/lineage_X.txt" % data_dir]
     expect_names = ["Lineage_X", "lineage_X", "lineage_X"]
-    rule_dict_json = {"min_alt": 4, "max_ref": 6, "s:E484K": "alt"}
-    rule_dict_csv = {"s:E484K": "alt"}
+    rule_dict_json = {"default": {"min_alt": 4, "max_ref": 6, "s:E484K": "alt"}}
+    rule_dict_csv = {"default": {"s:E484K": "alt"}}
     rule_dict_txt = None
     expect_rules = [rule_dict_json, rule_dict_csv, rule_dict_txt]
 
@@ -248,8 +248,8 @@ def test_count_and_classify():
     oth_string = "gaaattcgcccgta-gctcgcaatag"
     seqs = [Seq(ref_string), Seq(alt_string), Seq(alt_plus_string), Seq(oth_string)]
 
-    rules = {"min_alt": 1, "max_ref": 1, "snp2": "alt"}
-    expect_classify = [False, False, True, False]
+    rules = {"default": {"min_alt": 1, "max_ref": 1, "snp2": "alt"}}
+    expect_classify = [False, False, "default", False]
     expect_counts = [{"ref": 5, "alt": 0, "ambig": 0, "oth": 1, "rules": 0, 'substitution': {'ref': 4, 'alt': 0, 'ambig': 0, 'oth': 0}, 'indel': {'ref': 1, 'alt': 0, 'ambig': 0, 'oth': 1}, "support": 0.0, "conflict": 0.8333},
                      {"ref": 1, "alt": 4, "ambig": 0, "oth": 1, "rules": 0, 'substitution': {'ref': 1, 'alt': 3, 'ambig': 0, 'oth': 0}, 'indel': {'ref': 0, 'alt': 1, 'ambig': 0, 'oth': 1}, "support": 0.6667, "conflict": 0.1667},
                      {"ref": 0, "alt": 5, "ambig": 0, "oth": 1, "rules": 3, 'substitution': {'ref': 0, 'alt': 4, 'ambig': 0, 'oth': 0}, 'indel': {'ref': 0, 'alt': 1, 'ambig': 0, 'oth': 1}, "support": 0.8333, "conflict": 0.0},