From 10522a3b338af4a2a863a1d04b83fc53c1dd9ad7 Mon Sep 17 00:00:00 2001
From: don <donkirkby@gmail.com>
Date: Wed, 17 Jan 2018 10:11:17 -0800
Subject: [PATCH] Switch from NOT to ! in resistance rules for #412.

Change resistance level numbers to match Conan's.
Make sure reported mutations have wild type.
---
 micall/hivdb/asi_algorithm.py      |  24 +-
 micall/hivdb/genreport.yaml        |  12 +-
 micall/hivdb/hcv_rules.yaml        | 344 ++++++++++++++---------------
 micall/tests/test_asi_algorithm.py |  10 +
 4 files changed, 202 insertions(+), 188 deletions(-)

diff --git a/micall/hivdb/asi_algorithm.py b/micall/hivdb/asi_algorithm.py
index fa8955122..cb1fe3aa6 100644
--- a/micall/hivdb/asi_algorithm.py
+++ b/micall/hivdb/asi_algorithm.py
@@ -179,14 +179,14 @@ def load_xml(self, file):
                 self.mutation_comments.append([gene_name, rules])
 
     def load_yaml(self, rules_config, genotype):
-        self.level_def = {'-2': 'Resistance Interpretation Not Available',
-                          '-1': 'Not Indicated',
+        self.level_def = {'-1': 'Resistance Interpretation Not Available',
                           '0': 'Sequence does not meet quality-control standards',
                           '1': 'Likely Susceptible',
-                          '2': 'Mutations Detected; Effect Unknown',
-                          '3': 'Resistance Possible',
-                          '4': 'Resistance Likely'}
-        self.global_range = [('-INF', '3', '1'), ('4', '7', '3'), ('8', 'INF', '4')]
+                          '2': 'Not Indicated',
+                          '3': 'Mutations Detected; Effect Unknown',
+                          '4': 'Resistance Possible',
+                          '5': 'Resistance Likely'}
+        self.global_range = [('-INF', '3', '1'), ('4', '7', '4'), ('8', 'INF', '5')]
         for drug in rules_config:
             drug_code = drug['code']
             drug_rules = []
@@ -311,7 +311,11 @@ def interpret(self, aaseq, region):
 
                     score = float(rule_result.score)
                     flags = rule_result.flags
-                    m = rule_result.residues
+                    # rule_result.residues doesn't always have wild types.
+                    m = {mutation
+                         for mutation_set in mutations
+                         for mutation in mutation_set
+                         if mutation in rule_result.residues}
                     raw_mutations[drug_class] |= m
 
                     for action, comment in actions:
@@ -332,11 +336,11 @@ def interpret(self, aaseq, region):
                                 scorerange = self.global_range
                             if score == 0:
                                 if 'Not available' in flags:
-                                    drug_result.level = -2
-                                elif 'Not indicated' in flags:
                                     drug_result.level = -1
-                                elif 'Effect unknown' in flags:
+                                elif 'Not indicated' in flags:
                                     drug_result.level = 2
+                                elif 'Effect unknown' in flags:
+                                    drug_result.level = 3
                             else:
                                 # use score range to determine level
                                 for low_score, high_score, level in scorerange:
diff --git a/micall/hivdb/genreport.yaml b/micall/hivdb/genreport.yaml
index e59ec929a..7548f5bd4 100644
--- a/micall/hivdb/genreport.yaml
+++ b/micall/hivdb/genreport.yaml
@@ -97,13 +97,13 @@
   known_regions: [NS3, NS5a, NS5b]
   resistance_level_colours:
     # these are 'name, bg_colour, fg_colour
-    -2: ['Resistance Interpretation Not Available', 0xFFFFFF, 0x000000]
-    -1: ['Not Indicated', 0xFFFFFF, 0x000000]
+    -1: ['Resistance Interpretation Not Available', 0xFFFFFF, 0x000000]
     0: ['Sequence does not meet quality-control standards', 0xFFFFFF, 0x000000]
-    1: ['Likely Susceptible',          0xDEFBDE, 0x000000]
-    2: ['Mutations Detected; Effect Unknown', 0xF8DE7E, 0x000000]
-    3: ['Resistance Possible',         0xF8DE7E, 0x000000]
-    4: ['Resistance Likely',           0xDD0000, 0xFFFFFF]
+    1: ['Likely Susceptible', 0xDEFBDE, 0x000000]
+    2: ['Not Indicated', 0xFFFFFF, 0x000000]
+    3: ['Mutations Detected; Effect Unknown', 0xF8DE7E, 0x000000]
+    4: ['Resistance Possible', 0xF8DE7E, 0x000000]
+    5: ['Resistance Likely', 0xDD0000, 0xFFFFFF]
 
   disclaimer_text: >
     Mutations in NS3, NS5A and NS5B were detected by deep sequencing of HCV.
diff --git a/micall/hivdb/hcv_rules.yaml b/micall/hivdb/hcv_rules.yaml
index 4805c6a78..07c1f3b4c 100644
--- a/micall/hivdb/hcv_rules.yaml
+++ b/micall/hivdb/hcv_rules.yaml
@@ -5,21 +5,21 @@
     region: NS3
     rules: SCORE FROM ( 36AM => 8, 54AS => 8, 55AI => 8, 107I => 4, 155K => 8,
        156ST => 8, 158I => 4, 168N => 4, 170FTV => 8,
-       NOT R155KR => "Effect unknown", NOT V36AMV => "Effect unknown",
-       NOT T54AST => "Effect unknown", NOT V55AIV => "Effect unknown",
-       NOT D168ND => "Effect unknown", NOT I170FTVI => "Effect unknown",
-       NOT V107IV => "Effect unknown", NOT A156STA => "Effect unknown",
-       NOT V158IV => "Effect unknown" )
+       R155!KR => "Effect unknown", V36!AMV => "Effect unknown",
+       T54!AST => "Effect unknown", V55!AIV => "Effect unknown",
+       D168!ND => "Effect unknown", I170!FTVI => "Effect unknown",
+       V107!IV => "Effect unknown", A156!STA => "Effect unknown",
+       V158!IV => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS3
     region: NS3
     rules: SCORE FROM ( 36MA => 8, 54CGSA => 8, 55A => 8, 107I => 4, 155CK => 8,
        156TVS => 8, 158I => 4, 170TA => 8, 175L => 4, 170I => 0,
-       NOT R155CKR => "Effect unknown", NOT V36MAV => "Effect unknown",
-       NOT T54CGSAT => "Effect unknown", NOT V55AV => "Effect unknown",
-       NOT V170TAIV => "Effect unknown", NOT V107IV => "Effect unknown",
-       NOT A156TVSA => "Effect unknown", NOT V158IV => "Effect unknown",
-       NOT M175LM => "Effect unknown" )
+       R155!CKR => "Effect unknown", V36!MAV => "Effect unknown",
+       T54!CGSAT => "Effect unknown", V55!AV => "Effect unknown",
+       V170!TAIV => "Effect unknown", V107!IV => "Effect unknown",
+       A156!TVSA => "Effect unknown", V158!IV => "Effect unknown",
+       M175!LM => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS3
     region: NS3
@@ -52,35 +52,35 @@
     region: NS5a
     rules: SCORE FROM ( 24RG => 4, 24N => 0, 26E => 0, 28AT => 8, 28SV => 4,
        30EHKNRYDG => 8, 30T => 4, 30L => 0, 31IMV => 8, 54R => 4, 58D => 8,
-       58PR => 4, 92K => 0, 93CHNS => 8, 93F => 0, NOT H54RH => "Effect unknown",
-       NOT Y93CHNSFY => "Effect unknown", NOT K24RGNK => "Effect unknown",
-       NOT A92KA => "Effect unknown", NOT K26EK => "Effect unknown",
-       NOT M28ATSVM => "Effect unknown", NOT H58DPRH => "Effect unknown",
-       NOT Q30EHKNRYDGTLQ => "Effect unknown", NOT L31IMVL => "Effect unknown" )
+       58PR => 4, 92K => 0, 93CHNS => 8, 93F => 0, H54!RH => "Effect unknown",
+       Y93!CHNSFY => "Effect unknown", K24!RGNK => "Effect unknown",
+       A92!KA => "Effect unknown", K26!EK => "Effect unknown",
+       M28!ATSVM => "Effect unknown", H58!DPRH => "Effect unknown",
+       Q30!EHKNRYDGTLQ => "Effect unknown", L31!IMVL => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS5a
     region: NS5a
     rules: SCORE FROM ( 28MT => 4, 29XS => 4, 30GHPQ => 4, 31FV => 8, 31IM => 4,
        32X => 8, 32L => 4, 58S => 4, 62D => 4, 92K => 4, 93H => 8, 93N => 4,
-       NOT P32XLP => "Effect unknown", NOT Q62DQ => "Effect unknown",
-       NOT Y93HNY => "Effect unknown", NOT A92KA => "Effect unknown",
-       NOT P58SP => "Effect unknown", NOT L28MTL => "Effect unknown",
-       NOT P29XSP => "Effect unknown", NOT R30GHPQR => "Effect unknown",
-       NOT L31FVIML => "Effect unknown" )
+       P32!XLP => "Effect unknown", Q62!DQ => "Effect unknown",
+       Y93!HNY => "Effect unknown", A92!KA => "Effect unknown",
+       P58!SP => "Effect unknown", L28!MTL => "Effect unknown",
+       P29!XSP => "Effect unknown", R30!GHPQR => "Effect unknown",
+       L31!FVIML => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS5a
     region: NS5a
     rules: SCORE FROM ( 28SC => 8, 31M => 8, 92R => 8, 93H => 8,
-       NOT C92RC => "Effect unknown", NOT F28SCF => "Effect unknown",
-       NOT Y93HY => "Effect unknown", NOT L31ML => "Effect unknown" )
+       C92!RC => "Effect unknown", F28!SCF => "Effect unknown",
+       Y93!HY => "Effect unknown", L31!ML => "Effect unknown" )
   - genotype: '3'
     reference: HCV3-S52-NS5a
     region: NS5a
     rules: SCORE FROM ( 28T => 0, 28V => 0, 30K => 8, 30S => 4, 30TV => 0,
        31FIMV => 8, 31P => 4, 62ALIRPT => 4, 93H => 8,
-       NOT Y93HY => "Effect unknown", NOT M28TVM => "Effect unknown",
-       NOT S62ALIRPTS => "Effect unknown", NOT A30KSTVA => "Effect unknown",
-       NOT L31FIMVPL => "Effect unknown" )
+       Y93!HY => "Effect unknown", M28!TVM => "Effect unknown",
+       S62!ALIRPTS => "Effect unknown", A30!KSTVA => "Effect unknown",
+       L31!FIMVPL => "Effect unknown" )
   - genotype: '4'
     reference: HCV4-ED43-NS5a
     region: NS5a
@@ -106,24 +106,24 @@
     rules: SCORE FROM ( 307R => 4, 314H => 8, 316Y => 8, 395G => 8, 414ITV => 8,
        444K => 8, 444D => 0, 446KQ => 8, 448CH => 8, 450V => 4, 553TV => 8,
        553I => 4, 554S => 8, 556GR => 8, 558R => 4, 559GINV => 4, 561H => 8,
-       NOT Y448CHY => "Effect unknown", NOT A450VA => "Effect unknown",
-       NOT A553TVIA => "Effect unknown", NOT G554SG => "Effect unknown",
-       NOT A395GA => "Effect unknown", NOT S556GRS => "Effect unknown",
-       NOT G558RG => "Effect unknown", NOT D559GINVD => "Effect unknown",
-       NOT Y561HY => "Effect unknown", NOT G307RG => "Effect unknown",
-       NOT M414ITVM => "Effect unknown", NOT C316YC => "Effect unknown",
-       NOT L314HL => "Effect unknown", NOT N444KDN => "Effect unknown",
-       NOT E446KQE => "Effect unknown" )
+       Y448!CHY => "Effect unknown", A450!VA => "Effect unknown",
+       A553!TVIA => "Effect unknown", G554!SG => "Effect unknown",
+       A395!GA => "Effect unknown", S556!GRS => "Effect unknown",
+       G558!RG => "Effect unknown", D559!GINVD => "Effect unknown",
+       Y561!HY => "Effect unknown", G307!RG => "Effect unknown",
+       M414!ITVM => "Effect unknown", C316!YC => "Effect unknown",
+       L314!HL => "Effect unknown", N444!KDN => "Effect unknown",
+       E446!KQE => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS5b
     region: NS5b
     rules: SCORE FROM ( 307R => 0, 316HNY => 8, 316W => 4, 368T => 8, 411S => 8,
        414ITV => 8, 445FY => 4, 448CH => 8, 553V => 8, 556G => 8, 556R => 4,
-       559G => 8, NOT S368TS => "Effect unknown", NOT Y448CHY => "Effect unknown",
-       NOT K307RK => "Effect unknown", NOT D559GD => "Effect unknown",
-       NOT A553VA => "Effect unknown", NOT N411SN => "Effect unknown",
-       NOT C316HNYWC => "Effect unknown", NOT C445FYC => "Effect unknown",
-       NOT M414ITVM => "Effect unknown", NOT S556GRS => "Effect unknown" )
+       559G => 8, S368!TS => "Effect unknown", Y448!CHY => "Effect unknown",
+       K307!RK => "Effect unknown", D559!GD => "Effect unknown",
+       A553!VA => "Effect unknown", N411!SN => "Effect unknown",
+       C316!HNYWC => "Effect unknown", C445!FYC => "Effect unknown",
+       M414!ITVM => "Effect unknown", S556!GRS => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS5b
     region: NS5b
@@ -155,15 +155,15 @@
     reference: HCV1A-H77-NS5a
     region: NS5a
     rules: SCORE FROM ( 28AGT => 8, 28V => 0, 30DEGHR => 8, 30KY => 4, 30L => 0,
-       31IMFV => 8, 58D => 8, 93CHNS => 8, NOT H58DH => "Effect unknown",
-       NOT M28AGTVM => "Effect unknown", NOT Y93CHNSY => "Effect unknown",
-       NOT Q30DEGHRKYLQ => "Effect unknown", NOT L31IMFVL => "Effect unknown" )
+       31IMFV => 8, 58D => 8, 93CHNS => 8, H58!DH => "Effect unknown",
+       M28!AGTVM => "Effect unknown", Y93!CHNSY => "Effect unknown",
+       Q30!DEGHRKYLQ => "Effect unknown", L31!IMFVL => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS5a
     region: NS5a
     rules: SCORE FROM ( 28M => 4, 31FMV => 8, 93H => 8,
-       NOT L28ML => "Effect unknown", NOT Y93HY => "Effect unknown",
-       NOT L31FMVL => "Effect unknown" )
+       L28!ML => "Effect unknown", Y93!HY => "Effect unknown",
+       L31!FMVL => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS5a
     region: NS5a
@@ -172,15 +172,15 @@
     reference: HCV3-S52-NS5a
     region: NS5a
     rules: SCORE FROM ( 30DK => 8, 31FM => 8, 93H => 8,
-       NOT Y93HY => "Effect unknown", NOT A30DKA => "Effect unknown",
-       NOT L31FML => "Effect unknown" )
+       Y93!HY => "Effect unknown", A30!DKA => "Effect unknown",
+       L31!FML => "Effect unknown" )
   - genotype: '4'
     reference: HCV4-ED43-NS5a
     region: NS5a
     rules: SCORE FROM ( 30HF => 8, 30S => 0, 31V => 8, 31I => 4, 32L => 4,
-       58D => 8, 93H => 8, NOT P32LP => "Effect unknown",
-       NOT P58DP => "Effect unknown", NOT Y93HY => "Effect unknown",
-       NOT L30HFSL => "Effect unknown", NOT M31VIM => "Effect unknown" )
+       58D => 8, 93H => 8, P32!LP => "Effect unknown",
+       P58!DP => "Effect unknown", Y93!HY => "Effect unknown",
+       L30!HFSL => "Effect unknown", M31!VIM => "Effect unknown" )
   - genotype: '5'
     reference: HCV5-SA13-NS5a
     region: NS5a
@@ -202,19 +202,19 @@
     rules: SCORE FROM ( 36ALM => 4, 56H => 8, 56F => 4, 107I => 4, 122GT => 4,
        122R => 0, 155GIKS => 4, 156GLTV => 8, 156M => 4, 156S => 0, 158A => 4,
        168AEFGHIKLTVY => 8, 168CNS => 4, 170V => 4, 170T => 0,
-       NOT D168AEFGHIKLTVYCNSD => "Effect unknown",
-       NOT R155GIKSR => "Effect unknown", NOT V36ALMV => "Effect unknown",
-       NOT Y56HFY => "Effect unknown", NOT S122GTRS => "Effect unknown",
-       NOT V107IV => "Effect unknown", NOT A156GLTVMSA => "Effect unknown",
-       NOT I170VTI => "Effect unknown", NOT V158AV => "Effect unknown" )
+       D168!AEFGHIKLTVYCNSD => "Effect unknown",
+       R155!GIKSR => "Effect unknown", V36!ALMV => "Effect unknown",
+       Y56!HFY => "Effect unknown", S122!GTRS => "Effect unknown",
+       V107!IV => "Effect unknown", A156!GLTVMSA => "Effect unknown",
+       I170!VTI => "Effect unknown", V158!AV => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS3
     region: NS3
     rules: SCORE FROM ( 56H => 8, 56F => 4, 107I => 4, 155GTW => 8, 155K => 0,
        156TV => 8, 156G => 4, 168AFGHIKLTV => 8, 168ENY => 4,
-       NOT Y56HFY => "Effect unknown", NOT A156TVGA => "Effect unknown",
-       NOT V107IV => "Effect unknown", NOT R155GTWKR => "Effect unknown",
-       NOT D168AFGHIKLTVENYD => "Effect unknown" )
+       Y56!HFY => "Effect unknown", A156!TVGA => "Effect unknown",
+       V107!IV => "Effect unknown", R155!GTWKR => "Effect unknown",
+       D168!AFGHIKLTVENYD => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS3
     region: NS3
@@ -223,19 +223,19 @@
     reference: HCV3-S52-NS3
     region: NS3
     rules: SCORE FROM ( 77S => 8, 168QR => 8, 178R => 8,
-       NOT Q168QRQ => "Effect unknown", NOT Q178RQ => "Effect unknown",
-       NOT V170V => "Effect unknown", NOT Y56Y => "Effect unknown",
-       NOT S122S => "Effect unknown", NOT R155R => "Effect unknown",
-       NOT A156A => "Effect unknown", NOT N77SN => "Effect unknown" )
+       Q168!QRQ => "Effect unknown", Q178!RQ => "Effect unknown",
+       V170!V => "Effect unknown", Y56!Y => "Effect unknown",
+       S122!S => "Effect unknown", R155!R => "Effect unknown",
+       A156!A => "Effect unknown", N77!SN => "Effect unknown" )
   - genotype: '4'
     reference: HCV4-ED43-NS3
     region: NS3
     rules: SCORE FROM ( 107I => 4, 122G => 4, 156GMTV => 4, 158I => 4, 168AV => 8,
-       168CEGNY => 4, 170I => 4, NOT D168AVCEGNYD => "Effect unknown",
-       NOT R155R => "Effect unknown", NOT Y56Y => "Effect unknown",
-       NOT T122GT => "Effect unknown", NOT V107IV => "Effect unknown",
-       NOT A156GMTVA => "Effect unknown", NOT V170IV => "Effect unknown",
-       NOT V158IV => "Effect unknown" )
+       168CEGNY => 4, 170I => 4, D168!AVCEGNYD => "Effect unknown",
+       R155!R => "Effect unknown", Y56!Y => "Effect unknown",
+       T122!GT => "Effect unknown", V107!IV => "Effect unknown",
+       A156!GMTVA => "Effect unknown", V170!IV => "Effect unknown",
+       V158!IV => "Effect unknown" )
   - genotype: '5'
     reference: HCV5-SA13-NS3
     region: NS3
@@ -256,19 +256,19 @@
     region: NS5a
     rules: SCORE FROM ( 24RGN => 4, 28AGT => 8, 28V => 4, 30EGHKNRY => 8,
        30LT => 4, 31IMV => 8, 31P => 4, 32L => 8, 38F => 8, 58D => 8, 58P => 4,
-       92P => 8, 92T => 4, 93CHNS => 8, 93F => 4, NOT P32LP => "Effect unknown",
-       NOT S38FS => "Effect unknown", NOT K24RGNK => "Effect unknown",
-       NOT A92PTA => "Effect unknown", NOT H58DPH => "Effect unknown",
-       NOT M28AGTVM => "Effect unknown", NOT Y93CHNSFY => "Effect unknown",
-       NOT Q30EGHKNRYLTQ => "Effect unknown", NOT L31IMVPL => "Effect unknown" )
+       92P => 8, 92T => 4, 93CHNS => 8, 93F => 4, P32!LP => "Effect unknown",
+       S38!FS => "Effect unknown", K24!RGNK => "Effect unknown",
+       A92!PTA => "Effect unknown", H58!DPH => "Effect unknown",
+       M28!AGTVM => "Effect unknown", Y93!CHNSFY => "Effect unknown",
+       Q30!EGHKNRYLTQ => "Effect unknown", L31!IMVPL => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS5a
     region: NS5a
     rules: SCORE FROM ( 28M => 4, 31IV => 8, 31M => 4, 31F => 0, 32L => 0,
        58D => 8, 92K => 8, 92T => 4, 93H => 8, 93C => 4, 93S => 0,
-       NOT P32LP => "Effect unknown", NOT L28ML => "Effect unknown",
-       NOT P58DP => "Effect unknown", NOT A92KTA => "Effect unknown",
-       NOT Y93HCSY => "Effect unknown", NOT L31IVMFL => "Effect unknown" )
+       P32!LP => "Effect unknown", L28!ML => "Effect unknown",
+       P58!DP => "Effect unknown", A92!KTA => "Effect unknown",
+       Y93!HCSY => "Effect unknown", L31!IVMFL => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS5a
     region: NS5a
@@ -301,21 +301,21 @@
     region: NS5a
     rules: SCORE FROM ( 24R => 4, 28TV => 8, 28A => 4, 30EKRY => 8, 30HLNT => 0,
        31V => 8, 31MI => 0, 32L => 4, 54Y => 4, 58D => 8, 58PR => 4,
-       93CFHLNS => 8, NOT P32LP => "Effect unknown",
-       NOT H54YH => "Effect unknown", NOT K24RK => "Effect unknown",
-       NOT H58DPRH => "Effect unknown", NOT M28TVAM => "Effect unknown",
-       NOT Y93CFHLNSY => "Effect unknown", NOT Q30EKRYHLNTQ => "Effect unknown",
-       NOT L31VMIL => "Effect unknown" )
+       93CFHLNS => 8, P32!LP => "Effect unknown",
+       H54!YH => "Effect unknown", K24!RK => "Effect unknown",
+       H58!DPRH => "Effect unknown", M28!TVAM => "Effect unknown",
+       Y93!CFHLNSY => "Effect unknown", Q30!EKRYHLNTQ => "Effect unknown",
+       L31!VMIL => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS5a
     region: NS5a
     rules: SCORE FROM ( 28T => 8, 28M => 4, 29X => 8, 30GHPQ => 4, 31FV => 8,
        31MT => 4, 31I => 0, 32X => 4, 54Y => 4, 58AS => 4, 92E => 4, 93HNS => 8,
-       NOT P32XP => "Effect unknown", NOT Q54YQ => "Effect unknown",
-       NOT Y93HNSY => "Effect unknown", NOT A92EA => "Effect unknown",
-       NOT P58ASP => "Effect unknown", NOT L28TML => "Effect unknown",
-       NOT P29XP => "Effect unknown", NOT R30GHPQR => "Effect unknown",
-       NOT L31FVMTIL => "Effect unknown" )
+       P32!XP => "Effect unknown", Q54!YQ => "Effect unknown",
+       Y93!HNSY => "Effect unknown", A92!EA => "Effect unknown",
+       P58!ASP => "Effect unknown", L28!TML => "Effect unknown",
+       P29!XP => "Effect unknown", R30!GHPQR => "Effect unknown",
+       L31!FVMTIL => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS5a
     region: NS5a
@@ -328,8 +328,8 @@
     reference: HCV4-ED43-NS5a
     region: NS5a
     rules: SCORE FROM ( 28V => 8, 28S => 4, 31I => 4, 31L => 0, 58S => 4,
-       58AP => 0, NOT P58SAPP => "Effect unknown", NOT L28VSL => "Effect unknown",
-       NOT M31ILM => "Effect unknown" )
+       58AP => 0, P58!SAPP => "Effect unknown", L28!VSL => "Effect unknown",
+       M31!ILM => "Effect unknown" )
   - genotype: '5'
     reference: HCV5-SA13-NS5a
     region: NS5a
@@ -351,22 +351,22 @@
     rules: SCORE FROM ( 36AMT => 4, 36L => 0, 43L => 8, 55I => 4, 56H => 4,
        80KL => 4, 80R => 0, 132V => 4, 155GKTW => 8, 155S => 4, 156T => 8,
        156GVS => 4, 168AEFHILNTVY => 8, 334S => 4, 342P => 4, 357K => 4,
-       406AI => 4, 449I => 4, 470S => 4, NOT T449IT => "Effect unknown",
-       NOT V36AMTLV => "Effect unknown", NOT E357KE => "Effect unknown",
-       NOT V406AIV => "Effect unknown", NOT D168AEFHILNTVYD => "Effect unknown",
-       NOT P470SP => "Effect unknown", NOT F43LF => "Effect unknown",
-       NOT P334SP => "Effect unknown", NOT Q80KLRQ => "Effect unknown",
-       NOT S342PS => "Effect unknown", NOT V55IV => "Effect unknown",
-       NOT Y56HY => "Effect unknown", NOT I132VI => "Effect unknown",
-       NOT R155GKTWSR => "Effect unknown", NOT A156TGVSA => "Effect unknown" )
+       406AI => 4, 449I => 4, 470S => 4, T449!IT => "Effect unknown",
+       V36!AMTLV => "Effect unknown", E357!KE => "Effect unknown",
+       V406!AIV => "Effect unknown", D168!AEFHILNTVYD => "Effect unknown",
+       P470!SP => "Effect unknown", F43!LF => "Effect unknown",
+       P334!SP => "Effect unknown", Q80!KLRQ => "Effect unknown",
+       S342!PS => "Effect unknown", V55!IV => "Effect unknown",
+       Y56!HY => "Effect unknown", I132!VI => "Effect unknown",
+       R155!GKTWSR => "Effect unknown", A156!TGVSA => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS3
     region: NS3
     rules: SCORE FROM ( 56H => 4, 155K => 8, 156V => 8, 156T => 4, 156S => 0,
        168AFHKTVY => 8, 168ILN => 4, 168E => 0, 357K => 4,
-       NOT Y56HY => "Effect unknown", NOT D168AFHKTVYILNED => "Effect unknown",
-       NOT R155KR => "Effect unknown", NOT A156VTSA => "Effect unknown",
-       NOT E357KE => "Effect unknown" )
+       Y56!HY => "Effect unknown", D168!AFHKTVYILNED => "Effect unknown",
+       R155!KR => "Effect unknown", A156!VTSA => "Effect unknown",
+       E357!KE => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS3
     region: NS3
@@ -379,8 +379,8 @@
     reference: HCV4-ED43-NS3
     region: NS3
     rules: SCORE FROM ( 56H => 8, 155C => 8, 156TV => 8, 168HV => 8,
-       NOT Y56HY => "Effect unknown", NOT D168HVD => "Effect unknown",
-       NOT R155CR => "Effect unknown", NOT A156TVA => "Effect unknown" )
+       Y56!HY => "Effect unknown", D168!HVD => "Effect unknown",
+       R155!CR => "Effect unknown", A156!TVA => "Effect unknown" )
   - genotype: '5'
     reference: HCV5-SA13-NS3
     region: NS3
@@ -401,53 +401,53 @@
     region: NS5b
     rules: SCORE FROM ( 61G => 4, 112T => 4, 159F => 4, 237G => 4, 282T => 8,
        320V => 4, 321I => 4, 321A => 4, 355H => 4, 473T => 4,
-       NOT A112TA => "Effect unknown", NOT L320VL => "Effect unknown",
-       NOT Q355HQ => "Effect unknown", NOT V321IAV => "Effect unknown",
-       NOT S473TS => "Effect unknown", NOT S282TS => "Effect unknown",
-       NOT L159FL => "Effect unknown", NOT C316C => "Effect unknown",
-       NOT E237GE => "Effect unknown", NOT D61GD => "Effect unknown" )
+       A112!TA => "Effect unknown", L320!VL => "Effect unknown",
+       Q355!HQ => "Effect unknown", V321!IAV => "Effect unknown",
+       S473!TS => "Effect unknown", S282!TS => "Effect unknown",
+       L159!FL => "Effect unknown", C316!C => "Effect unknown",
+       E237!GE => "Effect unknown", D61!GD => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS5b
     region: NS5b
     rules: SCORE FROM ( 142S => 4, 282T => 8, 321I => 4,
-       NOT L320L => "Effect unknown", NOT V321IV => "Effect unknown",
-       NOT S282TS => "Effect unknown", NOT C316C => "Effect unknown",
-       NOT N142SN => "Effect unknown", NOT L159L => "Effect unknown" )
+       L320!L => "Effect unknown", V321!IV => "Effect unknown",
+       S282!TS => "Effect unknown", C316!C => "Effect unknown",
+       N142!SN => "Effect unknown", L159!L => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS5b
     region: NS5b
-    rules: SCORE FROM ( 282T => 8, NOT L320L => "Effect unknown",
-       NOT V321V => "Effect unknown", NOT S282TS => "Effect unknown",
-       NOT C316C => "Effect unknown", NOT L159L => "Effect unknown" )
+    rules: SCORE FROM ( 282T => 8, L320!L => "Effect unknown",
+       V321!V => "Effect unknown", S282!TS => "Effect unknown",
+       C316!C => "Effect unknown", L159!L => "Effect unknown" )
   - genotype: '3'
     reference: HCV3-S52-NS5b
     region: NS5b
     rules: SCORE FROM ( 142T => 4, 159F => 4, 237G => 4, 282T => 8, 314IFP => 4,
-       321A => 4, 355H => 4, NOT L320L => "Effect unknown",
-       NOT V321AV => "Effect unknown", NOT Q355HQ => "Effect unknown",
-       NOT S282TS => "Effect unknown", NOT L159FL => "Effect unknown",
-       NOT C316C => "Effect unknown", NOT L314IFPL => "Effect unknown",
-       NOT N142TN => "Effect unknown", NOT E237GE => "Effect unknown" )
+       321A => 4, 355H => 4, L320!L => "Effect unknown",
+       V321!AV => "Effect unknown", Q355!HQ => "Effect unknown",
+       S282!TS => "Effect unknown", L159!FL => "Effect unknown",
+       C316!C => "Effect unknown", L314!IFPL => "Effect unknown",
+       N142!TN => "Effect unknown", E237!GE => "Effect unknown" )
   - genotype: '4'
     reference: HCV4-ED43-NS5b
     region: NS5b
     rules: SCORE FROM ( 237G => 4, 282T => 8, 321I => 4,
-       NOT L320L => "Effect unknown", NOT V321IV => "Effect unknown",
-       NOT S282TS => "Effect unknown", NOT C316C => "Effect unknown",
-       NOT E237GE => "Effect unknown", NOT L159L => "Effect unknown" )
+       L320!L => "Effect unknown", V321!IV => "Effect unknown",
+       S282!TS => "Effect unknown", C316!C => "Effect unknown",
+       E237!GE => "Effect unknown", L159!L => "Effect unknown" )
   - genotype: '5'
     reference: HCV5-SA13-NS5b
     region: NS5b
-    rules: SCORE FROM ( 282T => 8, 289I => 4, NOT L320L => "Effect unknown",
-       NOT M289IM => "Effect unknown", NOT V321V => "Effect unknown",
-       NOT S282TS => "Effect unknown", NOT C316C => "Effect unknown",
-       NOT L159L => "Effect unknown" )
+    rules: SCORE FROM ( 282T => 8, 289I => 4, L320!L => "Effect unknown",
+       M289!IM => "Effect unknown", V321!V => "Effect unknown",
+       S282!TS => "Effect unknown", C316!C => "Effect unknown",
+       L159!L => "Effect unknown" )
   - genotype: '6'
     reference: HCV6-EUHK2-NS5b
     region: NS5b
-    rules: SCORE FROM ( 282T => 8, NOT L320L => "Effect unknown",
-       NOT V321V => "Effect unknown", NOT S282TS => "Effect unknown",
-       NOT C316C => "Effect unknown", NOT L159L => "Effect unknown" )
+    rules: SCORE FROM ( 282T => 8, L320!L => "Effect unknown",
+       V321!V => "Effect unknown", S282!TS => "Effect unknown",
+       C316!C => "Effect unknown", L159!L => "Effect unknown" )
   name: SOF-EPC
 - code: SOF-HAR
   genotypes:
@@ -456,18 +456,18 @@
     region: NS5b
     rules: SCORE FROM ( 61G => 4, 112T => 4, 159F => 4, 237G => 4, 282T => 8,
        320V => 4, 321I => 4, 321A => 4, 355H => 4, 473T => 4,
-       NOT A112TA => "Effect unknown", NOT L320VL => "Effect unknown",
-       NOT Q355HQ => "Effect unknown", NOT V321IAV => "Effect unknown",
-       NOT S473TS => "Effect unknown", NOT S282TS => "Effect unknown",
-       NOT L159FL => "Effect unknown", NOT C316C => "Effect unknown",
-       NOT E237GE => "Effect unknown", NOT D61GD => "Effect unknown" )
+       A112!TA => "Effect unknown", L320!VL => "Effect unknown",
+       Q355!HQ => "Effect unknown", V321!IAV => "Effect unknown",
+       S473!TS => "Effect unknown", S282!TS => "Effect unknown",
+       L159!FL => "Effect unknown", C316!C => "Effect unknown",
+       E237!GE => "Effect unknown", D61!GD => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS5b
     region: NS5b
     rules: SCORE FROM ( 142S => 4, 282T => 8, 321I => 4,
-       NOT L320L => "Effect unknown", NOT V321IV => "Effect unknown",
-       NOT S282TS => "Effect unknown", NOT C316C => "Effect unknown",
-       NOT N142SN => "Effect unknown", NOT L159L => "Effect unknown" )
+       L320!L => "Effect unknown", V321!IV => "Effect unknown",
+       S282!TS => "Effect unknown", C316!C => "Effect unknown",
+       N142!SN => "Effect unknown", L159!L => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS5b
     region: NS5b
@@ -501,21 +501,21 @@
     rules: SCORE FROM ( 36L => 4, 43LIV => 4, 54S => 4, 80KR => 8, 80GHMIL => 4,
        122GR => 8, 122ANIT => 4, 155KT => 8, 155GIMQSW => 4, 156GTV => 8,
        156LMS => 4, 168AEHV => 8, 168CFGIKLNSTY => 4, 170T => 8, 170V => 4,
-       NOT Q80KRGHMILQ => "Effect unknown", NOT R155KTGIMQSWR => "Effect unknown",
-       NOT V36LV => "Effect unknown", NOT T54ST => "Effect unknown",
-       NOT D168AEHVCFGIKLNSTYD => "Effect unknown",
-       NOT S122GRANITS => "Effect unknown", NOT F43LIVF => "Effect unknown",
-       NOT A156GTVLMSA => "Effect unknown", NOT I170TVI => "Effect unknown" )
+       Q80!KRGHMILQ => "Effect unknown", R155!KTGIMQSWR => "Effect unknown",
+       V36!LV => "Effect unknown", T54!ST => "Effect unknown",
+       D168!AEHVCFGIKLNSTYD => "Effect unknown",
+       S122!GRANITS => "Effect unknown", F43!LIVF => "Effect unknown",
+       A156!GTVLMSA => "Effect unknown", I170!TVI => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS3
     region: NS3
     rules: SCORE FROM ( 41R => 8, 43SIV => 8, 43L => 4, 80KR => 8, 80HIM => 4,
        80GL => 0, 122AIRT => 8, 155KGQTW => 8, 155C => 4, 155IM => 0, 156GTV => 8,
        156S => 4, 168AEFGHINQTVY => 8, 168KL => 4, 170T => 4, 170A => 0,
-       NOT Q80KRHIMGLQ => "Effect unknown", NOT R155KGQTWCIMR => "Effect unknown",
-       NOT D168AEFGHINQTVYKLD => "Effect unknown", NOT Q41RQ => "Effect unknown",
-       NOT S122AIRTS => "Effect unknown", NOT F43SIVLF => "Effect unknown",
-       NOT A156GTVSA => "Effect unknown", NOT V170TAV => "Effect unknown" )
+       Q80!KRHIMGLQ => "Effect unknown", R155!KGQTWCIMR => "Effect unknown",
+       D168!AEFGHINQTVYKLD => "Effect unknown", Q41!RQ => "Effect unknown",
+       S122!AIRTS => "Effect unknown", F43!SIVLF => "Effect unknown",
+       A156!GTVSA => "Effect unknown", V170!TAV => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS3
     region: NS3
@@ -528,7 +528,7 @@
     reference: HCV4-ED43-NS3
     region: NS3
     rules: SCORE FROM ( 155K => 8, 156G => 8, 156M => 0,
-       NOT R155KR => "Effect unknown", NOT A156GMA => "Effect unknown" )
+       R155!KR => "Effect unknown", A156!GMA => "Effect unknown" )
   - genotype: '5'
     reference: HCV5-SA13-NS3
     region: NS3
@@ -548,16 +548,16 @@
     reference: HCV1A-H77-NS3
     region: NS3
     rules: SCORE FROM ( 36AGILM => 8, 54AS => 8, 132V => 4, 155GMTK => 8,
-       156STV => 8, 168N => 4, NOT I132VI => "Effect unknown",
-       NOT T54AST => "Effect unknown", NOT D168ND => "Effect unknown",
-       NOT V36AGILMV => "Effect unknown", NOT R155GMTKR => "Effect unknown",
-       NOT A156STVA => "Effect unknown" )
+       156STV => 8, 168N => 4, I132!VI => "Effect unknown",
+       T54!AST => "Effect unknown", D168!ND => "Effect unknown",
+       V36!AGILMV => "Effect unknown", R155!GMTKR => "Effect unknown",
+       A156!STVA => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS3
     region: NS3
     rules: SCORE FROM ( 36GILMA => 8, 54SA => 8, 155K => 8, 156FTVS => 8,
-       NOT A156FTVSA => "Effect unknown", NOT R155KR => "Effect unknown",
-       NOT V36GILMAV => "Effect unknown", NOT T54SAT => "Effect unknown" )
+       A156!FTVSA => "Effect unknown", R155!KR => "Effect unknown",
+       V36!GILMAV => "Effect unknown", T54!SAT => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS3
     region: NS3
@@ -590,52 +590,52 @@
     region: NS5a
     rules: SCORE FROM ( 24RTM => 4, 28GT => 8, 28V => 4, 30EK => 8, 30HLR => 4,
        31MV => 8, 31I => 4, 32L => 8, 58D => 8, 58P => 4, 92K => 4, 93CHNRSW => 8,
-       NOT P32LP => "Effect unknown", NOT K24RTMK => "Effect unknown",
-       NOT A92KA => "Effect unknown", NOT H58DPH => "Effect unknown",
-       NOT M28GTVM => "Effect unknown", NOT Y93CHNRSWY => "Effect unknown",
-       NOT Q30EKHLRQ => "Effect unknown", NOT L31MVIL => "Effect unknown" )
+       P32!LP => "Effect unknown", K24!RTMK => "Effect unknown",
+       A92!KA => "Effect unknown", H58!DPH => "Effect unknown",
+       M28!GTVM => "Effect unknown", Y93!CHNRSWY => "Effect unknown",
+       Q30!EKHLRQ => "Effect unknown", L31!MVIL => "Effect unknown" )
   - genotype: 1B
     reference: HCV1B-Con1-NS5a
     region: NS5a
     rules: SCORE FROM ( 24K => 0, 30S => 0, 31MVI => 4, 58RT => 0, 92K => 8,
-       93CHNS => 4, NOT Q24KQ => "Effect unknown", NOT P58RTP => "Effect unknown",
-       NOT A92KA => "Effect unknown", NOT Y93CHNSY => "Effect unknown",
-       NOT R30SR => "Effect unknown", NOT L31MVIL => "Effect unknown" )
+       93CHNS => 4, Q24!KQ => "Effect unknown", P58!RTP => "Effect unknown",
+       A92!KA => "Effect unknown", Y93!CHNSY => "Effect unknown",
+       R30!SR => "Effect unknown", L31!MVIL => "Effect unknown" )
   - genotype: '2'
     reference: HCV2-JFH-1-NS5a
     region: NS5a
     rules: SCORE FROM ( 28S => 8, 31V => 8, 31MI => 4, 31L => 0, 58A => 0,
-       58S => 0, 92T => 8, 93HN => 8, NOT C92TC => "Effect unknown",
-       NOT P58ASP => "Effect unknown", NOT F28SF => "Effect unknown",
-       NOT Y93HNY => "Effect unknown", NOT L31VMILL => "Effect unknown" )
+       58S => 0, 92T => 8, 93HN => 8, C92!TC => "Effect unknown",
+       P58!ASP => "Effect unknown", F28!SF => "Effect unknown",
+       Y93!HNY => "Effect unknown", L31!VMILL => "Effect unknown" )
   - genotype: '3'
     reference: HCV3-S52-NS5a
     region: NS5a
     rules: SCORE FROM ( 30K => 8, 30V => 4, 31M => 8, 31VP => 4, 38P => 4,
-       58L => 4, 92K => 4, 93HS => 8, 93NR => 4, NOT S38PS => "Effect unknown",
-       NOT P58LP => "Effect unknown", NOT E92KE => "Effect unknown",
-       NOT Y93HSNRY => "Effect unknown", NOT A30KVA => "Effect unknown",
-       NOT L31MVPL => "Effect unknown" )
+       58L => 4, 92K => 4, 93HS => 8, 93NR => 4, S38!PS => "Effect unknown",
+       P58!LP => "Effect unknown", E92!KE => "Effect unknown",
+       Y93!HSNRY => "Effect unknown", A30!KVA => "Effect unknown",
+       L31!MVPL => "Effect unknown" )
   - genotype: '4'
     reference: HCV4-ED43-NS5a
     region: NS5a
     rules: SCORE FROM ( 28T => 4, 30HS => 4, 31V => 4, 32L => 4, 93CHNSW => 4,
-       NOT P32LP => "Effect unknown", NOT L28TL => "Effect unknown",
-       NOT Y93CHNSWY => "Effect unknown", NOT L30HSL => "Effect unknown",
-       NOT M31VM => "Effect unknown" )
+       P32!LP => "Effect unknown", L28!TL => "Effect unknown",
+       Y93!CHNSWY => "Effect unknown", L30!HSL => "Effect unknown",
+       M31!VM => "Effect unknown" )
   - genotype: '5'
     reference: HCV5-SA13-NS5a
     region: NS5a
-    rules: SCORE FROM ( NOT L28L => "Effect unknown", NOT P58P => "Effect unknown",
-       NOT A92A => "Effect unknown", NOT T93T => "Effect unknown",
-       NOT Q30Q => "Effect unknown", NOT L31L => "Effect unknown" )
+    rules: SCORE FROM ( L28!L => "Effect unknown", P58!P => "Effect unknown",
+       A92!A => "Effect unknown", T93!T => "Effect unknown",
+       Q30!Q => "Effect unknown", L31!L => "Effect unknown" )
   - genotype: '6'
     reference: HCV6-EUHK2-NS5a
     region: NS5a
-    rules: SCORE FROM ( 31V => 8, 32ALQR => 8, NOT P32ALQRP => "Effect unknown",
-       NOT A92A => "Effect unknown", NOT T58T => "Effect unknown",
-       NOT F28F => "Effect unknown", NOT T93T => "Effect unknown",
-       NOT R30R => "Effect unknown", NOT L31VL => "Effect unknown" )
+    rules: SCORE FROM ( 31V => 8, 32ALQR => 8, P32!ALQRP => "Effect unknown",
+       A92!A => "Effect unknown", T58!T => "Effect unknown",
+       F28!F => "Effect unknown", T93!T => "Effect unknown",
+       R30!R => "Effect unknown", L31!VL => "Effect unknown" )
   - genotype: 6E
     reference: HCV6-EUHK2-NS5a
     region: NS5a
diff --git a/micall/tests/test_asi_algorithm.py b/micall/tests/test_asi_algorithm.py
index 9202af675..04424d619 100644
--- a/micall/tests/test_asi_algorithm.py
+++ b/micall/tests/test_asi_algorithm.py
@@ -130,6 +130,16 @@ def test_mutations(self):
 
         self.assertEqual(expected_mutations, result.mutations)
 
+    def test_mutations_have_wildtype(self):
+        aa_seq = [[amino] for amino in self.asi.stds['RT']]
+        self.assertEqual(['M'], aa_seq[40])
+        aa_seq[40] = ['L', 'R']
+        expected_mutations = {'NRTI': ['M41L'], 'NNRTI': []}
+
+        result = self.asi.interpret(aa_seq, 'RT')
+
+        self.assertEqual(expected_mutations, result.mutations)
+
     def test_drug_classes(self):
         aa_seq = [[]] * 440
         compared_attrs = ('code', 'name', 'drug_class')