# HG changeset patch
# User public-health-bioinformatics
# Date 1578355908 18000
# Node ID 1e0389317446aa50773a00772c2bfcfbbe18ba3c
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
diff -r 000000000000 -r 1e0389317446 amino2consensus.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/amino2consensus.py Mon Jan 06 19:11:48 2020 -0500
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import csv
+
+
+AMINO_ACIDS = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y', '*']
+
+
+def determine_amino(amino_counts, threshold):
+ amino = ""
+ total_count = sum(amino_counts.values())
+ amino_with_max_counts = sorted(amino_counts, key=amino_counts.get, reverse=True)[0]
+ if total_count == 0:
+ amino = "#"
+ elif (amino_counts[amino_with_max_counts] / float(total_count)) > threshold:
+ amino = amino_with_max_counts
+ else:
+ amino = "@"
+ return amino
+
+
+def determine_first_region(amino_file):
+ with open(amino_file) as f:
+ reader = csv.DictReader(f)
+ row = next(reader)
+ region = row['region']
+ return region
+
+
+def main(args):
+ current_region = determine_first_region(args.amino)
+ seq = []
+ with open(args.amino) as f:
+ reader = csv.DictReader(f)
+ for row in reader:
+ if row['region'] == current_region:
+ amino_counts = {}
+ for amino_acid in AMINO_ACIDS:
+ amino_counts[amino_acid] = int(row[amino_acid])
+ amino = determine_amino(amino_counts, args.threshold)
+ seq.append(amino)
+ else:
+ print(">" + current_region)
+ print(''.join(seq))
+ current_region = row['region']
+ seq = []
+ amino_counts = {}
+ for amino_acid in AMINO_ACIDS:
+ amino_counts[amino_acid] = int(row[amino_acid])
+ amino = determine_amino(amino_counts, args.threshold)
+ seq.append(amino)
+ print(">" + current_region)
+ print(''.join(seq))
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser()
+ parser.add_argument("amino", help="MiCall amino.csv output file")
+ parser.add_argument("--threshold", default=0.15, type=float, help="Threshold for calling")
+ args = parser.parse_args()
+ main(args)
diff -r 000000000000 -r 1e0389317446 amino2consensus.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/amino2consensus.xml Mon Jan 06 19:11:48 2020 -0500
@@ -0,0 +1,29 @@
+
+
+
+ macros.xml
+
+
+
+ echo "@TOOL_VERSION@"
+
+ '${consensus}'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 1e0389317446 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Jan 06 19:11:48 2020 -0500
@@ -0,0 +1,12 @@
+
+ 0.1rc2
+
+ fastq,fastq.gz,fastqsanger,fastqsanger.gz
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 1e0389317446 resistance.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/resistance.py Mon Jan 06 19:11:48 2020 -0500
@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+
+import argparse
+from pprint import pprint
+
+
+import yaml
+
+
+HCV_RULES_VERSION = "1.8"
+
+
+def load_rules_config(rules_config, genotype, backup_genotype=None):
+ rules = {
+ 'drug_class': {},
+ 'drugs': {}
+ }
+ rules['alg_name'] = 'HCV_RULES'
+ rules['alg_version'] = HCV_RULES_VERSION
+ rules['level_def'] = {
+ '-1': 'Resistance Interpretation Not Available',
+ '0': 'Sequence does not meet quality-control standards',
+ '1': 'Likely Susceptible',
+ '2': 'Not Indicated',
+ '3': 'Mutations Detected; Effect Unknown',
+ '4': 'Resistance Possible',
+ '5': 'Resistance Likely'
+ }
+ rules['global_range'] = [('-INF', '3', '1'), ('4', '7', '4'), ('8', 'INF', '5')]
+ for drug in rules_config:
+ drug_code = drug['code']
+ drug_rules = []
+ region = None
+ for genotype_config in drug['genotypes']:
+ region = genotype_config['region']
+ rule_text = genotype_config['rules']
+ if genotype_config['genotype'] == genotype:
+ rules['gene_def'][genotype_config['reference']] = [region]
+ break
+ elif genotype_config['genotype'] == backup_genotype:
+ rules['gene_def'].setdefault(genotype_config['reference'], [region])
+ break
+ else:
+ rule_text = 'SCORE FROM ( TRUE => "Not available" )'
+ drug_rules.append((rule_text, [('scorerange', 'useglobalrange')]))
+ try:
+ rules['drug_class'][region].append(drug_code)
+ except KeyError:
+ rules['drug_class'][region] = [drug_code]
+ rules['drugs'][drug_code] = (drug['name'], drug_rules)
+ return rules
+
+
+def main(args):
+ with open(args.rules) as f:
+ rules = load_rules_config(yaml.safe_load(f), None)
+ pprint(rules)
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser()
+ parser.add_argument("consensus", help="Consensus fasta")
+ parser.add_argument("--rules", help="Rules file (yaml)")
+ args = parser.parse_args()
+ main(args)
diff -r 000000000000 -r 1e0389317446 test-data/1234A-V3LOOP.align.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1234A-V3LOOP.align.csv Mon Jan 06 19:11:48 2020 -0500
@@ -0,0 +1,3 @@
+refname,qcut,rank,count,offset,seq
+HIV1B-env-seed,15,0,9,876,TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
+HIV1B-env-seed,15,1,1,876,TGTATAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
diff -r 000000000000 -r 1e0389317446 test-data/1234A-V3LOOP.amino.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1234A-V3LOOP.amino.csv Mon Jan 06 19:11:48 2020 -0500
@@ -0,0 +1,494 @@
+seed,region,q-cutoff,query.aa.pos,refseq.aa.pos,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*
+HIV1B-env-seed,gp120,15,4,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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diff -r 000000000000 -r 1e0389317446 test-data/1234A-V3LOOP.conseq.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1234A-V3LOOP.conseq.csv Mon Jan 06 19:11:48 2020 -0500
@@ -0,0 +1,8 @@
+region,q-cutoff,consensus-percent-cutoff,offset,sequence
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diff -r 000000000000 -r 1e0389317446 test-data/1234A-V3LOOP.insert.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1234A-V3LOOP.insert.csv Mon Jan 06 19:11:48 2020 -0500
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diff -r 000000000000 -r 1e0389317446 test-data/1234A-V3LOOP.nuc.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1234A-V3LOOP.nuc.csv Mon Jan 06 19:11:48 2020 -0500
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diff -r 000000000000 -r 1e0389317446 test-data/1234A-V3LOOP_S1_L001_R1_001.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1234A-V3LOOP_S1_L001_R1_001.fastq Mon Jan 06 19:11:48 2020 -0500
@@ -0,0 +1,40 @@
+@M01234:01:000000000-AAAAA:1:1101:01234:0001 1:N:0:1
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++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
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+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0005 1:N:0:1
+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+@M01234:01:000000000-AAAAA:1:1101:01234:0006 1:N:0:1
+TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
++
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++
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++
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+HCV-3b,HCV3-S52-p7,15,879,12,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,26,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,880,13,28,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,881,14,28,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,882,15,0,0,0,0,0,26,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,883,16,0,0,0,23,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,884,17,0,0,0,0,0,0,0,0,0,0,0,0,0,27,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,885,18,0,0,0,0,0,28,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,886,19,0,0,0,0,19,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,887,20,0,0,0,0,0,0,0,16,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,888,21,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,18,0,0
+HCV-3b,HCV3-S52-p7,15,889,22,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,21,0
+HCV-3b,HCV3-S52-p7,15,890,23,0,0,0,0,0,0,0,0,0,22,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,891,24,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,28,0,0,0
+HCV-3b,HCV3-S52-p7,15,892,25,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,22,0,0,0
+HCV-3b,HCV3-S52-p7,15,893,26,0,0,0,0,15,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,894,27,0,19,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,895,28,23,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,896,29,23,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,897,30,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,19,0,0
+HCV-3b,HCV3-S52-p7,15,898,31,0,0,0,0,0,0,22,0,0,0,0,0,0,0,0,0,0,0,0,1,0
+HCV-3b,HCV3-S52-p7,15,899,32,0,0,0,0,0,0,0,21,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,900,33,0,0,0,0,0,0,0,0,0,0,0,0,0,0,23,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,901,34,0,0,0,0,0,24,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,902,35,0,0,0,0,0,0,0,0,0,0,0,0,0,0,22,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,903,36,0,0,0,0,0,0,0,0,0,22,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,904,37,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,24,0,0,0
+HCV-3b,HCV3-S52-p7,15,905,38,0,0,0,0,0,0,0,0,0,0,0,0,19,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,906,39,0,0,0,0,0,0,0,0,0,21,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,907,40,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,26,0,0,0
+HCV-3b,HCV3-S52-p7,15,908,41,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,23,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,909,42,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,25,0
+HCV-3b,HCV3-S52-p7,15,910,43,0,0,0,0,0,28,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,911,44,0,0,0,0,0,0,0,0,0,31,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,912,45,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,27,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,913,46,0,0,0,0,0,30,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,914,47,0,0,0,0,0,0,0,0,0,29,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,915,48,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,26,0,0
+HCV-3b,HCV3-S52-p7,15,916,49,0,0,0,0,0,0,0,0,0,0,0,0,25,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,917,50,0,0,0,0,0,0,0,0,0,22,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,918,51,22,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,919,52,0,0,0,0,0,0,0,0,0,23,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,920,53,0,0,0,0,0,0,0,0,0,23,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,921,54,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,23,0,0,0
+HCV-3b,HCV3-S52-p7,15,922,55,0,0,0,0,0,0,0,0,0,21,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,923,56,0,0,0,0,0,0,0,0,0,24,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,924,57,0,0,0,0,0,0,0,0,0,25,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,925,58,0,0,0,0,0,0,0,0,0,0,0,0,26,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,926,59,0,0,0,0,0,0,20,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,927,60,0,0,0,0,0,0,0,0,0,0,0,0,0,0,25,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,928,61,20,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,929,62,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,22,0
+HCV-3b,HCV3-S52-p7,15,930,63,23,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+HCV-3b,HCV3-S52-p7,15,,64,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
diff -r 000000000000 -r 1e0389317446 test-data/HCV294-consensus.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HCV294-consensus.fasta Mon Jan 06 19:11:48 2020 -0500
@@ -0,0 +1,20 @@
+>HCV3-S52-Core
+MSTLPKPQRQTQRNTPRRPQNVKFPGGGQIVGGVYVLPRRGPRLGVRAVRKTSERSQPRERRQPIPKARPREGRSWAQPGYPWPLYGNEGCGWAGWLLSPRGSRPSWGPNDPRRRSRNLGKVIDTLTCGFADLMGYIPLIGAPVGGVARALAHGVRALEDGVNYATGNLPGCSFSIFLLALFSCLTCPASA#
+>HCV3-S52-E1
+RNASGLYMLTNDCSNGSIVYEADEVILHLPGCVPCVAD#I#TSCWTPVSPTIAVKRPGVTTASIRSHVDMLVGAATLCSALYVGDLCGAVFLVGQAFTFRPRRHITVQTCNCSIYPGHVSGHRMAWDMMMNWSPAVGLVISHLMRLPQTFFDLIAGAHWGVMAGLAYFSMQGNWAKVCIVLVMFSGVDA#
+>HCV3-S52-E2
+############################QLVNSNGSWHINSTALNCRDSLNTGFIAGLIYYTKFNSTGCPERMSRCKSIADFNQGWGPLTDANISGPSEDRPYCWHYPPRPCSTVNASKVCGPVYCFTPSPVVVGTTDAKGLPTYSFGANESDVFLLTSLRPPPGRWFGCVWMNSTGFVKTCGAPPCNIYGGTGGTDNKT#LTCPTDCFRKHPAATYARCGSGPWLTPRCLVDYPYRLWHFPCTLNFSIFKVRMFVGGVEHRFSAACNWTRGERCSLEDRDRSEQQPLLHSTTDSLILPCSFTPMPALSTGLIHLHQNIVDVQYLYGVGSGMVGWVLKWELVVLVFLLLADARVCVALWMMLLISQAEA#
+>HCV3-S52-NS2
+WTGEDDATIGAGVLLLFGFFTLSPWYKHWISRLIWWNQYAICRSEAALQVWVPPLLVRGGRDSVILLTSLLYPSLIFDITKLLIAVLGPLYLIQVALTSTPYFVRAHVLIRICMLVRSAMGGKYVQMAVLTVGRWFNTYLYDHLSPMQDWAAEGLKELAVATEPVIFSPMETKVITWGADTAACGDILCGLPVSARLGHEVLLGPADDYKTMGWRLL#
+>HCV3-S52-NS3
+SPISAYAQQTRGLLGTIVTSLTGRDKNVVTGEVQVLSTATQTFLGTTVGGVMWTVYHGAGSRTLASNKRPALQMYTNVDQDLVGWPAPAGTKSLDPCTCGASDLYLVTREADVLPARRRGDSTASLLSPRPLSCLKGSSGGPVMCPSGHVVGIFRAAVCTRGVAKALQFIPVEALSTQVRSPSFSDNSTPPAVPEAYQVGYLHAPTGSGKSTKVPAAYVAQGYSVLVLNPSVAATLGFGMYMSKAYGIDPNIRTGTRTITTGAKLTYSTYGKFLADGGCSGGAYDVIICDECHAQDATSILGIGTVLDQAETAGVRLTVLATATPPGSITVPHPNIEEVALTNDGEIPFYGKAIPLATIKGGRHLIFCHSKKKCDELATKLRGMGVNAVAFYRGLDVSVIPTSGDVVVCATDALMTGYTGDFDSVIDSNVAVEQYVDFSLDPTFSIETHTIPQDAVARSQRRGRTGRGRPGIYRFVTPGERPSGMFDSAVLCECYDAGCSWYDLQPAETTVRLRAYLSTPGLPVCQDHLDFWESVFTGLTHIDAHFLSQAKQQGLNFAYLVAYQATVCARAKANPPSWDEMWKCLIRLKPTLQGPTPLLYRLGAIQNDICTTHPITKYIMACMSADLEVTT#
+>HCV3-S52-NS4a
+SAWVLVGGVLAALAAYCLSVGCVVIIGHIELGGKPALVPDREVLYQQYDEMEEC#
+>HCV3-S52-NS4b
+SQSAPYIEQAQAIAQQFKDKVLGLLQRASQQEAEIRPIVQSHWQKVEAFWQKHMWNFVSGIQYLAGLSTLPGNPAVASLMAFTASVTSPLTTNQTMFFNILGGWVATHLAGPAASSAFVVSGLAGAAVGGIGIGRVLLDVLAGYGAGVSGALVAFKIMGGELPTTEDMVNLLPAILSPGALVVGVICAAVLRRHVGPGEGAVQWMNRLIAFASRGNHVSPTHYVPESDAAAKVTALLSSLTVTRLLRRLHQWITEDYPSPC#
+>HCV3-S52-NS5a
+NGDWLHDIWDWVCTVLSDFKTWLSAKIMPKMPGIPFFSCQKGYKGVWRGDGVMTTRCPCGKDLTGHVKNGSMRIAGSGLCANVWHGTFPINEYTTGPGTPVPAYNYSRALWRVTSDSYVEVRRIGDAHFVVGATNDGLKIPCQVPAPEFFTELDGVRLHRYAPPCKPLLRDEITFSVGLHSYAVGSQLPCEPEPDVAVLTSMLRDPAHITAATAARRLARGSPPSEASSSASQLSAASLKATCHTHGLYPDAELIDANLLWRQEMGSTITRVESETKVVILDSFEPLRADEDDSELSVPAECFKKPPKYPPALPIWARPDYNPPLLPPWKDPTYEPPVVHGCALPPTRPTPVPPPRRKRTIKLDGSNVSAALLALAERSFPSTKPEGTGTSSSEFGTDTTAESNDPLEADGGSDVESHSSMPPLEGEPGDPDLDADSWSTVSDSEEQSVVCC#
+>HCV3-S52-NS5b
+SMSYSWTGAIITPCSAEEEKLPISPLSNSLLRHHNLVYSTSSRSAAARQKKVTFDRLQVLDDHYKNVLKEVKERASGVKGRLLSFEEACSLVPPHSARSKYGYSAKDVRSLSSKAINQIRSVWEDLLEDNTTPISTTIMAKNEVFSVNPAKGGRKPARLIVYPDLGVRVCEKRALYDVIQKLSIATMGSAYGFQYSPKQRVEHLLRMWTSKKTPLGFSYDTRCFDSTVTEHDIRMEEEIYQCCDLEPEARKAINALTERLYIGGPLYNSKGLQCGYRRCRASGVLPTSFGNTITCYIKATAASRAAGLKNPSFLVCGDDLVVIAESCGVEEDRAALRAFTEAMTRYSAPPGDAPQPIYDLELISSCSSNVSVAHDGAGKRYYYLTRDPETPLARAAWETARHTPVNSWLGNIIMFAPTIWVRMVFMTHFFSILQAQEQLEKALDFEMYGATYSVTPLDLPAIIERLHGLSAFSLHSYSPTELNRVAGALRKLGIPPLRAWRHRARAVRAKLIAQGGKARICGLYLFNWAVRTKTKLTPLPAASRLDLSSWFTVGVGGNDIYHSVSHARTRHLLLCLLLLTVGVGIFLLPAR#
+>HCV3-S52-p7
+AMENLVMLNALSAAGEQGFIWYLVVFCAAWHIRGRLVPLVTYGLTGLWPLALLVLLLPHRAYA#
diff -r 000000000000 -r 1e0389317446 test-data/hcv_rules.1.8.yaml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hcv_rules.1.8.yaml Mon Jan 06 19:11:48 2020 -0500
@@ -0,0 +1,677 @@
+- code: ASV
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS3
+ region: NS3
+ rules: SCORE FROM ( V36GLM => 4, V36!AGLMV => "Effect unknown", T54S => 4,
+ V55A => 4, Q80KLR => 4, Q80!KLQR => "Effect unknown", S122GINT => 4,
+ S122!GINRST => "Effect unknown", R155GQ => 4, R155K => 8,
+ R155!GKQR => "Effect unknown", A156!A => "Effect unknown", D168AEGVY => 8,
+ D168FHNT => 4, D168CIKLMPQRSW => "Effect unknown", I170T => 4 )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS3
+ region: NS3
+ rules: SCORE FROM ( V36GM => 4, V36!AGLMV => "Effect unknown", T54S => 4,
+ Y56HL => 4, Y56!HLY => "Effect unknown", N77S => 4, Q80K => 8, Q80LR => 4,
+ Q80!KLQR => "Effect unknown", S122DGINT => 4,
+ S122!DGINST => "Effect unknown", R155GQ => 4, R155K => 8,
+ R155!GKQR => "Effect unknown", A156ST => 4, A156V => 8,
+ A156!ASTV => "Effect unknown", D168ACEGHVY => 8, D168FNT => 4,
+ D168IKLMPQRSW => "Effect unknown", V170A => 4 )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '3'
+ reference: HCV3-S52-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '4'
+ reference: HCV4-ED43-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '5'
+ reference: HCV5-SA13-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ name: Asunaprevir
+- code: DCV
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS5a
+ region: NS5a
+ rules: SCORE FROM ( K24R => 4, K24T => 8, M28AGT => 8, M28V => 4,
+ M28!AGILMTV => "Effect unknown", Q30DEGHKNRY => 8, Q30T => 4,
+ Q30AFMSW => "Effect unknown", L31IMV => 8, L31!ILMV => "Effect unknown",
+ P32L => 8, P32!LP => "Effect unknown", H54RY => 4,
+ H54!CHNRY => "Effect unknown", H58D => 8, H58PV => 4,
+ H58AEFGIKMTW => "Effect unknown", A92K => 8, A92P => 4,
+ A92!AKPTV => "Effect unknown", Y93CHNST => 8, Y93FR => 4,
+ Y93!CFHNRSTY => "Effect unknown" )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS5a
+ region: NS5a
+ rules: SCORE FROM ( L28AMT => 4, L28!AILMTV => "Effect unknown", P29S => 4,
+ P29d => 8, R30G => 8, R30HKQ => 4, R30!GHKLPQRST => "Effect unknown",
+ L31FIMW => 4, L31V => 8, L31!FILMVW => "Effect unknown", P32d => 8,
+ P32!LP => "Effect unknown", Q54H => 4, P58LS => 4, Q62E => 4, A92E => 4,
+ A92K => 8, A92!AEKPTV => "Effect unknown", Y93H => 8, Y93N => 4,
+ Y93!CFHLNY => "Effect unknown" )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS5a
+ region: NS5a
+ rules: SCORE FROM ( F28CS => 8, F28!CFILS => "Effect unknown", L31M => 8,
+ L31!LM => "Effect unknown", C92R => 8, C92!CR => "Effect unknown",
+ Y93H => 8, Y93!HY => "Effect unknown" )
+ - genotype: '3'
+ reference: HCV3-S52-NS5a
+ region: NS5a
+ rules: SCORE FROM ( M28K => 8, M28T => 4, M28!IKMTV => "Effect unknown",
+ A30EK => 8, A30SV => 4, A30!AEKRSTV => "Effect unknown", L31FIMV => 8,
+ L31P => 4, L31!FILMPV => "Effect unknown", P58H => 4, S62AILPRT => 4,
+ S62CEFGHMVWY => "Effect unknown", E92G => 4, Y93H => 8,
+ Y93!HY => "Effect unknown" )
+ - genotype: '4'
+ reference: HCV4-ED43-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '5'
+ reference: HCV5-SA13-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ name: Daclatasvir
+- code: DAS
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS5b
+ region: NS5b
+ rules: SCORE FROM ( G307R => 4, L314H => 8, L314!HL => "Effect unknown",
+ C316Y => 8, C316!CY => "Effect unknown", A395G => 8,
+ A395!AG => "Effect unknown", M414ITV => 8, M414!IMTV => "Effect unknown",
+ N444K => 8, N444!KN => "Effect unknown", E446KQ => 8,
+ E446!EKQ => "Effect unknown", Y448CH => 8, Y448!CHY => "Effect unknown",
+ A450V => 4, A553I => 4, A553TV => 8, A553!AITV => "Effect unknown",
+ G554S => 8, G554!DGS => "Effect unknown", S556GR => 8,
+ S556!GRS => "Effect unknown", G558R => 4, D559GINV => 4,
+ D559!DGINV => "Effect unknown", Y561H => 8, Y561!HY => "Effect unknown",
+ L588F => 4 )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS5b
+ region: NS5b
+ rules: SCORE FROM ( C316HNY => 8, C316!CHNY => "Effect unknown", S368T => 8,
+ A395!A => "Effect unknown", N411S => 8, M414ITV => 8,
+ M414!IMTV => "Effect unknown", D444!D => "Effect unknown", C445F => 4,
+ Y448CH => 8, Y448!CHY => "Effect unknown", A553V => 8,
+ A553!AV => "Effect unknown", S556G => 8, S556R => 4,
+ S556!GRS => "Effect unknown", D559G => 8, D559!DG => "Effect unknown" )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS5b
+ region: NS5b
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '3'
+ reference: HCV3-S52-NS5b
+ region: NS5b
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '4'
+ reference: HCV4-ED43-NS5b
+ region: NS5b
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '5'
+ reference: HCV5-SA13-NS5b
+ region: NS5b
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS5b
+ region: NS5b
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ name: Dasabuvir
+- code: EBV
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS5a
+ region: NS5a
+ rules: SCORE FROM ( K24R => 4, M28AGT => 8, M28V => 4,
+ M28!AGMTV => "Effect unknown", Q30DEGHKR => 8, Q30LY => 4,
+ Q30!DEGHKLQRY => "Effect unknown", L31FIMV => 8,
+ L31!FILMV => "Effect unknown", H58D => 8, H58!DH => "Effect unknown",
+ E62D => 4, Y93CHN => 8, Y93S => 4, Y93!CFHNSY => "Effect unknown",
+ D427N => 4 )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS5a
+ region: NS5a
+ rules: SCORE FROM ( L28M => 4, R30Q => 8, L31FMV => 8,
+ L31!FLMV => "Effect unknown", P58S => 4, Y93H => 8,
+ Y93!CHY => "Effect unknown" )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '3'
+ reference: HCV3-S52-NS5a
+ region: NS5a
+ rules: SCORE FROM ( A30DK => 8, A30!ADK => "Effect unknown", L31FM => 8,
+ L31!FLM => "Effect unknown", P58S => 4, P58!PS => "Effect unknown",
+ S62APT => 4, S62!APST => "Effect unknown", Y93H => 8,
+ Y93!HY => "Effect unknown" )
+ - genotype: '4'
+ reference: HCV4-ED43-NS5a
+ region: NS5a
+ rules: SCORE FROM ( L28MST => 4, L30FH => 8, L30RS => 4,
+ L30!FHLPRS => "Effect unknown", M31I => 4, M31V => 8,
+ M31!IMV => "Effect unknown", P32L => 4, H54Y => 4, P58D => 8, P58TY => 4,
+ P58!DPTY => "Effect unknown", Y93C => 4, Y93H => 8,
+ Y93!CHY => "Effect unknown" )
+ - genotype: '5'
+ reference: HCV5-SA13-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ name: Elbasvir
+- code: GLP
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS3
+ region: NS3
+ rules: SCORE FROM ( V36AFM => 4, V36!AFLMV => "Effect unknown", V55AI => 4,
+ V55!AIV => "Effect unknown", Y56H => 4, Q80KL => 4,
+ Q80!KLQR => "Effect unknown", I132V => 4, R155KT => 4,
+ R155!KMRSTV => "Effect unknown", A156GV => 4, A156T => 8,
+ A156!AGTV => "Effect unknown", D168AFY => 8, D168EHTV => 4,
+ D168!ADEFHNTVY => "Effect unknown" )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS3
+ region: NS3
+ rules: SCORE FROM ( Y56F => 4, A156TV => 8, A156!ASTV => "Effect unknown",
+ D168FTV => 4, D168K => 8, D168!ADEFHKTVY => "Effect unknown", E176G => 4 )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS3
+ region: NS3
+ rules: SCORE FROM ( I132L => 4, A156MTV => 8, A156!AMTV => "Effect unknown",
+ D168EFHT => 4, D168!ADEFHSTVY => "Effect unknown" )
+ - genotype: '3'
+ reference: HCV3-S52-NS3
+ region: NS3
+ rules: SCORE FROM ( T54S => 4, Y56HN => 4, Y56!HNY => "Effect unknown",
+ Q80KR => 8, Q80!KQR => "Effect unknown", V107I => 4, L132I => 4,
+ A156G => 8, A156!AG => "Effect unknown", A166T => 8, A166SY => 4,
+ A166!ASTY => "Effect unknown", Q168K => 4, Q168LR => 8,
+ Q168!HKLQR => "Effect unknown", D186LR => 4, D186!DLR => "Effect unknown",
+ I366V => 4 )
+ - genotype: '4'
+ reference: HCV4-ED43-NS3
+ region: NS3
+ rules: SCORE FROM ( Y56H => 4, G90R => 4, R155C => 4, A156TV => 8,
+ A156!ATV => "Effect unknown", D168H => 8, D168V => 4,
+ D168!DHV => "Effect unknown" )
+ - genotype: '5'
+ reference: HCV5-SA13-NS3
+ region: NS3
+ rules: SCORE FROM ( A156!A => "Effect unknown", D168E => 4,
+ D168!DE => "Effect unknown" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS3
+ region: NS3
+ rules: SCORE FROM ( L80R => 8, L80!LR => "Effect unknown",
+ A156M => 4, A156!AM => "Effect unknown", D168AGHVY => 8,
+ D168!ADGHVY => "Effect unknown" )
+ name: Glecaprevir
+- code: GZR
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS3
+ region: NS3
+ rules: SCORE FROM ( V36ALM => 4, V36!AILMV => "Effect unknown", Q41R => 4,
+ I48V => 4, V55A => 4, Y56F => 4, Y56H => 8, Y56!FHY => "Effect unknown",
+ Q80KL => 8, Q80S => 4, Q80!KLQRS => "Effect unknown", V107I => 4,
+ S122GT => 4, S122!AGRST => "Effect unknown", I132V => 4, R155GIS => 4,
+ R155KQTW => 8, R155!GIKQRSTW => "Effect unknown", A156GLTV => 8,
+ A156!AGLSTV => "Effect unknown", V158A => 4, D168!CDMPQRSW => 8,
+ D168C => 4, D168MPQRW => "Effect unknown", I170V => 4, T185S => 4,
+ E357GK => 4 )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS3
+ region: NS3
+ rules: SCORE FROM ( T54S => 4, Y56H => 8, Y56F => 4,
+ Y56!FHY => "Effect unknown", Q80L => 4, V107I => 4, S122NRT => 4,
+ S122!AGNRST => "Effect unknown", V132IL => 4, V132!ILV => "Effect unknown",
+ R155GTW => 8, R155Q => 4, R155!EGKNQRSTW => "Effect unknown", A156TV => 8,
+ A156!AGSTV => "Effect unknown", D168AEFGHIKLTV => 8, D168NY => 4,
+ D168CMPQRW => "Effect unknown", V170I => 4, T185S => 4, E357K => 4 )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '3'
+ reference: HCV3-S52-NS3
+ region: NS3
+ rules: SCORE FROM ( Y56H => 4, A156TV => 8, A156!ATV => "Effect unknown",
+ Q168!HQR => "Effect unknown", Q178R => 4 )
+ - genotype: '4'
+ reference: HCV4-ED43-NS3
+ region: NS3
+ rules: SCORE FROM ( V107I => 4, A156MTV => 4, A156!AMTV => "Effect unknown",
+ D168AV => 8, D168EG => 4, D168!ADEGV => "Effect unknown", V170I => 4 )
+ - genotype: '5'
+ reference: HCV5-SA13-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS3
+ region: NS3
+ rules: SCORE FROM ( V36IL => 4, V36!ILV => "Effect unknown", Y56H => 4,
+ L80KQ => 4, L80!KLQ => "Effect unknown", I132L => 4, A156MTV => 4,
+ A156!AMTV => "Effect unknown", D168CEY => 4, D168!CDEY => "Effect unknown",
+ I170V => 4 )
+ name: Grazoprevir
+- code: LDV
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS5a
+ region: NS5a
+ rules: SCORE FROM ( K24R => 4, M28AGT => 8, M28V => 4,
+ M28!AGILMTV => "Effect unknown", Q30EGHKNRY => 8, Q30LT => 4,
+ Q30ADFMPSW => "Effect unknown", L31IMV => 8, L31P => 4,
+ L31!ILMPV => "Effect unknown", P32L => 8, P32!LP => "Effect unknown",
+ S38F => 8, S38!FST => "Effect unknown", H58D => 8, H58PR => 4,
+ H58!CDHPQRY => "Effect unknown", A92K => 8, A92!AKPTV => "Effect unknown",
+ Y93CHLNRSTW => 8, Y93F => 4, Y93ADEGIKMPQV => "Effect unknown" )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS5a
+ region: NS5a
+ rules: SCORE FROM ( L28M => 4, L31IMV => 4, L31!FILMV => "Effect unknown",
+ P58D => 8, P58!DPQRST => "Effect unknown", A92K => 8, A92T => 4,
+ A92!AEKTV => "Effect unknown", Y93CS => 4, Y93HN => 8,
+ Y93!CFHLNSY => "Effect unknown" )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '3'
+ reference: HCV3-S52-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '4'
+ reference: HCV4-ED43-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '5'
+ reference: HCV5-SA13-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ name: Ledipasvir
+- code: OMB
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS5a
+ region: NS5a
+ rules: SCORE FROM ( K24R => 4, M28A => 4, M28TV => 8,
+ M28!AMTV => "Effect unknown", Q30EKRY => 8,
+ Q30!EHKLNQRTY => "Effect unknown", L31V => 8, L31!ILMV => "Effect unknown",
+ P32L => 4, H54Y => 4, H58D => 8, H58PR => 4, H58!DHPR => "Effect unknown",
+ E62D => 4, Y93CFHLNS => 8, Y93!CFHLNSY => "Effect unknown" )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS5a
+ region: NS5a
+ rules: SCORE FROM ( L28M => 4, L28T => 8, L28!LMT => "Effect unknown",
+ P29d => 8, P29!P => "Effect unknown", R30Q => 4, L31FMV => 4,
+ L31!FILMTV => "Effect unknown", Q54Y => 4, P58S => 4, Y93HN => 8,
+ Y93S => 4, Y93!HNSY => "Effect unknown" )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '3'
+ reference: HCV3-S52-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '4'
+ reference: HCV4-ED43-NS5a
+ region: NS5a
+ rules: SCORE FROM ( L28S => 4, L28V => 8, L28!LSV => "Effect unknown",
+ M31I => 4, P58S => 4 )
+ - genotype: '5'
+ reference: HCV5-SA13-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ name: Ombitasvir
+- code: PIB
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS5a
+ region: NS5a
+ rules: SCORE FROM ( K24EQR => 4, K24!EKQR => "Effect unknown", M28ATV => 4,
+ M28G => 8, M28!AGMTV => "Effect unknown", P29QR => 4,
+ P29!PQR => "Effect unknown", Q30Dd => 8, Q30EGHKLR => 4,
+ Q30!DEGHKLQRY => "Effect unknown", L31M => 4, H58CDY => 4,
+ H58!CDHPRY => "Effect unknown", E62A => 8, E62!ADE => "Effect unknown",
+ Y93HN => 8, Y93!CFHLNSY => "Effect unknown" )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS5a
+ region: NS5a
+ rules: SCORE FROM ( L28M => 4, P29d => 4, R30Q => 4, L31K => 4, P32KNRT => 4,
+ P32d => 8, P32!KNPRT => "Effect unknown" )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS5a
+ region: NS5a
+ rules: SCORE FROM ( L31M => 4 )
+ - genotype: '3'
+ reference: HCV3-S52-NS5a
+ region: NS5a
+ rules: SCORE FROM ( S24FG => 4, S24!FGS => "Effect unknown", M28GK => 4,
+ M28!GKMT => "Effect unknown", P29Q => 4, A30GK => 4,
+ A30!AGK => "Effect unknown", L31FIM => 4, L31!FILM => "Effect unknown",
+ E92!E => "Effect unknown", Y93H => 4, Y93!HY => "Effect unknown" )
+ - genotype: '4'
+ reference: HCV4-ED43-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => 0 )
+ - genotype: '5'
+ reference: HCV5-SA13-NS5a
+ region: NS5a
+ rules: SCORE FROM ( T93A => 4, T93!TA => "Effect unknown" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS5a
+ region: NS5a
+ rules: SCORE FROM ( TRUE => 0 )
+ name: Pibrentasvir
+- code: PAR
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS3
+ region: NS3
+ rules: SCORE FROM ( V36AMT => 4, V36!ALMTV => "Effect unknown", F43L => 8,
+ F43!FL => "Effect unknown", V55I => 4, Y56H => 4, Q80KL => 4,
+ Q80!KLQR => "Effect unknown", I132V => 4, R155GKTW => 8, R155SV => 4,
+ R155!GKMRSTVW => "Effect unknown", A156G => 4, A156T => 8,
+ A156!AGT => "Effect unknown", D168!CDGMPQRSW => 8,
+ D168CGMPQRSW => "Effect unknown", P334S => 4, S342P => 4, E357K => 4,
+ V406AI => 4, V406!AIV => "Effect unknown", T449I => 4, P470S => 4 )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS3
+ region: NS3
+ rules: SCORE FROM ( Y56FH => 4, R155K => 8, R155!KR => "Effect unknown",
+ A156T => 4, A156V => 8, A156!ASTV => "Effect unknown", D168AFHKTVY => 8,
+ D168ILN => 4, D168CGMPQRSW => "Effect unknown", E357K => 4 )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '3'
+ reference: HCV3-S52-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '4'
+ reference: HCV4-ED43-NS3
+ region: NS3
+ rules: SCORE FROM ( Y56H => 8, Y56!HY => "Effect unknown", R155C => 8,
+ R155!CR => "Effect unknown", A156TV => 8, A156!ATV => "Effect unknown",
+ D168HV => 8, D168!DHV => "Effect unknown" )
+ - genotype: '5'
+ reference: HCV5-SA13-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ name: Paritaprevir
+- code: SOF-EPC
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS5b
+ region: NS5b
+ rules: SCORE FROM ( D61G => 4, S62N => 4, D66G => 4, F101L => 4, A112T => 4,
+ N142T => 4, L159F => 4, L159!FL => "Effect unknown", E202G => 4,
+ E237G => 4, S282GRT => 8, S282!GRST => 4, C316HR => 4,
+ C316!CHR => "Effect unknown", L320IV => 4, L320!ILV => "Effect unknown",
+ V321AFI => 4, V321!AFIV => "Effect unknown", Q355H => 4, F415Y => 4,
+ S473T => 4, N590d => 4 )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS5b
+ region: NS5b
+ rules: SCORE FROM ( N142S => 4, L159!L => "Effect unknown", S282GRT => 8,
+ S282!GRST => 4, C316!C => "Effect unknown",
+ L320!L => "Effect unknown", V321!V => "Effect unknown", K355T => 4 )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS5b
+ region: NS5b
+ rules: SCORE FROM ( L159!L => "Effect unknown", S282GRT => 8,
+ S282!GRST => 4, C316!C => "Effect unknown",
+ M289I => 4, L320!L => "Effect unknown", V321!V => "Effect unknown" )
+ - genotype: '3'
+ reference: HCV3-S52-NS5b
+ region: NS5b
+ rules: SCORE FROM ( K100R => 4, R120C => 4, N142ST => 4, L159F => 4,
+ L159!FL => "Effect unknown", E237G => 4, S282GRT => 8,
+ S282!GRST => 4, L314FIP => 4, C316!C => "Effect unknown",
+ L320FI => 4, L320!FIL => "Effect unknown", V321A => 4,
+ V321!AV => "Effect unknown", Q355HR => 4 )
+ - genotype: '4'
+ reference: HCV4-ED43-NS5b
+ region: NS5b
+ rules: SCORE FROM ( L159!L => "Effect unknown", E237G => 4, S282GRT => 8,
+ S282!GRST => 4, C316!C => "Effect unknown",
+ L320!L => "Effect unknown", V321I => 4, V321!IV => "Effect unknown" )
+ - genotype: '5'
+ reference: HCV5-SA13-NS5b
+ region: NS5b
+ rules: SCORE FROM ( L159!L => "Effect unknown", S282GRT => 8,
+ S282!GRST => 4, M289I => 4, C316!C => "Effect unknown",
+ L320!L => "Effect unknown", V321!V => "Effect unknown" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS5b
+ region: NS5b
+ rules: SCORE FROM ( L159!L => "Effect unknown", S282GRT => 8,
+ S282!GRST => 4, C316!C => "Effect unknown",
+ L320!L => "Effect unknown", V321!V => "Effect unknown" )
+ - genotype: 6E
+ reference: HCV6-EUHK2-NS5b
+ region: NS5b
+ rules: SCORE FROM ( TRUE => "Data not available" )
+ name: Sofosbuvir in Epclusa
+- code: SOF-HAR
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS5b
+ region: NS5b
+ rules: SCORE FROM ( D61G => 4, S62N => 4, D66G => 4, F101L => 4, A112T => 4,
+ N142T => 4, L159F => 4, L159!FL => "Effect unknown", E202G => 4,
+ E237G => 4, S282GRT => 8, S282!GRST => 4, C316HR => 4,
+ C316!CHR => "Effect unknown", L320IV => 4, L320!ILV => "Effect unknown",
+ V321AFI => 4, V321!AFIV => "Effect unknown", Q355H => 4, F415Y => 4,
+ S473T => 4, N590d => 4 )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS5b
+ region: NS5b
+ rules: SCORE FROM ( N142S => 4, L159!L => "Effect unknown", S282GRT => 8,
+ S282!GRST => 4, C316!C => "Effect unknown",
+ L320!L => "Effect unknown", V321!V => "Effect unknown", K355T => 4 )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS5b
+ region: NS5b
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '3'
+ reference: HCV3-S52-NS5b
+ region: NS5b
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '4'
+ reference: HCV4-ED43-NS5b
+ region: NS5b
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '5'
+ reference: HCV5-SA13-NS5b
+ region: NS5b
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS5b
+ region: NS5b
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ name: Sofosbuvir in Harvoni
+- code: SIM
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS3
+ region: NS3
+ rules: SCORE FROM ( A5V => 4, V36L => 4, Q41R => 4, T54S => 4, V71A => 4,
+ Q80KR => 8, Q80L => 4, Q80!KLQR => "Effect unknown", G120S => 4,
+ S122ACGIT => 4, S122NR => 8, S122!ACGINRST => "Effect unknown", R123M => 4,
+ I132L => 4, R155GQ => 4, R155KT => 8, R155!GKQRT => "Effect unknown",
+ A156GTV => 8, A156!AGTV => "Effect unknown", D168AEHV => 8, D168FT => 4,
+ D168!ADEFHTV => "Effect unknown", I170T => 8, I170V => 4,
+ I170!ITV => "Effect unknown", N174RS => 4, T178I => 4, T343N => 4,
+ T344I => 4, L356F => 4, A477T => 4, V511I => 4, G534S => 4, E555D => 4,
+ V629I => 4 )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS3
+ region: NS3
+ rules: SCORE FROM ( A39T => 4, F43ISV => 8, F43!FILSV => "Effect unknown",
+ T46S => 4, V48I => 4, S61L => 4, Q80H => 4, Q80KR => 8,
+ Q80!GHKLQR => "Effect unknown", Q86R => 4, R117C => 4, S122AGIT => 4,
+ S122R => 8, S122!AGIRST => "Effect unknown", R155GKQTW => 8,
+ R155!GIKMQRTW => "Effect unknown", A156GTV => 8, A156S => 4,
+ A156!AGSTV => "Effect unknown", D168AEHINQTVY => 8, D168F => 4,
+ D168CKLMPRSW => "Effect unknown", V170IT => 4,
+ V170!AITV => "Effect unknown", S174F => 4, S280P => 4, T344A => 4,
+ T358F => 4, G383S => 4, I426V => 4, T448A => 4, I472V => 4, V535A => 4,
+ P574AS => 4, V629I => 4 )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '3'
+ reference: HCV3-S52-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '4'
+ reference: HCV4-ED43-NS3
+ region: NS3
+ rules: SCORE FROM ( Q80!Q => "Effect unknown", T122!T => "Effect unknown",
+ R155K => 8, R155!KR => "Effect unknown", A156G => 8,
+ A156!AGM => "Effect unknown", D168!D => "Effect unknown",
+ V170!V => "Effect unknown" )
+ - genotype: '5'
+ reference: HCV5-SA13-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS3
+ region: NS3
+ rules: SCORE FROM ( TRUE => "Not indicated" )
+ name: Simeprevir
+- code: VEL
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS5a
+ region: NS5a
+ rules: SCORE FROM ( K24MT => 4, K24CDFHILPVWY => "Effect unknown", M28AV => 4,
+ M28GT => 8, M28!AGILMTV => "Effect unknown", Q30EK => 8, Q30GHLRT => 4,
+ Q30ADFMNPW => "Effect unknown", L31F => 4, L31IMV => 8,
+ L31!FILMV => "Effect unknown", P32L => 8, P32!LP => "Effect unknown",
+ S38Y => 4, H58D => 8, H58NPR => 4, H58!CDHLNPQRY => "Effect unknown",
+ S85N => 4, A92K => 8, A92!AKPTV => "Effect unknown", Y93CHNRSW => 8,
+ Y93LT => 4, Y93ADEGIKMPQV => "Effect unknown", L153V => 4 )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS5a
+ region: NS5a
+ rules: SCORE FROM ( Q24K => 4, L31IMV => 4, L31!FILMV => "Effect unknown",
+ P58T => 4, A92K => 8, A92!AEKPTV => "Effect unknown", Y93CRST => 4,
+ Y93HN => 8, Y93!CFHLNRSTY => "Effect unknown" )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS5a
+ region: NS5a
+ rules: SCORE FROM ( F28C => 4, F28S => 8, F28!CFLSV => "Effect unknown",
+ L31IM => 4, L31V => 8, L31!ILMV => "Effect unknown", P58A => 4, C92RS => 4,
+ C92T => 8, C92!ACKNRST => "Effect unknown", Y93F => 4, Y93HN => 8,
+ Y93!CFHLNSTY => "Effect unknown" )
+ - genotype: '3'
+ reference: HCV3-S52-NS5a
+ region: NS5a
+ rules: SCORE FROM ( S14E => 4, M28V => 4, M28T => 8,
+ M28!LMTV => "Effect unknown", A30HRV => 4, A30K => 8,
+ A30!AHKQRSV => "Effect unknown", L31FM => 8, L31PV => 4,
+ L31!FLMPV => "Effect unknown", S38PY => 4, S38!PSY => "Effect unknown",
+ V52M => 4, P58GLT => 4, P58!AGHLPST => "Effect unknown", H85Y => 4,
+ E92K => 4, Y93HS => 8, Y93NR => 4, Y93!FHNRSY => "Effect unknown",
+ S103DP => 4, A291P => 4, S379P => 4, S385Q => 4, R404K => 4, P407S => 4 )
+ - genotype: '4'
+ reference: HCV4-ED43-NS5a
+ region: NS5a
+ rules: SCORE FROM ( L28T => 8, L28!LMTV => "Effect unknown", L30R => 4,
+ M31V => 4, P32L => 4, H54R => 4, Y93CW => 4, Y93HNS => 8,
+ Y93!CHNSWY => "Effect unknown" )
+ - genotype: '5'
+ reference: HCV5-SA13-NS5a
+ region: NS5a
+ rules: SCORE FROM ( L31I => 4 )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS5a
+ region: NS5a
+ rules: SCORE FROM ( F28MV => 4, F28!AFMV => "Effect unknown", L31IM => 4,
+ L31V => 8, L31!ILMV => "Effect unknown", P32ALQR => 8,
+ P32!ALPQR => "Effect unknown", T58GH => 4, T58!AGHPST => "Effect unknown",
+ A92T => 4, T93AHNS => 4, T93!ACFHLNSTY => "Effect unknown" )
+ name: Velpatasvir
+- code: VOX
+ genotypes:
+ - genotype: 1A
+ reference: HCV1A-H77-NS3
+ region: NS3
+ rules: SCORE FROM ( V36AG => 4, V36!AGILMV => "Effect unknown", Q41R => 4,
+ F43S => 4, Q80K => 4, R155G => 4, R155W => 8,
+ R155!AGKRTW => "Effect unknown", A156GIMPDV => 4, A156LT => 8,
+ A156!AGILMPSTV => "Effect unknown", D168AFITV => 4, D168KLR => 8,
+ D168CMPQW => "Effect unknown" )
+ - genotype: 1B
+ reference: HCV1B-Con1-NS3
+ region: NS3
+ rules: SCORE FROM ( V36AM => 4, V36!AIMSV => "Effect unknown", S122D => 4,
+ R155W => 8, R155!KRW => "Effect unknown", A156S => 4, A156TV => 8,
+ A156!ASTV => "Effect unknown", D168VY => 4,
+ D168!ADEGVY => "Effect unknown", V170A => 4 )
+ - genotype: '2'
+ reference: HCV2-JFH-1-NS3
+ region: NS3
+ rules: SCORE FROM ( F43V => 4, A156LTV => 8, A156!AGLTV => "Effect unknown" )
+ - genotype: '3'
+ reference: HCV3-S52-NS3
+ region: NS3
+ rules: SCORE FROM ( Q41K => 8, Q41R => 4, Q41!KQR => "Effect unknown",
+ V55A => 4, Q80K => 8, Q80!KQR => "Effect unknown", A156TV => 8,
+ A156!ATV => "Effect unknown", Q168R => 4, Q168!HKQR => "Effect unknown",
+ L175M => 4, A294V => 4 )
+ - genotype: '4'
+ reference: HCV4-ED43-NS3
+ region: NS3
+ rules: SCORE FROM ( Q41R => 4, A156LTV => 8, A156!ALTV => "Effect unknown",
+ D168ETV => 4, D168!DEKTV => "Effect unknown", T185S => 4, T382S => 4 )
+ - genotype: '5'
+ reference: HCV5-SA13-NS3
+ region: NS3
+ rules: SCORE FROM ( A156!A => "Effect unknown", D168AK => 4, D168HRY => 8,
+ D168!ADEHKRVY => "Effect unknown" )
+ - genotype: '6'
+ reference: HCV6-EUHK2-NS3
+ region: NS3
+ rules: SCORE FROM ( Q41KR => 4, Q41!KQR => "Effect unknown", Y56H => 4,
+ A156!A => "Effect unknown", D168AEH => 4,
+ D168!ADEHVY => "Effect unknown" )
+ name: Voxilaprevir