Mercurial > repos > public-health-bioinformatics > micall_lite
changeset 0:023064145bea draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
| author | public-health-bioinformatics |
|---|---|
| date | Mon, 06 Jan 2020 19:10:15 -0500 |
| parents | |
| children | bb549c5eaf34 |
| files | amino2consensus.py macros.xml micall_lite.xml resistance.py test-data/1234A-V3LOOP.align.csv test-data/1234A-V3LOOP.amino.csv test-data/1234A-V3LOOP.conseq.csv test-data/1234A-V3LOOP.insert.csv test-data/1234A-V3LOOP.nuc.csv test-data/1234A-V3LOOP_S1_L001_R1_001.fastq test-data/1234A-V3LOOP_S1_L001_R1_001.fastq.gz test-data/1234A-V3LOOP_S1_L001_R2_001.fastq test-data/1234A-V3LOOP_S1_L001_R2_001.fastq.gz test-data/HCV294-amino.csv test-data/HCV294-consensus.fasta test-data/hcv_rules.1.8.yaml |
| diffstat | 16 files changed, 6084 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/amino2consensus.py Mon Jan 06 19:10:15 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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jan 06 19:10:15 2020 -0500 @@ -0,0 +1,12 @@ +<macros> + <token name="@TOOL_VERSION@">0.1rc2</token> + <token name="@INTYPES@"> + fastq,fastq.gz,fastqsanger,fastqsanger.gz + </token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + </citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/micall_lite.xml Mon Jan 06 19:10:15 2020 -0500 @@ -0,0 +1,148 @@ +<tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy0"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement> + </requirements> + <version_command>echo "@TOOL_VERSION@"</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + #if str( $fastq_input.fastq_input_selector ) == "paired": + #if $fastq_input.reads1.is_of_type("fastq.gz", "fastqsanger.gz"): + #set unzipped = False + #set reads1 = $fastq_input.reads1.element_identifier + '_R1.fastq.gz' + #else if $fastq_input.reads1.is_of_type("fastq", "fastqsanger"): + #set unzipped = True + #set reads1 = $fastq_input.reads1.element_identifier + '_R1.fastq' + #end if + ln -s '$fastq_input.reads1' '$reads1' && + #if $fastq_input.reads2.is_of_type("fastq.gz", "fastqsanger.gz"): + #set unzipped = False + #set reads2 = $fastq_input.reads2.element_identifier + '_R2.fastq.gz' + #else if $fastq_input.reads2.is_of_type("fastq", "fastqsanger"): + #set unzipped = True + #set reads2 = $fastq_input.reads2.element_identifier + '_R2.fastq' + #end if + ln -s '$fastq_input.reads2' '$reads2' && + #else if str( $fastq_input.fastq_input_selector ) == "paired_collection": + #if $fastq_input.pair.forward.is_of_type("fastq.gz", "fastqsanger.gz"): + #set unzipped = False + #set reads1 = $fastq_input.pair.element_identifier + '_R1.fastq.gz' + #else if $fastq_input.pair.forward.is_of_type("fastq", "fastqsanger"): + #set unzipped = True + #set reads1 = $fastq_input.pair.element_identifier + '_R1.fastq' + #end if + ln -s '$fastq_input.pair.forward' '$reads1' && + #if $fastq_input.pair.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): + #set unzipped = False + #set reads2 = $fastq_input.pair.element_identifier + '_R2.fastq.gz' + #else if $fastq_input.pair.reverse.is_of_type("fastq", "fastqsanger"): + #set unzipped = True + #set reads2 = $fastq_input.pair.element_identifier + '_R2.fastq' + #end if + ln -s '$fastq_input.pair.reverse' '$reads2' && + #end if + + mkdir 'outdir' && + micall + --threads \${GALAXY_SLOTS:-1} + #if $unzipped: + --unzipped + #end if + --readlen ${readlen} + '${reads1}' + '${reads2}' + --outdir 'outdir' + ]]> + </command> + <inputs> + <conditional name="fastq_input"> + <param name="fastq_input_selector" type="select" label="Paired Reads or Paired Collection" > + <option selected="true" value="paired">Paired</option> + <option value="paired_collection">Paired Collection</option> + </param> + <when value="paired"> + <param format="@INTYPES@" name="reads1" type="data" label="Select first set of reads"/> + <param format="@INTYPES@" name="reads2" type="data" label="Select second set of reads"/> + </when> + <when value="paired_collection"> + <param format="@INTYPES@" name="pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/> + </when> + </conditional> + <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" /> + </inputs> + <outputs> + <data name="align" label="align" format="csv" from_work_dir="outdir/*.align.csv" /> + <data name="amino" label="amino" format="csv" from_work_dir="outdir/*.amino.csv" /> + <data name="conseq" label="conseq" format="csv" from_work_dir="outdir/*.conseq.csv" /> + <data name="insert" label="insert" format="csv" from_work_dir="outdir/*.insert.csv" /> + <data name="nuc" label="nuc" format="csv" from_work_dir="outdir/*.nuc.csv" /> + </outputs> + <tests> + <test> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq" /> + <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq" /> + </conditional> + <param name="readlen" value="51" /> + <output name="align" value="1234A-V3LOOP.align.csv" /> + <output name="amino" value="1234A-V3LOOP.amino.csv" /> + <output name="conseq" value="1234A-V3LOOP.conseq.csv" /> + <output name="insert" value="1234A-V3LOOP.insert.csv" /> + <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> + </test> + <test> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" /> + <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" /> + </conditional> + <param name="readlen" value="51" /> + <output name="align" value="1234A-V3LOOP.align.csv" /> + <output name="amino" value="1234A-V3LOOP.amino.csv" /> + <output name="conseq" value="1234A-V3LOOP.conseq.csv" /> + <output name="insert" value="1234A-V3LOOP.insert.csv" /> + <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> + </test> + <test> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired_collection" /> + <param name="pair" > + <collection type="paired"> + <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq" /> + <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq" /> + </collection> + </param> + </conditional> + <param name="readlen" value="51" /> + <output name="align" value="1234A-V3LOOP.align.csv" /> + <output name="amino" value="1234A-V3LOOP.amino.csv" /> + <output name="conseq" value="1234A-V3LOOP.conseq.csv" /> + <output name="insert" value="1234A-V3LOOP.insert.csv" /> + <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> + </test> + <test> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired_collection" /> + <param name="pair" > + <collection type="paired"> + <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" /> + <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" /> + </collection> + </param> + </conditional> + <param name="readlen" value="51" /> + <output name="align" value="1234A-V3LOOP.align.csv" /> + <output name="amino" value="1234A-V3LOOP.amino.csv" /> + <output name="conseq" value="1234A-V3LOOP.conseq.csv" /> + <output name="insert" value="1234A-V3LOOP.insert.csv" /> + <output name="nuc" value="1234A-V3LOOP.nuc.csv" /> + </test> + </tests> + <help><![CDATA[ + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/resistance.py Mon Jan 06 19:10:15 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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1234A-V3LOOP.align.csv Mon Jan 06 19:10:15 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1234A-V3LOOP.amino.csv Mon Jan 06 19:10:15 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 +HIV1B-env-seed,gp120,15,5,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +HIV1B-env-seed,gp120,15,6,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +HIV1B-env-seed,gp120,15,7,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +HIV1B-env-seed,gp120,15,8,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +HIV1B-env-seed,gp120,15,9,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +HIV1B-env-seed,gp120,15,10,7,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +HIV1B-env-seed,gp120,15,11,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +HIV1B-env-seed,gp120,15,12,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +HIV1B-env-seed,gp120,15,13,10,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1234A-V3LOOP.conseq.csv Mon Jan 06 19:10:15 2020 -0500 @@ -0,0 +1,8 @@ +region,q-cutoff,consensus-percent-cutoff,offset,sequence +HIV1B-env-seed,15,MAX,876,TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG +HIV1B-env-seed,15,0.010,876,TGTAYAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG +HIV1B-env-seed,15,0.020,876,TGTAYAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG +HIV1B-env-seed,15,0.050,876,TGTAYAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG +HIV1B-env-seed,15,0.100,876,TGTAYAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG +HIV1B-env-seed,15,0.200,876,TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG +HIV1B-env-seed,15,0.250,876,TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1234A-V3LOOP.insert.csv Mon Jan 06 19:10:15 2020 -0500 @@ -0,0 +1,1 @@ +seed,region,qcut,left,insert,count,before
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1234A-V3LOOP_S1_L001_R1_001.fastq Mon Jan 06 19:10:15 2020 -0500 @@ -0,0 +1,40 @@ +@M01234:01:000000000-AAAAA:1:1101:01234:0001 1:N:0:1 +TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0002 1:N:0:1 +TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0003 1:N:0:1 +TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0004 1:N:0:1 +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 ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0007 1:N:0:1 +TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0008 1:N:0:1 +TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0009 1:N:0:1 +TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0010 1:N:0:1:fifth_base_differs +TGTATAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGG ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1234A-V3LOOP_S1_L001_R2_001.fastq Mon Jan 06 19:10:15 2020 -0500 @@ -0,0 +1,40 @@ +@M01234:01:000000000-AAAAA:1:1101:01234:0001 2:N:0:1 +CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0002 2:N:0:1 +CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0003 2:N:0:1 +CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0004 2:N:0:1 +CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0005 2:N:0:1 +CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0006 2:N:0:1 +CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0007 2:N:0:1 +CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0008 2:N:0:1 +CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0009 2:N:0:1 +CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTGTACA ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@M01234:01:000000000-AAAAA:1:1101:01234:0010 2:N:0:1:fifth_base_differs +CCCTGGTCCTATATGTATACTTTTTCTTGTATTGTTGTTGGGTCTTATACA ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HCV294-consensus.fasta Mon Jan 06 19:10:15 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#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hcv_rules.1.8.yaml Mon Jan 06 19:10:15 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