--- a/amino2consensus.py	Wed Feb 26 22:19:50 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-#!/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)

--- a/resistance.py	Wed Feb 26 22:19:50 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,68 +0,0 @@
-#!/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)

--- a/tool_data_table_conf.xml.test	Wed Feb 26 22:19:50 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<?xml version="1.0"?>
-<tables>
-    <!-- Locations of MiCall-Lite projects files in the required format -->
-    <table name="micall_lite_projects_files" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="${__HERE__}/test-data/micall_lite_projects_files.loc" />
-    </table>
-</tables>