diff resistance.py @ 0:023064145bea draft

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"

--- /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)