# HG changeset patch
# User dfornika
# Date 1582842692 0
# Node ID 4ff24c044fed1912aebf01bbc8bdcd06ff1bf495
# Parent c0cdaa42b5412b6c3ec5a5151c8c1506a8423a68
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
diff -r c0cdaa42b541 -r 4ff24c044fed amino2consensus.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/amino2consensus.py Thu Feb 27 22:31:32 2020 +0000
@@ -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 c0cdaa42b541 -r 4ff24c044fed macros.xml
--- a/macros.xml Thu Feb 27 18:37:19 2020 +0000
+++ b/macros.xml Thu Feb 27 22:31:32 2020 +0000
@@ -5,8 +5,6 @@
-
-
diff -r c0cdaa42b541 -r 4ff24c044fed resistance.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/resistance.py Thu Feb 27 22:31:32 2020 +0000
@@ -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 c0cdaa42b541 -r 4ff24c044fed tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu Feb 27 22:31:32 2020 +0000
@@ -0,0 +1,8 @@
+
+
+
+
+