--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/modules/typing.py	Wed Jan 22 08:41:44 2020 -0500
@@ -0,0 +1,62 @@
+import os.path
+import functools
+
+import utils
+
+def simplify_data_by_gene(data_by_gene):
+    cleaned_data_by_gene = {}
+    for counter, data in data_by_gene.items():
+        cleaned_data_by_gene[data['header']] = {'gene_identity': data['gene_identity'], 'gene_coverage': data['gene_coverage'], 'gene_depth': data['gene_mean_read_coverage']}
+    return cleaned_data_by_gene
+
+
+def possible_types(data_by_gene, typing_rules_file, min_gene_coverage, min_gene_identity, min_gene_depth):
+    data_by_gene = simplify_data_by_gene(data_by_gene)
+
+    possible_pathotypes = []
+    with open(typing_rules_file, 'rtU') as reader:
+        genes = []
+        for line in reader:
+            line = line.splitlines()[0]
+            if len(line) > 0:
+                line = line.split('\t')
+                if line[0].startswith('#'):
+                    genes = map(str.lower, line[1:])
+                else:
+                    profile = line[1:]
+                    congruence = []
+                    for x, gene_requirement in enumerate(profile):
+                        gene_requirement = True if gene_requirement == '1' else False if gene_requirement == '0' else None
+                        if gene_requirement is None:
+                            congruence.append(True)
+                        else:
+                            if data_by_gene[genes[x]]['gene_coverage'] >= min_gene_coverage and data_by_gene[genes[x]]['gene_identity'] >= min_gene_identity and data_by_gene[genes[x]]['gene_depth'] >= min_gene_depth:
+                                gene_present = True
+                            else:
+                                gene_present = False
+
+                            if gene_present == gene_requirement:
+                                congruence.append(True)
+                            else:
+                                congruence.append(False)
+                    if all(congruence):
+                        possible_pathotypes.append(line[0])
+    return possible_pathotypes
+
+
+module_timer = functools.partial(utils.timer, name='Module Typing')
+
+
+@module_timer
+def typing(data_by_gene, typing_rules_file, min_gene_coverage, min_gene_identity, min_gene_depth, outdir):
+    possible_pathotypes = possible_types(data_by_gene, typing_rules_file, min_gene_coverage, min_gene_identity, min_gene_depth)
+    with open(os.path.join(outdir, 'patho_typing.report.txt'), 'wt') as writer:
+        if len(possible_pathotypes) > 0:
+            writer.write('\n'.join(possible_pathotypes) + '\n')
+            print '\n' + 'Pathotypes found:' + '\n'
+            print '\n'.join(possible_pathotypes) + '\n'
+        else:
+            writer.write('NA' + '\n')
+            print '\n' + 'It was not possible to identify any possible pathotype match' + '\n'
+
+    return None, None