Merge pull request #62 from jodyphelan/master

TB-Profiler IO

hAMRonization/TBProfilerIO.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+import json
+from .Interfaces import hAMRonizedResultIterator
+
+required_metadata = ['analysis_software_version',
+                     'reference_database_version']
+
+
+class TBProfilerIterator(hAMRonizedResultIterator):
+
+    def __init__(self, source, metadata):
+        metadata['analysis_software_name'] = 'TBProfiler'
+        self.metadata = metadata
+
+        self.field_mapping = {
+                'filename': 'input_file_name', 
+                'gene': 'gene_symbol',
+                'gene': 'gene_name',
+                'drug': 'drug_class',
+                'type': 'genetic_variation_type',
+                'frequency': 'variant_frequency',
+                'db_name': 'reference_database_id',
+                'db_version': 'reference_database_version',
+                'tbprofiler_version': 'analysis_software_version'
+
+                }
+
+        super().__init__(source, self.field_mapping, self.metadata)
+
+    def parse(self, handle):
+        """
+        Read each and return it
+        """
+        # skip any manually specified fields for later
+        json_obj = json.load(handle)
+        for variant in json_obj["dr_variants"]:
+            for drug in variant["drugs"]:
+                result = {
+                    'filename': handle.name,
+                    'gene': variant['gene'],
+                    'gene_name': variant['gene'],
+                    'drug': drug['drug'],
+                    'type': 'variant', 
+                    'frequency': variant['freq'],
+                    'db_name': json_obj['db_version']['name'],
+                    'db_version': json_obj['db_version']['commit'],
+                    'tbprofiler_version': json_obj['tbprofiler_version']
+                }
+                yield self.hAMRonize(result, self.metadata)
+