fix indentation

fmalmeida · fmalmeida · commit 9931b4201b7c · 2023-02-28T11:24:52.000+01:00
diff --git a/falmeida_py/mges_function.py b/falmeida_py/mges_function.py
@@ -17,43 +17,40 @@ def mges_stats(bacannot_summary):
 
         # init MGE annotation dictionary
         bacannot_summary[sample]['MGE'] = {}
-
-        # load annotation stats
-        if os.path.exists(f"{results_dir}/integron_finder"):
             
-            # integron_finder
-            if os.path.exists(f"{results_dir}/integron_finder/{sample}_integrons.gff"):
-
-                # init integron_finder annotation dictionary
-                bacannot_summary[sample]['MGE']['integron_finder'] = {}
-
-                # load integron_finder results
-                results = pd.read_csv(
-                    f"{results_dir}/integron_finder/{sample}_integrons.gff",
-                    sep='\t',
-                    header=None,
-                    names=[
-                        'chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'frame', 'atts'
-                    ]
-                )
-
-                # number of integron_finder annotations
-                total_number = len(results.index)
-                bacannot_summary[sample]['MGE']['integron_finder']['total'] = total_number
-
-                # per integron info
-                bacannot_summary[sample]['MGE']['integron_finder'] = {}
-                if int(results.shape[0]) > 0:
-                    for seq in [ str(x) for x in results['chr'].unique() ]:
-                        
-                        bacannot_summary[sample]['MGE']['integron_finder'][seq] = {}
-                        for index, row in results[results['chr'] == seq].reset_index().iterrows():
-                            id = row['atts'].split(';')[0].split('=')[-1]
-                            bacannot_summary[sample]['MGE']['integron_finder'][seq][id] = {}
-                            bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['id'] = id
-                            bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['contig'] = row['chr']
-                            bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['start'] = row['start']
-                            bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['end'] = row['end']
-                            bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['type'] = row['atts'].split(';')[1].split('=')[-1]
-                            bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['source'] = row['source']
-                            bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['product'] = row['type']
+        # integron_finder
+        if os.path.exists(f"{results_dir}/integron_finder/{sample}_integrons.gff"):
+
+            # init integron_finder annotation dictionary
+            bacannot_summary[sample]['MGE']['integron_finder'] = {}
+
+            # load integron_finder results
+            results = pd.read_csv(
+                f"{results_dir}/integron_finder/{sample}_integrons.gff",
+                sep='\t',
+                header=None,
+                names=[
+                    'chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'frame', 'atts'
+                ]
+            )
+
+            # number of integron_finder annotations
+            total_number = len(results.index)
+            bacannot_summary[sample]['MGE']['integron_finder']['total'] = total_number
+
+            # per integron info
+            bacannot_summary[sample]['MGE']['integron_finder'] = {}
+            if int(results.shape[0]) > 0:
+                for seq in [ str(x) for x in results['chr'].unique() ]:
+                    
+                    bacannot_summary[sample]['MGE']['integron_finder'][seq] = {}
+                    for index, row in results[results['chr'] == seq].reset_index().iterrows():
+                        id = row['atts'].split(';')[0].split('=')[-1]
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id] = {}
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['id'] = id
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['contig'] = row['chr']
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['start'] = row['start']
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['end'] = row['end']
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['type'] = row['atts'].split(';')[1].split('=')[-1]
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['source'] = row['source']
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['product'] = row['type']
