added create_keggcharter_input.py

desktop/src/mmonitor/userside/create_keggcharter_input.py

@@ -0,0 +1,29 @@
+import glob
+
+import pandas as pd
+
+"""
+This method takes as input to
+@param path_to_prokka_output: Path to the output of prokka that contains the tsv files that will get concatenated
+@param output_path: Path to safe the final tsv file to. That tsv file can then used as input for keggcharter and has the columns with EC_number nad taxonomy
+"""
+
+
+def create_keggcharter_input(path_to_prokka_output, output_path):
+    keggcharter_sheet = {'taxonomy': ['']}
+    df = pd.DataFrame(keggcharter_sheet)
+    df_list = []
+    df.to_csv(output_path, sep='\t')
+    for tsv in glob.glob(f"{path_to_prokka_output}/tsvs/*.tsv"):
+        data = pd.read_csv(tsv, sep='\t')
+        tax = tsv.split('.tsv')[0]
+        tax = tax.split('/')[-1]
+        tax = tax.replace('_', ' ')
+        tax = tax.replace('.fasta', ' ')
+        print(tax)
+        data["taxonomy"] = tax
+        df_list.append(data)
+    df = pd.concat(df_list)
+    df.to_csv(output_path, sep='\t')
+
+# create_keggcharter_input("/Users/timolucas/Desktop/kegg_test/",'/Users/timolucas/Desktop/kegg_test/test.tsv')