init

dnasp2popart.py

@@ -0,0 +1,30 @@
+from collections import defaultdict
+import re
+
+data = defaultdict(lambda : 0)
+hap_list = set()
+
+with open("16S.arp", "r") as f:
+    sample_array = f.read().split("}\n")
+    for sample in sample_array:
+        sample_data = sample.split("\n")
+        if len(sample_data[0].split('"'))>1:
+            # Sample name
+            sample_name = sample_data[0].split('"')[1]
+            data[sample_name] = defaultdict(lambda : 0);
+            data[sample_name]["sample_size"] = sample_data[1].split('=')[1].strip()
+            for hap in sample_data[3:]:
+                if hap:
+                    data[sample_name][hap.split()[0].strip()] = hap.split()[1].strip()
+                    hap_list.add(hap.split()[0].strip())
+
+with open("output.csv", "w+") as f:
+    hap_list = sorted(list(hap_list), key=lambda x : int(x.split('_')[1]))
+    key_list = sorted(data.keys())
+    f.write("sample_name, " + ", ".join(key_list) + "\n")
+    f.write("sample_size, " + ", ".join([data[key]["sample_size"] for key in key_list]) + "\n")
+    for hap in hap_list:
+        f.write(hap)
+        for key in key_list:
+            f.write(", " + str(data[key][hap]))
+        f.write("\n")