adding bare bones haplo fxns file

piranha/analysis/haplo_functions.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+import csv
+from Bio import SeqIO
+import collections
+from piranha.utils.config import *
+import os
+
+from piranha.utils.log_colours import green,cyan,red
+
+
+def parse_partition_file(partition_file):
+
+    partitions = collections.defaultdict(set)
+    with open(partition_file, "r") as f:
+        part = ""
+        for l in f:
+            l=l.rstrip("\n")
+            if l[0] == "#":
+                part = l.lstrip("#")
+            else:
+                read_id = l.split("\t")[0]
+                partitions[part].add(read_id)
+
+    return partitions