From 3e5c617d78b4c86ee0b1ab33fffe755bccc22a34 Mon Sep 17 00:00:00 2001
From: aineniamh <aine.otoole@ed.ac.uk>
Date: Tue, 7 Nov 2023 13:58:28 +0000
Subject: [PATCH] adding bare bones haplo fxns file

---
 piranha/analysis/haplo_functions.py | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 piranha/analysis/haplo_functions.py

diff --git a/piranha/analysis/haplo_functions.py b/piranha/analysis/haplo_functions.py
new file mode 100644
index 0000000..62ad948
--- /dev/null
+++ b/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
\ No newline at end of file