From 1d5f21b8a0e4f181bf5e2654c4292c99ce3371d5 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 5 Jun 2020 17:44:56 -0500
Subject: [PATCH] Segmentmodel_from_lists will now guess stacks based on
connectivity if not supplied
---
mrdna/readers/segmentmodel_from_lists.py | 13 ++++++++++++-
1 file changed, 12 insertions(+), 1 deletion(-)
diff --git a/mrdna/readers/segmentmodel_from_lists.py b/mrdna/readers/segmentmodel_from_lists.py
index 51b2877..96f610a 100644
--- a/mrdna/readers/segmentmodel_from_lists.py
+++ b/mrdna/readers/segmentmodel_from_lists.py
@@ -261,7 +261,18 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
raise ValueError("The 'orientation' array is not properly formatted")
if stack is None:
- stack = find_stacks(coordinate, orientation)
+ if orientation is not None:
+ stack = find_stacks(coordinate, orientation)
+ else:
+ ## Guess stacking based on 3' connectivity
+ stack = np.array(three_prime,dtype=np.int) # Assume nts on 3' ends are stacked
+ _stack_below = _three_prime_list_to_five_prime(stack)
+ _has_bp = (basepair >= 0)
+ _nostack = np.where( (stack == -1)*_has_bp )[0]
+ _has_stack_below = _stack_below[basepair[_nostack]] >= 0
+ _nostack2 = _nostack[_has_stack_below]
+ stack[_nostack2] = basepair[_stack_below[basepair[_nostack2]]]
+
else:
try:
stack = np.array(stack,dtype=np.int)
--
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