From 616ca8e25568b140e4ef24f1068dbdf6ffada1e2 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 17 Jul 2018 16:43:56 -0500
Subject: [PATCH] Added 'read_model' to cadnano_segments
---
cadnano_segments.py | 33 +++++++++++++++++++++++++++++++++
1 file changed, 33 insertions(+)
diff --git a/cadnano_segments.py b/cadnano_segments.py
index 585b368..d0adeea 100644
--- a/cadnano_segments.py
+++ b/cadnano_segments.py
@@ -544,6 +544,39 @@ def decode_cadnano_part(json_data):
def package_archive( name, directory ):
...
+def read_model(json_data, sequence=None):
+ """ Read in data """
+ part = decode_cadnano_part(json_data)
+ model = cadnano_part(part,
+ max_basepairs_per_bead = 7,
+ max_nucleotides_per_bead = 4,
+ local_twist=False)
+ model._generate_strands() # TODO: move into model creation
+
+ # TODO
+ # try:
+ # model.set_cadnano_sequence()
+ # finally:
+ # ...
+ # if sequence is not None and len() :
+ # model.strands[0].set_sequence(seq)
+
+ if sequence is None or len(sequence) == 0:
+ ## default m13mp18
+ sequence = list(m13seq)
+ try:
+ model.strands[0].set_sequence(sequence)
+ except:
+ ...
+ else:
+ model.strands[0].set_sequence(sequence)
+
+ for s in model.segments:
+ s.randomize_unset_sequence()
+
+ return model
+
+
def run_simulation_protocol( output_name, job_id, json_data,
sequence=None,
remove_long_bonds=False,
--
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