From 465d369a9c8c58b0a291b6582a884d3c266ea700 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 27 Sep 2019 13:17:47 -0500
Subject: [PATCH] Added sequence to vHelix parser
---
mrdna/readers/__init__.py | 1 -
mrdna/readers/polygon_mesh.py | 21 +++++++++++++++++++++
2 files changed, 21 insertions(+), 1 deletion(-)
diff --git a/mrdna/readers/__init__.py b/mrdna/readers/__init__.py
index 31a6ced..4ac260c 100644
--- a/mrdna/readers/__init__.py
+++ b/mrdna/readers/__init__.py
@@ -13,7 +13,6 @@ def read_vhelix(maya_file, **model_parameters):
maya_bases = parse_maya_file(maya_file)
model = convert_maya_bases_to_segment_model( maya_bases, **model_parameters )
- model.set_sequence(m13seq*10)
return model
def read_list(infile,**model_parameters):
diff --git a/mrdna/readers/polygon_mesh.py b/mrdna/readers/polygon_mesh.py
index 2eb0015..7f96df1 100644
--- a/mrdna/readers/polygon_mesh.py
+++ b/mrdna/readers/polygon_mesh.py
@@ -13,6 +13,8 @@ maya_obj_registry_short = dict()
class MayaObj():
""" Class representing a node in a Maya ascii file """
+ seq_mapping = {str(i):c for c,i in zip('ATCG',range(4))}
+
def __init__(self, maya_lines):
self.parent = None
self.children = dict()
@@ -59,6 +61,11 @@ class MayaObj():
Ry = rotationAboutAxis( [0,1,0], ay, normalizeAxis=False )
Rz = rotationAboutAxis( [0,0,1], az, normalizeAxis=False )
self.orientation = Rz.dot(Ry.dot(Rx))
+ elif vals[1] == '".lb"':
+ try:
+ self.sequence = MayaObj.seq_mapping[vals[2][0]]
+ except:
+ pass
def _strip_maya_string(string):
return re.match('"\|?([a-zA-Z_0-9|]+)";?$', string).group(1)
@@ -138,6 +145,7 @@ def ParseMayaConnection(line, base_dict):
class MayaBase(MayaObj):
def __init__(self, maya_lines):
+ self.sequence = '?'
MayaObj.__init__(self, maya_lines)
self._parse_maya_lines(maya_lines)
self.basepair = None
@@ -371,6 +379,10 @@ def convert_maya_bases_to_segment_model(maya_bases, **model_parameters):
coord = np.zeros((len(maya_bases),3))
orientation = np.zeros((len(maya_bases),3,3))
bp,end3 = [-np.ones((len(maya_bases)),dtype=np.int) for i in range(2)]
+ sequence = []
+
+ seq_map = {'A':'T', 'C':'G', 'T':'A', 'G':'C'}
+
for i,b in zip(range(len(maya_bases)),maya_bases):
coord[i] = b.get_position()
@@ -380,6 +392,15 @@ def convert_maya_bases_to_segment_model(maya_bases, **model_parameters):
if b.end3 is not None:
end3[i] = base_to_index[ b.end3 ]
+ try:
+ s = b.sequence
+ if s == '?':
+ s = seq_map[s.basepair.sequence]
+ except:
+ s = 'T'
+ sequence.append( s )
+ if 'sequence' not in model_parameters:
+ model_parameters['sequence'] = sequence
return model_from_basepair_stack_3prime(coord, bp, None, end3,
orientation=orientation,
**model_parameters)
--
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