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Commit 2e5cefe3 authored by pinyili2's avatar pinyili2
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update code

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mrdna/readers/.DS_Store 0 → 100644
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− 0
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File added
mrdna/readers/__init__.py
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− 2
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......@@ -9,9 +9,7 @@ def read_cadnano(json_file, sequence=None, fill_sequence='T', **model_parameters
def read_cadnano_input(json_file,sequence=None,**model_parameters):
from .segmentmodel_from_cadnano import mrdna_model_from_cadnano
from .segmentmodel_from_lists import model_from_basepair_stack_3prime
return mrdna_model_from_cadnano(json_file,seq=sequence,**model_parameters)
def read_vhelix(maya_file, **model_parameters):
......
mrdna/readers/segmentmodel_from_cadnano.py
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− 29
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# -*- coding: utf-8 -*-
import pdb
import numpy as np
import os,sys
from glob import glob
......@@ -13,6 +12,7 @@ from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSe
from ..model.dna_sequence import m13 as m13seq
import json
import re
import pdb
......@@ -23,7 +23,26 @@ import re
## - helices that should be stacked across an empty region (crossovers from and end in the helix to another end in the helix)
## - circular constructs
def get_lattice(part):
lattice_type = None
_gt = part.getGridType()
try:
lattice_type = _gt.name.lower()
except:
if _gt == 1:
lattice_type = 'square'
elif _gt == 2:
lattice_type = 'honeycomb'
else:
print(lattice_type)
return lattice_type
def read_json_file(filename):
import cadnano
from cadnano.document import Document
try:
with open(filename) as ch:
json_data = json.load(ch)
......@@ -38,11 +57,7 @@ def read_json_file(filename):
# l = re.sub(r"(\w):", r'\1":', l)
content += l+"\n"
json_data = json.loads(content)
return json_data
def cadnano_parts(json_data):
import cadnano
from cadnano.document import Document
try:
doc = Document()
cadnano.fileio.v3decode.decode(doc, json_data)
......@@ -68,20 +83,6 @@ def cadnano_parts(json_data):
n_df=df.set_index("num")
return part
def get_lattice(part):
lattice_type = None
_gt = part.getGridType()
try:
lattice_type = _gt.name.lower()
except:
if _gt == 1:
lattice_type = 'square'
elif _gt == 2:
lattice_type = 'honeycomb'
else:
print("WARNING: unable to determine cadnano part lattice type")
return lattice_type
def get_helix_angle(part, helix_id, indices):
""" Get "start_orientation" for helix """
# import ipdb
......@@ -154,10 +155,11 @@ def gen_id_series(strand,part):
else:
df["threeprime_tuple"]=[(strand.connection3p().idNum(),str(strand.connection3p().idx5Prime()),strand.connection3p().isForward())]+L[0:-1]
## cadnano 3.1 sequence assign is wrong if there is insertion or deletion.
df["r"]=[np.array([df["x"][i],df["y"][i],df["z"][i]]) for i in df.index]
df["r"]=[np.array([df["x"][i],df["y"][i],df["z"][i]],dtype=np.float32) for i in df.index]
return [pd.Series(df.loc[i]) for i in df.index]
def gen_prop_table(part):
strand_set=[]
for i in part.getidNums():
......@@ -170,7 +172,7 @@ def gen_prop_table(part):
nt_prop=pd.DataFrame(id_series)
nt_prop.reset_index(names=list(range(len(nt_prop.index))),inplace=True)
nt_prop["seq"]=-1
ind_tuple=[(nt_prop["vh"][i],nt_prop["zid"][i],nt_prop["fwd"][i]) for i in nt_prop.index]
stacks=[]
for i in list(nt_prop["stack_tuple"]):
......@@ -187,7 +189,7 @@ def gen_prop_table(part):
tprime.append(ind_tuple.index(i))
nt_prop["threeprime"]=tprime
vhzid=list(zip(nt_prop["vh"],nt_prop["zid"]))
nt_prop["bp"]=-1
nt_prop["orientation"]=[get_helix_angle(part, helix_id, int(float(indices))) for helix_id,indices in vhzid]
nt_prop=nt_prop.fillna(-1)
for i in range(int(len(nt_prop.index)/2)):
......@@ -199,14 +201,11 @@ def gen_prop_table(part):
pass
return nt_prop
def mrdna_model_from_cadnano(json_file,seq=None,**model_parameters):
json_data=read_json_file(json_file)
part,decoder=cadnano_parts(json_data)
if decoder==2:
nt_prop=gen_prop_table(part)
elif decoder==3:
nt_prop=gen_prop_table(part)
part=read_json_file(json_file)
nt_prop=gen_prop_table(part)
if seq is None:
if nt_prop["seq"][0]==-1:
......
mrdna/readers/test.csv deleted 100644 → 0
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mrdna/readers/test/1.json 0 → 100644
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{"format":"3.1","date":"2024-08-09 00:08:58","name":"","parts":[{"name":"NaPart1","color":"#0066cc","is_visible":true,"active_phos":null,"crossover_span_angle":45,"max_vhelix_length":42,"neighbor_active_angle":"","grid_type":2,"virtual_helix_order":[0,1,2,3,4,5],"is_lattice":true,"virtual_helices":{"name":["vh0","vh1","vh2","vh3","vh4","vh5"],"is_visible":[true,true,true,true,true,true],"color":["#0066cc","#0066cc","#0066cc","#0066cc","#0066cc","#0066cc"],"eulerZ":[0.0,0.0,0.0,0.0,0.0,0.0],"neighbor_active_angle":[0.0,0.0,0.0,0.0,0.0,0.0],"neighbors":["[1, 5]","[0, 2]","[1, 3]","[2, 4]","[3, 5]","[0, 4]"],"bases_per_repeat":[21,21,21,21,21,21],"turns_per_repeat":[2,2,2,2,2,2],"repeat_hint":[2,2,2,2,2,2],"helical_pitch":[1.0,1.0,1.0,1.0,1.0,1.0],"minor_groove_angle":[180.0,180.0,180.0,180.0,180.0,180.0],"length":[42,42,42,42,42,42],"z":[0.0,0.0,0.0,0.0,0.0,0.0]},"origins":[[0.0,2.25,0.0],[-1.948557375,1.125,0.0],[-1.948557375,-1.125,0.0],[0.0,-2.25,0.0],[1.948557375,-1.125,0.0],[1.948557375,1.125,0.0]],"directions":[[0.0,0.0,1.0],[0.0,0.0,1.0],[0.0,0.0,1.0],[0.0,0.0,1.0],[0.0,0.0,1.0],[0.0,0.0,1.0]],"vh_list":[[0,42],[1,42],[2,42],[3,42],[4,42],[5,42]],"strands":{"indices":[[[[5,36]],[[5,30],[31,36]]],[[[1,30],[31,34]],[[1,15],[16,34]]],[[],[[1,16]]],[[[15,37]],[[15,37]]],[[[15,38]],[[18,23],[24,33]]],[[[14,23],[24,37]],[[15,30],[31,36]]]],"properties":[[["#0066cc"],["#0066cc","#0066cc"]],[["#0066cc","#0066cc"],["#0066cc","#0066cc"]],[[],["#0066cc"]],[["#0066cc"],["#0066cc"]],[["#0066cc"],["#0066cc","#0066cc"]],[["#0066cc","#0066cc"],["#0066cc","#0066cc"]]]},"insertions":[],"xovers":[[0,false,31,1,true,31],[1,true,30,0,false,30],[3,false,15,1,false,15],[4,true,38,5,false,36],[4,false,24,5,true,24],[5,true,23,4,false,23],[5,false,15,4,true,15]],"oligos":[{"id_num":0,"idx5p":36,"is_5p_fwd":false,"is_circular":false,"sequence":null,"name":"oligo7360","color":"#0066cc","length":10,"is_visible":true},{"id_num":1,"idx5p":1,"is_5p_fwd":true,"is_circular":false,"sequence":null,"name":"oligo6512","color":"#0066cc","length":56,"is_visible":true},{"id_num":3,"idx5p":15,"is_5p_fwd":true,"is_circular":false,"sequence":null,"name":"oligo8176","color":"#0066cc","length":23,"is_visible":true},{"id_num":1,"idx5p":34,"is_5p_fwd":false,"is_circular":false,"sequence":null,"name":"oligo8000","color":"#0066cc","length":19,"is_visible":true},{"id_num":2,"idx5p":16,"is_5p_fwd":false,"is_circular":false,"sequence":null,"name":"oligo5072","color":"#0066cc","length":16,"is_visible":true},{"id_num":3,"idx5p":37,"is_5p_fwd":false,"is_circular":false,"sequence":null,"name":"oligo5456","color":"#0066cc","length":38,"is_visible":true},{"id_num":0,"idx5p":5,"is_5p_fwd":true,"is_circular":false,"sequence":null,"name":"oligo0016","color":"#0066cc","length":32,"is_visible":true},{"id_num":5,"idx5p":14,"is_5p_fwd":true,"is_circular":false,"sequence":null,"name":"oligo5344","color":"#0066cc","length":16,"is_visible":true},{"id_num":5,"idx5p":30,"is_5p_fwd":false,"is_circular":false,"sequence":null,"name":"oligo4128","color":"#0066cc","length":46,"is_visible":true},{"id_num":4,"idx5p":33,"is_5p_fwd":false,"is_circular":false,"sequence":null,"name":"oligo1344","color":"#0066cc","length":24,"is_visible":true}],"instance_properties":[{"slice:position":[0.0,0.0],"grid:position":[0.0,0.0],"path:position":[0.0,0.0]}],"uuid":"0f339308432240cb80de80d28db856f3"}],"modifications":{}}
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mrdna/readers/test/ipykernel_launcher.json 0 → 100644
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mrdna/readers/test/loopout.sc 0 → 100644
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{
"version": "0.19.3",
"grid": "square",
"helices": [
{"grid_position": [0, 0], "max_offset": 48},
{"grid_position": [0, 1], "max_offset": 48}
],
"modifications_5p_in_design": {
"/5Biosg/": {
"display_text": "B",
"vendor_code": "/5Biosg/",
"location": "5'"
}
},
"strands": [
{
"color": "#0066cc",
"sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG",
"is_scaffold": true,
"domains": [
{"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]},
{"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]},
{"loopout": 3},
{"helix": 1, "forward": false, "start": 24, "end": 40}
]
},
{
"color": "#f74308",
"sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT",
"domains": [
{"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]},
{"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]}
]
},
{
"color": "#57bb00",
"sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC",
"domains": [
{"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]},
{"helix": 1, "forward": true, "start": 24, "end": 40}
],
"5prime_modification": "/5Biosg/"
}
]
}
\ No newline at end of file
mrdna/readers/test/s.csv 0 → 100644
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mrdna/readers/segmentmodel_from_cadnano_old.py → mrdna/readers/test/segmentmodel_from_cadnano_old.py
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......@@ -6,11 +6,11 @@ from glob import glob
import re
import pandas as pd
pd.options.mode.chained_assignment = None # default='warn'
from .segmentmodel_from_lists import model_from_basepair_stack_3prime
from ..segmentmodel_from_lists import model_from_basepair_stack_3prime
from ..arbdmodel.coords import readArbdCoords, readAvgArbdCoords, rotationAboutAxis
from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
from ..model.dna_sequence import m13 as m13seq
from ...arbdmodel.coords import readArbdCoords, readAvgArbdCoords, rotationAboutAxis
from ...segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
from ...model.dna_sequence import m13 as m13seq
import json
import re
......
mrdna/readers/test/seq0.txt 0 → 100644
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− 0
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Start,End,Color,Mod5,Sequence,Mod3,AbstractSequence
5[3],5[0],#0066cc,,????,,()
1[41],1[39],#0066cc,,???,,()
0[38],5[39],#b8056c,,??ATCCCTTATAAATCAAAAGACTGAGAGAGTTG,,"(,)"
0[23],1[38],#cc01d1,,CCCTTCCGAAATCGGCAAA??,,"(,)"
3[0],4[9],#cc0000,,??GACTCCAACGTCAACCCCAGTTTGAGGGCGA,,"(,)"
5[9],0[24],#000000,,AAAACCGTCTATCATGGCCATAG,,"(,)"
2[34],2[0],#888888,,??TCCTGTTTGATGGTACTATTAAAGAACGTG??,,()
0[39],0[41],#0066cc,,???,,()
5[22],5[23],#0066cc,,TGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCA,,"(,,,,,,,,,,)"
3[41],3[37],#0066cc,,?????,,()
1[3],0[2],#16e876,,??TTGGAACAAGAGTCCGGGAGATAGGGTTGAGTGTTGTTCCAGT???,,"(,)"
2[39],2[41],#0066cc,,???,,()
4[39],3[34],#888888,,CAGCAAGCGGTCCACGCTGGCAGGCGAAAA??,,"(,)"
4[0],4[3],#0066cc,,TGAT,,()
mrdna/readers/test/test.ipynb
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mrdna/readers/test/test.sc 0 → 100644
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{
"version": "0.19.3",
"grid": "honeycomb",
"helices": [
{"grid_position": [16, 12]},
{"grid_position": [15, 12]},
{"grid_position": [15, 13]},
{"grid_position": [16, 13]},
{"grid_position": [17, 13]},
{"grid_position": [17, 12]}
],
"strands": [
{
"color": "#0066cc",
"is_scaffold": true,
"domains": [
{"helix": 5, "forward": false, "start": 9, "end": 23},
{"helix": 4, "forward": true, "start": 9, "end": 16},
{"helix": 3, "forward": false, "start": 2, "end": 16},
{"helix": 2, "forward": true, "start": 2, "end": 19},
{"helix": 1, "forward": false, "start": 5, "end": 19},
{"helix": 0, "forward": true, "start": 5, "end": 37},
{"helix": 1, "forward": false, "start": 19, "end": 37},
{"helix": 2, "forward": true, "start": 19, "end": 33},
{"helix": 3, "forward": false, "start": 16, "end": 33},
{"helix": 4, "forward": true, "start": 16, "end": 40},
{"helix": 5, "forward": false, "start": 23, "end": 40}
]
},
{
"color": "#0066cc",
"is_scaffold": true,
"domains": [
{"helix": 0, "forward": true, "start": 39, "end": 42}
]
},
{
"color": "#cc0000",
"domains": [
{"helix": 1, "forward": true, "start": 3, "end": 21},
{"helix": 0, "forward": false, "start": 2, "end": 21}
]
},
{
"color": "#b8056c",
"domains": [
{"helix": 0, "forward": false, "start": 21, "end": 24},
{"helix": 1, "forward": true, "start": 21, "end": 39}
]
},
{
"color": "#f74308",
"domains": [
{"helix": 5, "forward": true, "start": 9, "end": 28},
{"helix": 0, "forward": false, "start": 24, "end": 28}
]
},
{
"color": "#1700de",
"domains": [
{"helix": 0, "forward": false, "start": 28, "end": 39},
{"helix": 5, "forward": true, "start": 28, "end": 40}
]
},
{
"color": "#0066cc",
"is_scaffold": true,
"domains": [
{"helix": 1, "forward": false, "start": 39, "end": 42}
]
},
{
"color": "#0066cc",
"is_scaffold": true,
"domains": [
{"helix": 2, "forward": true, "start": 39, "end": 42}
]
},
{
"color": "#888888",
"domains": [
{"helix": 2, "forward": false, "start": 0, "end": 35}
]
},
{
"color": "#0066cc",
"is_scaffold": true,
"domains": [
{"helix": 3, "forward": false, "start": 37, "end": 42}
]
},
{
"color": "#cc0000",
"domains": [
{"helix": 3, "forward": true, "start": 0, "end": 21},
{"helix": 4, "forward": false, "start": 9, "end": 21}
]
},
{
"color": "#888888",
"domains": [
{"helix": 4, "forward": false, "start": 21, "end": 40},
{"helix": 3, "forward": true, "start": 21, "end": 35}
]
},
{
"color": "#0066cc",
"is_scaffold": true,
"domains": [
{"helix": 4, "forward": true, "start": 0, "end": 4}
]
},
{
"color": "#0066cc",
"is_scaffold": true,
"domains": [
{"helix": 5, "forward": false, "start": 0, "end": 4}
]
}
]
}
\ No newline at end of file
mrdna/readers/test/test2.ipynb
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mrdna/readers/test/test3.ipynb
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......@@ -536,9 +536,7 @@
"cell_type": "code",
"execution_count": 62,
"id": "f666ffb1",
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [
{
"data": {
......@@ -2115,7 +2113,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
......@@ -2129,7 +2127,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.18"
"version": "3.8.19"
}
},
"nbformat": 4,
......
mrdna/readers/test/test_cad2.5.json 0 → 100644
+ 1
− 0
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{"format":"3.1","date":"2024-08-08 23:20:21","name":"","parts":[{"name":"NaPart1","color":"#0066cc","is_visible":true,"active_phos":null,"crossover_span_angle":45,"max_vhelix_length":42,"neighbor_active_angle":"","grid_type":2,"virtual_helix_order":[0,1,2,3,4,5],"is_lattice":true,"virtual_helices":{"name":["vh0","vh1","vh2","vh3","vh4","vh5"],"is_visible":[true,true,true,true,true,true],"color":["#0066cc","#0066cc","#0066cc","#0066cc","#0066cc","#0066cc"],"eulerZ":[0.0,0.0,0.0,0.0,0.0,0.0],"neighbor_active_angle":[0.0,0.0,0.0,0.0,0.0,0.0],"neighbors":["[1, 5]","[0, 2]","[1, 3]","[2, 4]","[3, 5]","[0, 4]"],"bases_per_repeat":[21,21,21,21,21,21],"turns_per_repeat":[2,2,2,2,2,2],"repeat_hint":[2,2,2,2,2,2],"helical_pitch":[1.0,1.0,1.0,1.0,1.0,1.0],"minor_groove_angle":[180.0,180.0,180.0,180.0,180.0,180.0],"length":[42,42,42,42,42,42],"z":[0.0,0.0,0.0,0.0,0.0,0.0]},"origins":[[-1.948557375,1.125,0.0],[0.0,2.25,0.0],[1.948557375,1.125,0.0],[1.948557375,-1.125,0.0],[0.0,-2.25,0.0],[-1.948557375,-1.125,0.0]],"directions":[[0.0,0.0,1.0],[0.0,0.0,1.0],[0.0,0.0,1.0],[0.0,0.0,1.0],[0.0,0.0,1.0],[0.0,0.0,1.0]],"vh_list":[[0,42],[1,42],[2,42],[3,42],[4,42],[5,42]],"strands":{"indices":[[[[0,2],[3,20],[21,35]],[]],[[],[[0,20],[21,41]]],[[[0,23],[24,41]],[]],[[],[[0,9],[10,23],[24,30],[31,41]]],[[[0,9],[10,30],[31,41]],[]],[[],[[0,2],[3,35],[36,41]]]],"properties":[[["#0066cc","#f7931e","#f7931e"],[]],[[],["#f7931e","#f7931e"]],[["#f7931e","#f7931e"],[]],[[],["#0066cc","#f7931e","#f7931e","#0066cc"]],[["#0066cc","#f7931e","#0066cc"],[]],[[],["#333333","#f7931e","#0066cc"]]]},"insertions":[],"xovers":[[0,true,20,1,false,20],[0,true,35,5,false,35],[1,false,0,2,true,0],[1,false,21,0,true,21],[2,true,23,3,false,23],[2,true,41,1,false,41],[3,false,10,4,true,10],[3,false,24,2,true,24],[3,false,31,4,true,31],[4,true,9,3,false,9],[4,true,30,3,false,30],[5,false,3,0,true,3]],"oligos":[{"id_num":4,"idx5p":0,"is_5p_fwd":true,"is_circular":false,"sequence":null,"name":"oligo3632","color":"#0066cc","length":20,"is_visible":true},{"id_num":3,"idx5p":30,"is_5p_fwd":false,"is_circular":true,"sequence":null,"name":"oligo8000","color":"#f7931e","length":192,"is_visible":true},{"id_num":3,"idx5p":41,"is_5p_fwd":false,"is_circular":false,"sequence":null,"name":"oligo0160","color":"#0066cc","length":22,"is_visible":true},{"id_num":5,"idx5p":41,"is_5p_fwd":false,"is_circular":false,"sequence":null,"name":"oligo7152","color":"#0066cc","length":6,"is_visible":true},{"id_num":0,"idx5p":0,"is_5p_fwd":true,"is_circular":false,"sequence":null,"name":"oligo8896","color":"#0066cc","length":3,"is_visible":true},{"id_num":5,"idx5p":2,"is_5p_fwd":false,"is_circular":false,"sequence":null,"name":"oligo1168","color":"#333333","length":3,"is_visible":true}],"instance_properties":[{"slice:position":[0.0,0.0],"grid:position":[0.0,0.0],"path:position":[-12.994158258098764,-4.331386086032921]}],"uuid":"7029b213616f4ab5a1adcbf0d3a59edb"}],"modifications":{}}
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mrdna/readers/test/test_insert.sc 0 → 100644
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