def parse_legacy(obj,mymodel):
"""
take a loaded legacy dictionary, decides between current filetype and legacy caDNAno 1.0 filetype
Parameters
----------
obj: dictionary object generated from a JSON file
See Also
--------
Examples
--------
"""
from assembly import Assembly
from part import Part
my_assembly = Assembly()
my_part = Part(my_assembly.createPartID())
vhelixlist = obj["vstrands"] # should rename to
name = obj["name"] # placeholder, not really used
# create dictionaries (keyed by vstrand #) of
# row/col, scaf array, stap array
vhToRowCol = {}
vhToScaf = {}
vhToStap = {}
vhNums = []
for helix in vhelixlist: # strand should be helix
num = helix["num"] # helix number
vhNums.append(num) # keep track of a list of helix numbers
row = helix["row"] # slice row for this helix
col = helix["col"] # slice column
scaf = helix["scaf"] # array of scaffold points
stap = helix["stap"] # array of staple pointers
vhToRowCol[num] = [row,col]
vhToScaf[num] = scaf
vhToStap[num] = stap
# extract scaffold 5' breakpoints
scafBreaks = []
for vh in vhNums:
scaf = vhToScaf[vh]
for i in range(len(scaf)):
base = scaf[i]
if (base[1] == -1) & (base[3] != -1):
scafBreaks.append([vh, i])
# extract staple 5' breakpoints
stapBreaks = []
for vh in vhNums:
stap = vhToStap[vh]
for i in range(len(stap)):
base = stap[i]
if (base[1] == -1) & (base[3] != -1):
stapBreaks.append([vh, i])
# extract scaffold paths, starting at 5' breakpoints
scafPaths = []
for scafBreak in scafBreaks:
path = []
[curr_vh, curr_base] = scafBreak
[next_vh, next_base] = vhToScaf[curr_vh][curr_base][2:4]
while next_base != -1:
[row, col] = vsToRowCol[curr_vs]
[x, y, z] = getScafCoord(row,col,curr_base)
path.append([curr_vs,curr_base,[x, y, z]])
# append midpoint for crossover
if (curr_vs != next_vs) & (curr_base == next_base):
(x1,y1,z1) = getScafCoord(row,col,curr_base)
[nextrow, nextcol] = vsToRowCol[next_vs]
(x2,y2,z2) = getScafCoord(nextrow,nextcol,next_base)
midxyz = [(x1+x2)/2,(y1+y2)/2,(z1+z2)/2]
path.append([curr_vs,curr_base,midxyz])
[curr_vs, curr_base] = [next_vs, next_base]
[next_vs, next_base] = vsToScaf[curr_vs][curr_base][2:4]
[row, col] = vsToRowCol[curr_vs]
[x, y, z] = getScafCoord(row,col,curr_base)
path.append([curr_vs,curr_base,[x, y, z]])
scafPaths.append(path)
# extract staple paths, starting at 5' breakpoints
stapPaths = []
for stapBreak in stapBreaks:
path = []
[curr_vs, curr_base] = stapBreak
[next_vs, next_base] = vsToStap[curr_vs][curr_base][2:4]
while next_base != -1:
[row, col] = vsToRowCol[curr_vs]
[x, y, z] = getStapCoord(row,col,curr_base)
path.append([curr_vs,curr_base, [x, y, z]])
# append midpoint for crossover
if (curr_vs != next_vs) & (curr_base == next_base):
(x1,y1,z1) = getStapCoord(row,col,curr_base)
[nextrow, nextcol] = vsToRowCol[next_vs]
(x2,y2,z2) = getStapCoord(nextrow,nextcol,next_base)
midxyz = [(x1+x2)/2,(y1+y2)/2,(z1+z2)/2]
path.append([curr_vs,curr_base,midxyz])
[curr_vs, curr_base] = [next_vs, next_base]
[next_vs, next_base] = vsToStap[curr_vs][curr_base][2:4]
[row, col] = vsToRowCol[curr_vs]
[x, y, z] = getStapCoord(row,col,curr_base)
path.append([curr_vs,curr_base, [x, y, z]])
stapPaths.append(path)
my_part.VHelix = vhelixlist
my_assembly.addPart(my_part)
return my_parts, my_assembly
