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draw.final.scaff.orders.py
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draw.final.scaff.orders.py
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from matplotlib import pyplot as plt
import sys
from common import *
from pprint import pprint
import maps
final_maps, lendict = maps.final_maps, maps.lendict
def plot_ord(scaff_ord, lendict, ypos):
lenlist = [lendict[i] for i in map(lambda s: s[1:], scaff_ord)]
colorlist = []
for i in scaff_ord:
if '-' in i: colorlist.append('r')
else: colorlist.append('g')
pos = 0
out = {}
for i in range(len(scaff_ord)):
scaff, lenx, col = scaff_ord[i], lenlist[i], colorlist[i]
plt.plot([pos, pos+lenx], [ypos, ypos], color=col, linewidth=2, alpha=.74)
plt.plot([pos+lenx, pos+lenx], [ypos+1, ypos-1], color='k', alpha=.74)
midpoint = (lenx * .5) + pos
if (i+1) % 2:
plt.text(midpoint-1e5,ypos-2, s=scaff, rotation=90, size=7)
else:
plt.text(midpoint-1e5, ypos+2, s = scaff, rotation=90, size=7)
out[scaff] = midpoint
pos+=lenx
plt.plot([0, 0], [ypos+1, ypos-1], color='k', alpha=.74)
return out
def connections(scaff_ord1, scaff_ord2, mids1, mids2, y1, y2):
#pprint(scaff_ord1)
#pprint(scaff_ord2)
#pprint(mids1)
#pprint(mids2)
# def amend_mids(x, newx):
# for i in x.keys():
# print i, x[i]
# newx[i] = x[i]
# if '-' in x:
# j = i.replace('-', "+")
# newx[j] = x[i]
# else:
# j = i.replace('+', "-")
# newx[j] = x[i]
# print j, newx[i], newx[j]
# return(newx)
# print len(mids1), len(mids2)
# mids1x = amend_mids(mids1, {})
# mids2x = amend_mids(mids2, {})
def flip(x):
if '-' in x: return x.replace('-', '+')
elif '+' in x: return x.replace('+', '-')
#print len(mids1), len(mids2)
#print
for i in scaff_ord1:
plotIT = 0
if i in mids1:
m1 = mids1[i]
plotIT+=1
elif flip(i) in mids1:
m1 = mids1[flip(i)]
plotIT+=1
if i in mids2:
m2 = mids2[i]
plotIT+=1
elif flip(i) in mids2:
m2 = mids2[flip(i)]
plotIT+=1
#print i
#pprint(mids1)
#pprint(mids2)
#print plotIT
if plotIT > 1: plt.plot([m1, m2], [y1, y2], color='k', alpha=.2)
pops = 'v2_genome IMPR_rils IM_ase IM_mse LVR SF SWC'.split()
#pprint(final_maps.keys())
for chrom in '1 2 3 4 5 6 7 8 9 10 11 12 13 14'.split():
p = pops
yidx = 100
mx = 0
p0_mid = plot_ord(final_maps[p[0]][chrom], lendict, yidx)
p1_mid = plot_ord(final_maps[p[1]][chrom], lendict, yidx-10)
p2_mid = plot_ord(final_maps[p[2]][chrom], lendict, yidx-20)
p3_mid = plot_ord(final_maps[p[3]][chrom], lendict, yidx-30)
p4_mid = plot_ord(final_maps[p[4]][chrom], lendict, yidx-40)
p5_mid = plot_ord(final_maps[p[5]][chrom], lendict, yidx-50)
p6_mid = plot_ord(final_maps[p[6]][chrom], lendict, yidx-60)
for i in [p0_mid, p1_mid, p2_mid, p3_mid, p4_mid, p5_mid, p6_mid]:
if max(i.values()) > mx: mx = max(i.values())
no_sign = lambda s: [i.replace('-','').replace('+','') for i in s]
complete = lambda s, ovlp: [i for i in s if i.replace('-','').replace('+','') in ovlp]
m0, m1, m2, m3, m4, m5, m6 = map(no_sign, [final_maps[p[i]][chrom] for i in range(7)])
f0, f1, f2, f3, f4, f5, f6 = [final_maps[p[i]][chrom] for i in range(7)]
ovlp01, ovlp12, ovlp23, ovlp34, ovlp45, ovlp56 = set(m0).intersection(m1), set(m1).intersection(m2), set(m2).intersection(m3), set(m3).intersection(m4), set(m4).intersection(m5), set(m5).intersection(m6)
m0complete, m1complete = complete(f0, ovlp01), complete(f1, ovlp01)
print m0, m1, ovlp01, m0complete, m1complete
connections(m0complete, m1complete, p0_mid, p1_mid, yidx, yidx-10)
m1complete, m2complete = complete(f1, ovlp12), complete(f2, ovlp12)
connections(m1complete, m2complete, p1_mid, p1_mid, yidx-10, yidx-20)
m2complete, m3complete = complete(f2, ovlp23), complete(f3, ovlp23)
connections(m2complete, m3complete, p2_mid, p3_mid, yidx-20, yidx-30)
m3complete, m4complete = complete(f3, ovlp34), complete(f4, ovlp34)
connections(m3complete, m4complete, p3_mid, p4_mid, yidx-30, yidx-40)
m4complete, m5complete = complete(f4, ovlp45), complete(f5, ovlp45)
connections(m4complete, m5complete, p4_mid, p5_mid, yidx-40, yidx-50)
m5complete, m6complete = complete(f5, ovlp56), complete(f6, ovlp56)
connections(m5complete, m6complete, p5_mid, p6_mid, yidx-50, yidx-60)
plt.xlim(xmin=-1250000, xmax = mx+1250000)
plt.title('Chromosome '+ chrom)
plt.show()
for chrom in '1 2 3 4 5 6 7 8 9 10 11 12 13 14'.split():
yidx = 100
mx = 0
for p in pops[1:]:
v2_mid = plot_ord(final_maps['v2_genome'][chrom], lendict, yidx)
p_mid = plot_ord(final_maps[p][chrom], lendict, yidx-10)
#m1, m2 = [i.replace('-','').replace('+','') for i in v2_mid.keys()], [i.replace('-','').replace('+','') for i in p_mid.keys()]
#for i in v2_mid.keys():
# if i not in p_mid: del(v2_mid[i])
#for i in p_mid.keys():
# if i not in v2_mid: del(p_mid[i])
#pprint([(i, v2_mid[i]) for i in final_maps['v2_genome'][chrom]])
#pprint([(i, p_mid[i]) for i in final_maps[p][chrom]])
#print '*'*40
if max(v2_mid.values()) > mx: mx = max(v2_mid.values())
if max(p_mid.values()) > mx: mx = max(p_mid.values())
#print map(len,[v2_mid, p_mid])
#print map(len, [final_maps['v2_genome'][chrom], final_maps[p][chrom]])
#print
m1, m2 = [i.replace('-','').replace('+','') for i in final_maps['v2_genome'][chrom]], [i.replace('-','').replace('+','') for i in final_maps[p][chrom]]
ovlp = set(m1).intersection(m2)
v2complete = [i for i in final_maps['v2_genome'][chrom] if i.replace('-','').replace('+','') in ovlp]
pcomplete = [i for i in final_maps[p][chrom] if i.replace('-','').replace('+','') in ovlp]
#print map(len, [v2complete, pcomplete])
connections(v2complete, pcomplete, v2_mid, p_mid, yidx, yidx-10)
yidx-=24
plt.xlim(xmin=-1250000, xmax = mx+1250000)
plt.title('Chromosome '+ chrom)
plt.show()
# z = 0
# for i in first:
# #print i, z
# if z == 1:
# orig = i[0].replace('scaffold order=', '').split()
# z+=1
# if 'individual=1 fitness=' in i[0]:
# z +=1
#
#
# fbest = [idx for idx, i in enumerate(first) if 'individual=1 fitness=' in i[0]]
# sbest = [idx for idx, i in enumerate(second) if 'individual=1 fitness=' in i[0]]
# pprint(sbest)
#
# origfitf, origfits = first[fbest[0]][0].replace('individual=1 fitness=', ''), second[sbest[0]][0].replace('individual=1 fitness=', '')
# ff, sf = first[fbest[-1]][0].replace('individual=1 fitness=', ''), second[sbest[-1]][0].replace('individual=1 fitness=', '')
#
# fend = first[fbest[-1]+1][0].replace('scaffold order=', '').split()
# send = second[sbest[-1]+1][0].replace('scaffold order=', '').split()
#
# print orig, origfitf, origfits
# print fend, ff
# print send, sf
# orig_mids = plot_ord(orig, lendict, 20)
# first_mids = plot_ord(fend, lendict, 10)
# second_mids = plot_ord(send, lendict, 0)
# connections(orig, fend, orig_mids, first_mids, 20, 10)
# connections(fend, send, first_mids, second_mids, 10, 0)
#