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josephhughes/Clusters.txt

Created October 7, 2015 14:10
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Generating a circular plot showing reassortment using the ETE toolkit
Raw
Clusters.txt
#Name Seg1 Seg2 Seg3 Seg4 Seg5 Seg6 Seg7 Seg8 Seg9 Seg10
1-8FRA2008-27 15 4 16 1 11 3 1 19 1 14
1-8FRA2008-28 15 4 16 1 11 3 1 19 1 14
1-8FRA2008-29 15 4 16 1 11 3 1 19 1 14
10RSArrrr-10 ? ?
11RSArrrr-11 15 6
12RSArrrr-12 ? ?
13RSArrrr-13 ? ?
14CAR1982-04 ? ? 1 1 1 ? ? 2 1 1
14POL2012-01 3 14 15 2 2 13 5 7 4 14
14RSArrrr-14 3 14 15 2 2 13 5 7 ? 14
14RUS2011-01 3 14 15 2 2 13 5 12 4 7
14SPA2012-01 3 14 15 2 2 13 5 7 4 14
15AUSDPP192 11 ? ? 5 7 ? ? ? ? 8
15ISR2006-11 3 8 8 8 2 11 ? 10 4 14
15RSArrrr-15 ? 8 8 8 ? 11 ? 12 4 7
16AUSDPP965 ? ? ? 5 ? 10 ? 13 12 8
16CHINABN96-16 2 17 2 12 9 17 15 17 15 12
16COR2004-01 2 17 2 12 9 17 15 17 15 12
16CYP2004-01 13 17 2 12 4 17 18 1 15 2
16CYP2006-01 10 17 7 1 4 17 18 1 11 1
16CYP2010-03 13 17 2 12 4 17 18 1 15 2
16GRE1999-13 2 17 2 12 12 17 18 1 16 2
16GRE2008-10 2 17 2 12 12 17 18 1 16 2
16IND-Goat-2010-Hisar 13 17 4 10 10 17 7 1 16 4
16ISR2001-18 2 17 2 12 9 17 15 17 15 12
16ISR2008-03 10 17 7 1 4 17 18 1 11 1
16NIG1982-10 ? ? 1 1 1 14 12 ? ? 14
16RSArrrr-16 2 17 2 12 9 17 15 17 15 12
16RSAvvvv-16 2 17 2 12 9 17 15 17 15 12
16TUR2000-01 2 17 2 12 12 17 18 1 16 2
17RSArrrr-17 ? ?
18RSArrrr-18 ? ?
19RSArrrr-19 13 ?
1ALG2006-01 1 1 1 1 1 1 1 20 1 1
1ALG2006-04 1 1 1 1 1 1 1 20 1 1
1ALG2008-10 1 1 1 1 1 1 1 20 1 1
1AUSCSIRO156 11 ? 12 7 ? ? 11 13 12 6
1CAR1982-01 14 ? 1 1 1 1 3 ? 1 1
1CHINASZ97-01 3 7 3 1 2 8 1 5 6 13
1FRA2007-18 1 1 1 1 1 1 1 20 1 1
1FRA2008-21 1 1 1 1 1 1 1 20 1 1
1FRA2008-22 1 1 1 1 1 1 1 20 1 1
1FRA2008-23 1 1 1 1 1 1 1 20 1 1
1FRA2008-24 15 1 16 1 1 3 1 20 1 1
1FRA2008-25 1 1 1 1 1 1 1 20 1 1
1FRA2008-26 1 1 1 1 1 1 1 20 1 1
1GIB2007-06 1 1 1 1 1 1 1 20 1 1
1GRE2001-01 13 6 11 12 4 7 13 1 15 2
1GRE2001-06 13 6 11 12 4 7 13 1 15 2
1GRE2001-10 13 6 11 12 4 7 13 1 15 2
1IND1992-01 12 6 4 10 12 7 9 1 ? 4
1LIB2007-06 1 1 17 1 1 1 1 2 1 1
1MOR2006-06 1 1 1 1 1 1 1 20 1 1
1MOR2007-01 1 1 1 1 1 1 1 20 1 1
1MOR2007-02 1 1 1 1 1 1 1 20 1 1
1MOR2007-03 1 1 1 1 1 1 1 20 1 1
1MOR2007-04 1 1 1 1 1 1 1 20 1 1
1MOR2009-01 1 1 1 1 1 1 1 20 1 1
1MOR2009-04 1 1 1 1 1 1 1 20 1 1
1MOR2009-06 1 1 1 1 1 1 1 20 1 1
1RSArrrr-01 3 7 3 1 2 8 1 5 6 13
1RSAvvvv-01 3 ? 5 ? 2 8 ? 4 6 3
1SPA2007-04 1 1 1 1 1 1 1 20 1 1
1SPA2007-05 1 1 1 1 1 1 1 20 1 1
1SPA2008-01 1 1 1 1 1 1 1 20 1 1
1SPA2009-01 1 1 1 1 1 1 1 20 1 1
1SUD1987-01 ? 7 ? 1 5 ? 1 15 9 13
1TUN2007-01 1 1 1 1 1 1 1 20 1 1
20RSArrrr-20 ? ?
21RSArrrr-21 ? 10
22RSArrrr-22 ? ?
23RSArrrr-23 ? ?
24RSArrrr-24 12 ?
25SWI2008-01 ? ?
26KUW2010-02 ? ?
2AUSCooktown2010 12 10 9 9 6 12 8 8 7 11
2AUSv72912008 12 10 9 9 6 12 8 8 7 11
2FRA2001-01 1 19 17 1 1 16 2 2 1 1
2FRA2001-03 1 19 17 1 1 16 2 2 1 1
2FRA2001-06 1 19 17 1 1 16 2 2 1 1
2IND1982-01 13 ? 4 ? 10 ? 9 1 16 4
2IND2003-02 5 19 13 3 3 5 4 16 5 14
2ISR2001-17 3 19 15 11 3 5 4 ? 6 14
2ITL2002-02 1 19 17 1 1 16 2 2 1 1
2ITL2002-07 1 19 17 1 1 16 2 2 1 1
2RSArrrr-02 5 19 13 3 3 5 4 16 5 14
2RSAvvvv-02 5 19 13 3 3 5 4 16 5 14
2SAD2001-01 1 19 17 1 1 16 2 2 1 1
2SAD2001-03 1 19 17 1 1 16 2 2 1 1
2SAD2002-02 1 19 17 1 1 16 2 2 1 1
2SPA2005-01 14 19 14 3 3 5 6 16 13 5
2SUD1983-05 ? 19 1 1 11 16 2 20 1 1
2TAIWANstrainKM 12 ? ? 9 12 12 ? 1 10 11
2TUN2000-01 1 19 17 1 1 16 2 2 1 1
3AUSDPP973 11 ? 12 5 7 ? ? ? 12 6
3CYP1958-01 9 11 15 6 10 14 10 15 13 9
3IND2003-08 13 ? 4 10 10 ? ? 1 16 2
3RSArrrr-03 9 11 15 6 10 14 10 15 13 9
4CHINAYTS-4 12 ? 4 9 12 ? ? ? 10 11
4CYP1969-01 4 2 3 2 11 4 16 18 2 13
4CYP2004-03 4 2 3 2 11 4 16 18 2 13
4CYP2011-01 15 2 16 12 12 18 1 1 14 14
4CYP2011-02 15 2 16 12 12 18 1 1 14 14
4CYP2011-03 15 2 16 12 12 18 1 1 14 14
4CYP2011-04 15 2 16 12 12 18 1 1 14 14
4CYP2011-05 15 2 16 12 12 18 1 1 14 14
4EGY1977-01 14 9 14 11 8 6 6 9 13 5
4FRA2003-01 1 18 17 1 1 18 3 3 1 1
4FRA200303.124 1 18 17 1 1 18 3 3 1 1
4FRA2003200 1 18 17 1 1 18 3 3 1 1
4GRE1979-01 4 2 3 2 11 4 16 18 2 13
4GRE1999-24 4 2 3 2 11 4 16 18 2 13
4GRE1999-26 4 2 3 2 11 4 16 18 2 13
4GRE2000-07 4 2 3 2 11 4 16 18 2 13
4GRE2000-08 4 2 3 2 11 4 16 18 2 13
4GRE2012-01 15 2 16 12 12 18 1 1 14 14
4GRE2012-02 15 2 16 12 12 18 1 1 14 14
4GRE2012-03 15 2 16 12 12 18 1 1 14 14
4ISR2006-12 10 2 7 1 9 4 17 17 11 13
24ISR2008-02 3 12 17 1 2 18 1 10 1 1
4MOR2004-02 1 18 17 1 1 18 3 3 1 1
4MOR2009-07 1 18 17 1 1 18 1 20 1 1
4MOR2009-08 1 18 17 1 1 18 1 20 1 1
4MOR2009-09 1 18 17 1 1 18 1 20 1 1
4MOR2009-10 15 18 16 1 1 18 1 19 1 1
4RSArrrr-04 4 2 3 2 11 4 16 18 2 13
4SPA2003-03 1 18 17 1 1 18 3 3 1 1
4SPA2004-02 1 18 17 1 1 18 3 3 1 1
4SPA2005-02 1 18 17 1 1 18 3 3 1 1
4SPA2010-01 1 18 17 1 1 18 1 20 1 1
4SUD1983-01 15 18 1 1 11 18 3 2 9 14
5RSArrrr-05 ? ?
6BT2-03 8 5 10 4 3 9 12 11 8 3
6NET2008-05 6 5 6 11 2 14 14 5 2 14
6P635 8 5 10 4 3 9 12 11 8 3
6RSArrrr-06 6 5 6 11 2 14 14 5 2 3
6RSAvvvv-06 6 5 6 11 2 14 14 5 2 3
6vac5011-60E 6 5 6 11 2 14 14 5 2 3
7RSArrrr-07 ? ?
8GRE2008-01 15 4 16 1 11 3 1 19 1 14
8ISR2008-13 15 4 16 1 11 3 1 19 1 14
8NET2006-04 15 4 16 1 11 3 1 19 1 14
8NET2007-01 15 4 16 1 11 3 1 19 1 14
8NET2008-03 15 4 16 1 11 3 1 19 1 14
8RSA1998-01 15 13 ? 4 5 ? ? 2 4 1
8RSArrrr-08 ? ? ? ? ? ? 17 4 3 ?
8UKG2007-06 15 4 16 1 11 3 1 19 1 14
8NET2006-11 15 4 16 1 11 3 1 19 1 14
9AUSDP0837 11 ? 12 7 ? ? 11 ? 12 6
9BOS2002-02 2 3 2 12 12 2 18 1 16 2
9BUL1999-01 2 3 2 12 12 2 18 1 16 2
9GRE1998-01 2 3 2 12 12 2 18 1 16 2
9GRE1999-06 2 3 2 12 12 2 18 1 16 2
9GRE1999-31 2 3 2 12 12 2 18 1 16 2
9INDstrainBBF 2 3 4 10 10 2 7 1 16 4
9INDstrainR1-2007 13 3 4 10 10 2 7 1 16 4
9ITL2003-01 14 16 5 2 2 15 17 4 3 3
9KOS2001-01 2 3 2 12 12 2 18 1 16 2
9KOS2001-03 2 3 2 12 12 2 18 1 16 2
9LIB2008-03 7 16 17 1 10 15 1 14 1 1
9LIB2008-08 7 16 17 1 10 15 1 14 1 1
9RSArrrr-09 14 16 5 2 2 15 17 4 3 3
9RSAvvv1-09 14 16 5 2 2 15 17 4 3 3
9SER2001-01 2 3 2 12 12 2 18 1 16 2
9TUR1998-02 2 3 2 12 12 2 18 1 16 2
9TUR2000-03 2 3 2 12 12 2 18 1 16 2
9TUR2001-02 2 3 2 12 12 2 18 1 16 2
BTV-11_DE 14 15 14 11 2 6 17 6 3 10
BTV-11_REF 14 15 14 11 2 6 17 6 3 10
BTV-11_VAC 14 15 14 11 2 6 17 6 3 10
BTV-2IT_L_ 1 19 17 1 1 16 2 2 1 1
BTV-2RSA_vacc_ 5 19 13 3 3 5 4 16 5 14
BTV-2RSA_WT_ 5 19 13 3 3 5 4 16 5 14
BTV-4IT_L_ 1 18 17 1 1 18 3 3 1 1
BTV-4RSA_vacc_ 14 9 14 11 8 6 6 9 13 5
BTV-9IT_L_ 2 3 2 12 12 2 18 1 16 2
BTV-9RSA_vacc_ 14 16 5 2 2 15 17 4 3 3
BTV-9RSA_WT_ 14 16 5 2 2 15 17 4 3 3
Raw
mappingClusters.py
from ete2 import Tree, TextFace, NodeStyle, TreeStyle, faces, AttrFace, CircleFace
# To operate with numbers efficiently
import numpy
from collections import defaultdict
import collections
import colorsys
import re
def rgb2hex(rgb):
return'#%02x%02x%02x'% rgb
def hls2hex(h, l, s):
return rgb2hex(tuple(map(lambda x: int(x*255), colorsys.hls_to_rgb(h, l, s))))
# Loads serotype info
try:
infile = open('Clusters.txt', "r")
except:
print "Invalid file. Please enter a correct file."
first_line = infile.readline()
first_line = first_line.rstrip()
segments = first_line.split("\t")
segments.pop(0)
# print segments
N = 21
print N
hexcolors = []
HSV_tuples = [(x*1.0/N, 0.5, 0.5) for x in range(N)]
for color in HSV_tuples:
print color[0]
hexcolor = hls2hex(color[0],color[1],color[2])
print hexcolor
hexcolors.append(hexcolor)
#RGB_tuples = hls2hex(tuple(map(lambda x: colorsys.hsv_to_rgb(*x), HSV_tuples)))
# Grey box color
hexcolors.append('#D3D3D3')
d={}
myhash = collections.defaultdict(dict)
all_val = []
for line in infile:
line = line.rstrip()
serotypes = line.split("\t")
seqid = serotypes.pop(0)
for idx, val in enumerate(serotypes):
print idx, val
all_val.append(val)
# print segments[idx]
if val.isdigit():
i = int(val)
elif val is '?':
i = 21
else:
i = 0
print segments[idx]
myhash[seqid][segments[idx]] = i
print i, hexcolors[i]
infile.close()
# print myhash
f = open('Seg-2.newick','r')
newickstring = f.read()
t = Tree(newickstring)
print "Tree after DELETING the nodes"
print t.get_ascii(show_internal=True)
segs = ["Seg1", "Seg2", "Seg3", "Seg4", "Seg5", "Seg6", "Seg7", "Seg8", "Seg9", "Seg10"]
print segments
for k in myhash:
print k
cnt = 0
for x in segs:
#print cnt
if x in myhash[k]:
if myhash[k][x]>0:
RGBcolor = hexcolors[myhash[k][x]]
col = segs.index(x)
print k , x, col, myhash[k][x], RGBcolor
if myhash[k][x]==21:
F = TextFace("?")
else:
F = TextFace(myhash[k][x])
# Set some attributes
#F.margin_top = 5
F.margin_right = 5
F.margin_left = 5
#F.margin_bottom = 5
F.border.width = 2
F.border.color = "white"
F.background.color = RGBcolor
#F.inner_background.color = RGBcolor
P = CircleFace(radius=14, color=RGBcolor, style="circle")
P.opacity = 1
n = t&k
n.add_face(F, column=col, position="aligned")
cnt += 1
ts = TreeStyle()
#ts.show_leaf_name = True
ts.show_leaf_name = False
##ts.show_scale = False
ts.show_scale = True
ts.draw_aligned_faces_as_table = True
# Set our custom layout function
for n in t.traverse():
nstyle = NodeStyle()
nstyle["fgcolor"] = "black"
nstyle["size"] = 0
n.set_style(nstyle)
# for circular
ts.mode = "c"
ts.allow_face_overlap=False
ts.draw_guiding_lines=False
# remove ts.scale for circular
ts.scale = 0.014
t.render("BTV_circularNoLabel.pdf", tree_style=ts, h=240, units="mm")
Raw
Seg-2.newick
(((((((((((1CAR1982-01:107.56225618684064,(((((((1FRA2008-25:1.1962150511248684,((1FRA2008-21:0.5896744029573684,1FRA2008-24:0.759421151759617):0.16947484033746552,1FRA2008-22:0.8440226176960905):0.35219243342877427):0.8540138066325431,1FRA2008-23:2.1351022321584407):2.198679125560825,(((1FRA2008-26:1.4275113190400708,(1SPA2009-01:1.4059685376189952,1SPA2008-01:0.4066530003156936):0.6868405226942773):1.260980274485875,1FRA2007-18:1.7714256569528493):0.8377976114488304,1SPA2007-05:2.1902180208544912):0.8896276763583639):2.7245619963014462,(1SPA2007-04:4.106041523359591,1GIB2007-06:4.4400593193895):1.6983661701546833):2.195039301512537,(1MOR2007-02:5.6378012846242385,(((1MOR2007-04:0.7045182450868754,1MOR2007-01:0.7045182450868754):2.9073857915758845,1MOR2007-03:3.6119040366627733):1.2157526895973199,1ALG2008-10:6.166579838283719):0.8101445583641755):2.4437812340164875):2.4065015446701246,(((1MOR2009-06:1.700497850304643,(1MOR2009-04:0.564441459718203,1MOR2009-01:0.5644414597182021):1.1360563905863992):3.6285584919350367,1MOR2006-06:2.4105074031569558):3.503769213298428,(1ALG2006-04:4.8353529538328575,(1TUN2007-01:4.341194204174392,1ALG2006-01:3.2570052924703212):1.5783476613625904):0.9119147646075376):3.82637418196836):53.10198063262838,1LIB2007-06:63.674938070340204):68.7196247557888):43.79271423366228,(1SUD1987-01:112.87292872640379,(1CHINASZ97-01:61.429705244521095,1RSArrrr-01:41.17347860817399):61.61160130529136):42.980330537357105):60.87108958494815,1RSAvvvv-01:173.16828135623166):2129.3881469985718,((((1GRE2001-10:1.173416623102252,1GRE2001-06:1.255552146716182):5.004989695182928,1GRE2001-01:6.093418866767964):103.6729280223459,1IND1992-01:100.18124536047996):489.0909716576167,1AUSCSIRO156:576.5219318253085):1761.7575729199941):3207.5092719091367,((((((2SPA2005-01:5.853620144319169,2ISR2001-17:1.4430566033654646):12.40958759836779,2RSAvvvv-02:6.153185257919837):37.69654662963377,(BTV-2RSA_WT_:4.2108791050559375,(2IND2003-02:25.139051614548094,BTV-2RSA_vacc_:-5.807381191875123):23.071827490508007):5.665370818257202):5.306682095496278,2RSArrrr-02:15.182932018809403):85.92396455328378,(2SUD1983-05:73.14980424104493,(((2FRA2001-01:2.285601109562343,2TUN2000-01:0.8729841805181895):0.8424949650126425,BTV-2IT_L_:2.046645013657713):2.4216398673170403,((2ITL2002-02:0.4858856760707617,2ITL2002-07:0.4858856760707617):3.180871774379165,((((2FRA2001-06:0.5421587219067607,2FRA2001-03:0.5421587219067447):0.44500508655045046,2SAD2002-02:1.3212956816033739):0.4416617346663436,2SAD2001-01:1.6780840418687237):0.8064645141162501,2SAD2001-03:2.484548555984979):0.6018986047092625):2.8822940287452266):85.34955495213056):52.29111012707841):2248.1117709415958,((2TAIWANstrainKM:146.73833470690712,(2AUSv72912008:6.243896409255516,2AUSCooktown2010:8.24252748386194):145.58136506014299):307.8904841423251,2IND1982-01:433.46260849102947):1938.5049752900486):3176.570109140748):2625.318914872818,((18RSArrrr-18:2059.4753187215783,(8RSArrrr-08:197.29886446352222,(((8NET2006-04:4.61436397647666,((8NET2007-01:1.2631456283282043,8NET2008-03:2.350072390819677):2.6225637341981347,8UKG2007-06:4.055456111328368):1.643096776852401):1.4627681220921502,8NET2006-11:3.0357576031229634):4.004866014503641,((((1-8FRA2008-28:1.3090589530475611,1-8FRA2008-27:1.3090589530475611):1.3509686846720053,1-8FRA2008-29:2.7449010121206427):4.547260854288023,8GRE2008-01:7.040279593992449):1.3570979282138076,8ISR2008-13:8.816382769753616):3.518980618244532):256.3831907857681):1861.8109735814692):1297.340642224363,23RSArrrr-23:3356.4726550037585):4772.658580183301):1842.4003471749438,(((3IND2003-08:239.74682430815412,3AUSDPP973:222.7475087708515):4020.110800892839,((13RSArrrr-13:2384.9180784434525,(16NIG1982-10:1451.5164732333265,(16AUSDPP965:334.570259624506,(((16COR2004-01:17.64345354701061,16CHINABN96-16:9.643453547010676):41.11942582018277,(16RSArrrr-16:7.535758733062266,(16ISR2001-18:30.32025142145338,16RSAvvvv-16:-0.10224934919550321):17.886394831572503):7.22712063413109):104.44067580352713,((16TUR2000-01:23.512064310243417,((16GRE1999-13:5.930346235786381,16GRE2008-10:15.099408521891771):6.23285999159398,((16CYP2004-01:2.594216920268032,16CYP2010-03:9.343019110548628):2.030710765510916,(16CYP2006-01:2.296548323869187,16ISR2008-03:4.297917249262739):4.992194100673128):12.042157163549895):10.513813592787741):44.35367752481715,16IND-Goat-2010-Hisar:77.86437290966684):91.33781333566021):189.36807337917926):1120.7792047108023):956.5692985708365):925.9950463099776,(3CYP1958-01:30.826929947879115,3RSArrrr-03:17.577376988314214):3277.335633687993):904.9445004475588):3756.8408994374986,(21RSArrrr-21:3719.972814720968,(((6P635:37.86866809286623,6BT2-03:29.174701363812417):140.97815932253587,(6RSArrrr-06:8.134678204781608,((6NET2008-05:2.656244494260587,6RSAvvvv-06:0.21909234172323622):3.259654613865516,6vac5011-60E:3.283315618632928):52.47203029446545):174.35115179175975):2204.536202361135,(14CAR1982-04:327.61840942981763,(14RSArrrr-14:32.63589309963722,((14POL2012-01:1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