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+112
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3 files changed

+112
-112
lines changed

‎ald.py

-1
Original file line numberDiff line numberDiff line change
@@ -101,7 +101,6 @@ def ld_decay(c, chrsize, ac_subpops, popdict, pop2color, var, min_maf=0.1,
101101
"""
102102
"""
103103
lddict = {}
104-
fig, ax = plt.subplots()
105104
for x in ac_subpops.keys():
106105
acu = ac_subpops[x]
107106
pos = var.pos

‎allel_class.py

+1
Original file line numberDiff line numberDiff line change
@@ -66,6 +66,7 @@ def miss(self, genotypes, positions, prctmiss):
6666
"""
6767
"""
6868
misscount = genotypes.count_missing(axis=1)
69+
# .20 will remove sites with > 20% missing data
6970
missarray = misscount <= (genotypes.n_samples * prctmiss)
7071
# remove missing
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self.gt = genotypes.compress(missarray, axis=0)

‎kirfol.meta.txt.csv

+111-111
Original file line numberDiff line numberDiff line change
@@ -1,188 +1,188 @@
11
Population,ID,ChromForm,Karyotype,2Ra,2Rs,3Ra,3Rb,3La
22
Sabtenga,02-07119,Folonzo,10220,1,0,2,2,0
3-
Kuiti,00-01522,Kiribina,01000,0,1,0,0,0
3+
Kuiti,00-01522,Kiribina,1000,0,1,0,0,0
44
Koubri,00-03530,Folonzo,10220,1,0,2,2,0
5-
Koubri,00-01481,Kiribina,00000,0,0,0,0,0
6-
Ividie,02-06477,Kiribina,00101,0,0,1,0,1
7-
Dirze,02-07231,Kiribina,00000,0,0,0,0,0
8-
Kuiti,00-01397,Kiribina,01000,0,1,0,0,0
5+
Koubri,00-01481,Kiribina,0,0,0,0,0,0
6+
Ividie,02-06477,Kiribina,101,0,0,1,0,1
7+
Dirze,02-07231,Kiribina,0,0,0,0,0,0
8+
Kuiti,00-01397,Kiribina,1000,0,1,0,0,0
99
Vi,02-06681,Folonzo,NN21N,N,N,2,1,N
1010
La,02-07687,Folonzo,NN2NN,N,N,2,N,N
11-
Pehele,02-05622,Kiribina,00000,0,0,0,0,0
12-
Bagre,02-07329,Kiribina,00000,0,0,0,0,0
13-
Siby,02-06439,Kiribina,00000,0,0,0,0,0
11+
Pehele,02-05622,Kiribina,0,0,0,0,0,0
12+
Bagre,02-07329,Kiribina,0,0,0,0,0,0
13+
Siby,02-06439,Kiribina,0,0,0,0,0,0
1414
La,02-07709,Folonzo,20220,2,0,2,2,0
15-
Kuiti,00-01528,Kiribina,00000,0,0,0,0,0
16-
Kuiti,02-06213,Kiribina,00000,0,0,0,0,0
17-
Kuiti,00-01396,Kiribina,00000,0,0,0,0,0
15+
Kuiti,00-01528,Kiribina,0,0,0,0,0,0
16+
Kuiti,02-06213,Kiribina,0,0,0,0,0,0
17+
Kuiti,00-01396,Kiribina,0,0,0,0,0,0
1818
Koubri,00-03541,Folonzo,10110,1,0,1,1,0
19-
Pehele,02-05628,Kiribina,00100,0,0,1,0,0
19+
Pehele,02-05628,Kiribina,100,0,0,1,0,0
2020
Koubri,00-01490,Folonzo,NN11N,N,N,1,1,N
21-
Kuiti,00-01518,Kiribina,00000,0,0,0,0,0
22-
Koubri,01-04358,Folonzo,00111,0,0,1,1,1
21+
Kuiti,00-01518,Kiribina,0,0,0,0,0,0
22+
Koubri,01-04358,Folonzo,111,0,0,1,1,1
2323
Kuiti,00-03426,Folonzo,10210,1,0,2,1,0
2424
Pehele,02-05666,Folonzo,002N0,0,0,2,N,0
25-
Koubri,00-01433,Kiribina,00000,0,0,0,0,0
26-
Kuiti,00-01398,Kiribina,00000,0,0,0,0,0
25+
Koubri,00-01433,Kiribina,0,0,0,0,0,0
26+
Kuiti,00-01398,Kiribina,0,0,0,0,0,0
2727
Koubri,00-01426,Kiribina,0000N,0,0,0,0,N
28-
Kuiti,00-01523,Kiribina,00000,0,0,0,0,0
29-
Ipendo,01-05798,Kiribina,00000,0,0,0,0,0
28+
Kuiti,00-01523,Kiribina,0,0,0,0,0,0
29+
Ipendo,01-05798,Folonzo,0,0,0,0,0,0
3030
La,02-07745,Folonzo,NN21N,N,N,2,1,N
31-
Dirze,02-07299,Kiribina,00000,0,0,0,0,0
31+
Dirze,02-07299,Kiribina,0,0,0,0,0,0
3232
Sabtenga,02-07108,Folonzo,10220,1,0,2,2,0
3333
Kuiti,02-06223,Folonzo,20221,2,0,2,2,1
34-
Dirze,02-07029,Kiribina,00000,0,0,0,0,0
35-
Koubri,00-01631,Kiribina,00000,0,0,0,0,0
36-
Bagre,02-07350,Kiribina,00000,0,0,0,0,0
34+
Dirze,02-07029,Kiribina,0,0,0,0,0,0
35+
Koubri,00-01631,Kiribina,0,0,0,0,0,0
36+
Bagre,02-07350,Kiribina,0,0,0,0,0,0
3737
Sabtenga,02-07195,Folonzo,20220,2,0,2,2,0
38-
Pehele,02-06377,Folonzo,00210,0,0,2,1,0
39-
Bagre,02-07327,Kiribina,01000,0,1,0,0,0
40-
Ividie,02-06649,Kiribina,00000,0,0,0,0,0
38+
Pehele,02-06377,Folonzo,210,0,0,2,1,0
39+
Bagre,02-07327,Kiribina,1000,0,1,0,0,0
40+
Ividie,02-06649,Kiribina,0,0,0,0,0,0
4141
La,02-07553,Folonzo,10210,1,0,2,1,0
42-
Kuiti,02-06217,Kiribina,00100,0,0,1,0,0
42+
Kuiti,02-06217,Kiribina,100,0,0,1,0,0
4343
Kuiti,02-06212,Folonzo,10210,1,0,2,1,0
44-
Koubri,00-01630,Kiribina,00000,0,0,0,0,0
45-
Pehele,02-05656,Kiribina,00000,0,0,0,0,0
46-
Pehele,02-06345,Kiribina,00000,0,0,0,0,0
44+
Koubri,00-01630,Kiribina,0,0,0,0,0,0
45+
Pehele,02-05656,Kiribina,0,0,0,0,0,0
46+
Pehele,02-06345,Kiribina,0,0,0,0,0,0
4747
Vi,02-06871,Folonzo,1020N,1,0,2,0,N
4848
Ipendo,01-06387,Folonzo,10110,1,0,1,1,0
49-
Vi,02-06861,Kiribina,00000,0,0,0,0,0
49+
Vi,02-06861,Kiribina,0,0,0,0,0,0
5050
Sabtenga,02-07111,Folonzo,NN21N,N,N,2,1,N
51-
Pehele,02-06409,Kiribina,00000,0,0,0,0,0
51+
Pehele,02-06409,Kiribina,0,0,0,0,0,0
5252
La,02-07539,Folonzo,NN221,N,N,2,2,1
53-
Kuiti,00-01525,Kiribina,00000,0,0,0,0,0
53+
Kuiti,00-01525,Kiribina,0,0,0,0,0,0
5454
Sabtenga,02-07106,Folonzo,20120,2,0,1,2,0
55-
Koubri,00-01488,Kiribina,00100,0,0,1,0,0
56-
Bagre,02-07358,Kiribina,00000,0,0,0,0,0
57-
La,02-07526,Folonzo,00200,0,0,2,0,0
58-
Dirze,02-07223,Kiribina,00000,0,0,0,0,0
59-
Pehele,02-06381,Kiribina,00000,0,0,0,0,0
60-
Vi,02-06837,Folonzo,00220,0,0,2,2,0
61-
Pehele,02-05664,Kiribina,00100,0,0,1,0,0
62-
Kuiti,00-01332,Kiribina,00000,0,0,0,0,0
63-
Pehele,02-05660,Kiribina,00000,0,0,0,0,0
64-
Koubri,00-01616,Kiribina,00000,0,0,0,0,0
65-
Koubri,00-01606,Kiribina,01000,0,1,0,0,0
66-
Kuiti,02-06222,Kiribina,00000,0,0,0,0,0
55+
Koubri,00-01488,Kiribina,100,0,0,1,0,0
56+
Bagre,02-07358,Kiribina,0,0,0,0,0,0
57+
La,02-07526,Folonzo,200,0,0,2,0,0
58+
Dirze,02-07223,Kiribina,0,0,0,0,0,0
59+
Pehele,02-06381,Kiribina,0,0,0,0,0,0
60+
Vi,02-06837,Folonzo,220,0,0,2,2,0
61+
Pehele,02-05664,Kiribina,100,0,0,1,0,0
62+
Kuiti,00-01332,Kiribina,0,0,0,0,0,0
63+
Pehele,02-05660,Kiribina,0,0,0,0,0,0
64+
Koubri,00-01616,Kiribina,0,0,0,0,0,0
65+
Koubri,00-01606,Kiribina,1000,0,1,0,0,0
66+
Kuiti,02-06222,Kiribina,0,0,0,0,0,0
6767
Kuiti,00-03773,Folonzo,NN210,N,N,2,1,0
68-
Ipendo,01-05791,Kiribina,00000,0,0,0,0,0
68+
Ipendo,01-05791,Folonzo,0,0,0,0,0,0
6969
Kuiti,00-04373,Folonzo,20210,2,0,2,1,0
7070
Pehele,02-06363,Folonzo,20100,2,0,1,0,0
71-
Kuiti,00-01516,Kiribina,00000,0,0,0,0,0
72-
Bagre,02-07397,Kiribina,00000,0,0,0,0,0
73-
Koubri,00-01612,Folonzo,01110,0,1,1,1,0
74-
Kuiti,00-01399,Kiribina,00000,0,0,0,0,0
75-
Kuiti,00-01334,Kiribina,00000,0,0,0,0,0
76-
Sabtenga,02-07104,Folonzo,00211,0,0,2,1,1
77-
Koubri,01-04360,Kiribina,00000,0,0,0,0,0
71+
Kuiti,00-01516,Kiribina,0,0,0,0,0,0
72+
Bagre,02-07397,Kiribina,0,0,0,0,0,0
73+
Koubri,00-01612,Folonzo,1110,0,1,1,1,0
74+
Kuiti,00-01399,Kiribina,0,0,0,0,0,0
75+
Kuiti,00-01334,Kiribina,0,0,0,0,0,0
76+
Sabtenga,02-07104,Folonzo,211,0,0,2,1,1
77+
Koubri,01-04360,Kiribina,0,0,0,0,0,0
7878
Sabtenga,02-07199,Folonzo,0021N,0,0,2,1,N
7979
Sabtenga,02-07110,Folonzo,10220,1,0,2,2,0
80-
Koubri,00-01482,Kiribina,00000,0,0,0,0,0
80+
Koubri,00-01482,Kiribina,0,0,0,0,0,0
8181
Vi,02-06851,Folonzo,20210,2,0,2,1,0
8282
Koubri,00-01432,Folonzo,NN200,N,N,2,0,0
83-
Sabtenga,02-07133,Kiribina,01000,0,1,0,0,0
83+
Sabtenga,02-07133,Kiribina,1000,0,1,0,0,0
8484
Kuiti,00-03385,Folonzo,NN210,N,N,2,1,0
85-
Koubri,00-01456,Folonzo,00110,0,0,1,1,0
85+
Koubri,00-01456,Folonzo,110,0,0,1,1,0
8686
Vi,02-06859,Folonzo,20200,2,0,2,0,0
8787
Sabtenga,02-07125,Folonzo,20221,2,0,2,2,1
8888
Pehele,02-05624,Folonzo,20210,2,0,2,1,0
8989
Kuiti,00-01526,Folonzo,20210,2,0,2,1,0
9090
Vi,02-06847,Kiribina,0000N,0,0,0,0,N
91-
Dirze,02-07053,Kiribina,00000,0,0,0,0,0
92-
Dirze,02-07079,Kiribina,00000,0,0,0,0,0
93-
Kuiti,00-01527,Kiribina,00000,0,0,0,0,0
94-
Koubri,00-01434,Kiribina,01100,0,1,1,0,0
95-
Dirze,02-07217,Kiribina,00000,0,0,0,0,0
91+
Dirze,02-07053,Kiribina,0,0,0,0,0,0
92+
Dirze,02-07079,Kiribina,0,0,0,0,0,0
93+
Kuiti,00-01527,Kiribina,0,0,0,0,0,0
94+
Koubri,00-01434,Kiribina,1100,0,1,1,0,0
95+
Dirze,02-07217,Kiribina,0,0,0,0,0,0
9696
Kuiti,00-04455,Folonzo,10220,1,0,2,2,0
97-
Pehele,02-06339,Kiribina,01000,0,1,0,0,0
97+
Pehele,02-06339,Kiribina,1000,0,1,0,0,0
9898
Vi,02-06821,Kiribina,0001N,0,0,0,1,N
9999
Pehele,02-05640,Folonzo,0020N,0,0,2,0,N
100-
Koubri,00-01611,Kiribina,00000,0,0,0,0,0
101-
Dirze,02-06905,Kiribina,00000,0,0,0,0,0
102-
Koubri,00-01607,Kiribina,00000,0,0,0,0,0
103-
Pehele,02-05632,Kiribina,00000,0,0,0,0,0
104-
Koubri,00-01459,Kiribina,00000,0,0,0,0,0
105-
Koubri,00-01455,Kiribina,02100,0,2,1,0,0
100+
Koubri,00-01611,Kiribina,0,0,0,0,0,0
101+
Dirze,02-06905,Kiribina,0,0,0,0,0,0
102+
Koubri,00-01607,Kiribina,0,0,0,0,0,0
103+
Pehele,02-05632,Kiribina,0,0,0,0,0,0
104+
Koubri,00-01459,Kiribina,0,0,0,0,0,0
105+
Koubri,00-01455,Kiribina,2100,0,2,1,0,0
106106
Kuiti,00-03776,Folonzo,20210,2,0,2,1,0
107107
Vi,02-06825,Folonzo,NN2NN,N,N,2,N,N
108108
Sabtenga,02-07107,Folonzo,1011N,1,0,1,1,N
109109
La,02-07747,Folonzo,10110,1,0,1,1,0
110110
Vi,02-06845,Folonzo,NN22N,N,N,2,2,N
111111
Vi,02-06809,Folonzo,20200,2,0,2,0,0
112112
Kuiti,02-06209,Folonzo,10220,1,0,2,2,0
113-
Koubri,01-04359,Kiribina,00000,0,0,0,0,0
113+
Koubri,01-04359,Kiribina,0,0,0,0,0,0
114114
Vi,02-06857,Folonzo,10210,1,0,2,1,0
115-
Bagre,02-07344,Kiribina,00000,0,0,0,0,0
116-
Dirze,02-06949,Kiribina,00000,0,0,0,0,0
115+
Bagre,02-07344,Kiribina,0,0,0,0,0,0
116+
Dirze,02-06949,Kiribina,0,0,0,0,0,0
117117
Ipendo,01-06389,Folonzo,20210,2,0,2,1,0
118118
Ipendo,01-06375,Folonzo,10220,1,0,2,2,0
119-
Pehele,02-06365,Kiribina,00000,0,0,0,0,0
119+
Pehele,02-06365,Kiribina,0,0,0,0,0,0
120120
Vi,02-06873,Folonzo,1020N,1,0,2,0,N
121-
Dirze,02-06753,Kiribina,00000,0,0,0,0,0
122-
Koubri,01-04357,Kiribina,00000,0,0,0,0,0
123-
Pehele,02-06371,Kiribina,00000,0,0,0,0,0
124-
Dirze,02-06915,Kiribina,00000,0,0,0,0,0
121+
Dirze,02-06753,Kiribina,0,0,0,0,0,0
122+
Koubri,01-04357,Kiribina,0,0,0,0,0,0
123+
Pehele,02-06371,Kiribina,0,0,0,0,0,0
124+
Dirze,02-06915,Kiribina,0,0,0,0,0,0
125125
Vi,02-06817,Folonzo,20220,2,0,2,2,0
126126
Pehele,02-06353,Kiribina,0000N,0,0,0,0,N
127-
Kuiti,00-03666,Folonzo,00120,0,0,1,2,0
127+
Kuiti,00-03666,Folonzo,120,0,0,1,2,0
128128
Sabtenga,02-07101,Folonzo,10210,1,0,2,1,0
129-
La,02-07529,Folonzo,00200,0,0,2,0,0
129+
La,02-07529,Kiribina,200,0,0,2,0,0
130130
Koubri,00-03830,Folonzo,10120,1,0,1,2,0
131-
Dirze,02-06897,Kiribina,00000,0,0,0,0,0
132-
Bagre,02-07343,Kiribina,00000,0,0,0,0,0
133-
Pehele,02-05630,Kiribina,00000,0,0,0,0,0
134-
Kuiti,00-01520,Kiribina,01000,0,1,0,0,0
135-
Bagre,02-07373,Kiribina,00000,0,0,0,0,0
136-
Vi,02-06801,Kiribina,00000,0,0,0,0,0
131+
Dirze,02-06897,Kiribina,0,0,0,0,0,0
132+
Bagre,02-07343,Kiribina,0,0,0,0,0,0
133+
Pehele,02-05630,Kiribina,0,0,0,0,0,0
134+
Kuiti,00-01520,Kiribina,1000,0,1,0,0,0
135+
Bagre,02-07373,Kiribina,0,0,0,0,0,0
136+
Vi,02-06801,Kiribina,0,0,0,0,0,0
137137
La,02-07537,Folonzo,20220,2,0,2,2,0
138-
Dirze,02-07095,Kiribina,00000,0,0,0,0,0
139-
Dirze,02-07293,Kiribina,00000,0,0,0,0,0
138+
Dirze,02-07095,Kiribina,0,0,0,0,0,0
139+
Dirze,02-07293,Kiribina,0,0,0,0,0,0
140140
Pehele,02-05652,Folonzo,NN200,N,N,2,0,0
141-
Koubri,00-01401,Kiribina,00000,0,0,0,0,0
142-
La,02-07544,Folonzo,00210,0,0,2,1,0
143-
Koubri,00-01613,Kiribina,00000,0,0,0,0,0
144-
Kuiti,00-04366,Folonzo,00220,0,0,2,2,0
141+
Koubri,00-01401,Kiribina,0,0,0,0,0,0
142+
La,02-07544,Folonzo,210,0,0,2,1,0
143+
Koubri,00-01613,Kiribina,0,0,0,0,0,0
144+
Kuiti,00-04366,Folonzo,220,0,0,2,2,0
145145
Koubri,00-01435,Folonzo,10200,1,0,2,0,0
146-
Bagre,02-07365,Kiribina,01000,0,1,0,0,0
146+
Bagre,02-07365,Kiribina,1000,0,1,0,0,0
147147
Pehele,02-05670,Folonzo,10100,1,0,1,0,0
148148
La,02-07557,Folonzo,NN2NN,N,N,2,N,N
149-
Koubri,00-01457,Kiribina,00000,0,0,0,0,0
150-
Koubri,00-01431,Kiribina,00000,0,0,0,0,0
151-
Bagre,02-07346,Kiribina,00000,0,0,0,0,0
149+
Koubri,00-01457,Kiribina,0,0,0,0,0,0
150+
Koubri,00-01431,Kiribina,0,0,0,0,0,0
151+
Bagre,02-07346,Kiribina,0,0,0,0,0,0
152152
Sabtenga,02-07146,Folonzo,20220,2,0,2,2,0
153-
Bagre,02-07363,Kiribina,00000,0,0,0,0,0
153+
Bagre,02-07363,Kiribina,0,0,0,0,0,0
154154
La,02-07703,Folonzo,10220,1,0,2,2,0
155155
Bagre,02-07341,Kiribina,0000N,0,0,0,0,N
156-
Ipendo,01-05793,Folonzo,00210,0,0,2,1,0
157-
Kuiti,00-01519,Kiribina,00000,0,0,0,0,0
156+
Ipendo,01-05793,Folonzo,210,0,0,2,1,0
157+
Kuiti,00-01519,Kiribina,0,0,0,0,0,0
158158
La,02-07549,Folonzo,2022N,2,0,2,2,N
159-
Bagre,02-07361,Kiribina,01000,0,1,0,0,0
160-
Kuiti,02-06221,Kiribina,00000,0,0,0,0,0
159+
Bagre,02-07361,Kiribina,1000,0,1,0,0,0
160+
Kuiti,02-06221,Kiribina,0,0,0,0,0,0
161161
Koubri,01-04362,Folonzo,NN210,N,N,2,1,0
162-
Kuiti,00-01331,Kiribina,00000,0,0,0,0,0
163-
Vi,02-06855,Folonzo,10120,1,0,1,2,0
164-
Bagre,02-07391,Kiribina,00000,0,0,0,0,0
165-
Kuiti,00-01517,Kiribina,00000,0,0,0,0,0
162+
Kuiti,00-01331,Kiribina,0,0,0,0,0,0
163+
Vi,02-06855,Kiribina,10120,1,0,1,2,0
164+
Bagre,02-07391,Kiribina,0,0,0,0,0,0
165+
Kuiti,00-01517,Kiribina,0,0,0,0,0,0
166166
Sabtenga,02-07112,Folonzo,10210,1,0,2,1,0
167-
Sabtenga,02-07193,Folonzo,00110,0,0,1,1,0
168-
Vi,02-06849,Kiribina,00000,0,0,0,0,0
169-
Koubri,00-01422,Kiribina,00000,0,0,0,0,0
167+
Sabtenga,02-07193,Folonzo,110,0,0,1,1,0
168+
Vi,02-06849,Kiribina,0,0,0,0,0,0
169+
Koubri,00-01422,Kiribina,0,0,0,0,0,0
170170
La,02-07580,Folonzo,10210,1,0,2,1,0
171-
Kuiti,00-03777,Kiribina,00000,0,0,0,0,0
171+
Kuiti,00-03777,Kiribina,0,0,0,0,0,0
172172
Vi,02-06695,Kiribina,0100N,0,1,0,0,N
173173
Koubri,00-03544,Folonzo,20200,2,0,2,0,0
174174
Vi,02-06673,Folonzo,NN2NN,N,N,2,N,N
175175
Sabtenga,02-07145,Folonzo,NN220,N,N,2,2,0
176176
Ipendo,01-06373,Folonzo,20220,2,0,2,2,0
177-
Dirze,02-07241,Kiribina,01000,0,1,0,0,0
177+
Dirze,02-07241,Kiribina,1000,0,1,0,0,0
178178
Vi,02-06839,Folonzo,20211,2,0,2,1,1
179179
Kuiti,00-04003,Folonzo,20210,2,0,2,1,0
180180
Vi,02-06829,Folonzo,20221,2,0,2,2,1
181-
Bagre,02-07351,Kiribina,00000,0,0,0,0,0
181+
Bagre,02-07351,Kiribina,0,0,0,0,0,0
182182
Pehele,02-06394,Folonzo,NN220,N,N,2,2,0
183183
Koubri,00-01421,Folonzo,10200,1,0,2,0,0
184184
Pehele,02-06341,Folonzo,2021N,2,0,2,1,N
185-
Kuiti,02-06207,Folonzo,00210,0,0,2,1,0
186-
Koubri,00-01413,Kiribina,00000,0,0,0,0,0
187-
Pehele,02-05634,Kiribina,00000,0,0,0,0,0
185+
Kuiti,02-06207,Folonzo,210,0,0,2,1,0
186+
Koubri,00-01413,Kiribina,0,0,0,0,0,0
187+
Pehele,02-05634,Kiribina,0,0,0,0,0,0
188188
La,02-07675,Folonzo,10200,1,0,2,0,0

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