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Clusters
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‎result/sims/machina_sims/cluster_m5.sh

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,6 @@ do
1111
do
1212
s=$(basename $f .tsv | sed -e s/reads_seed//g)
1313
echo Clustering seed $s pattern $p...
14-
$1 -a 0.0001 $f > input_m5/cluster_${p}_seed${s}.tsv 2> input_m5/cluster_${p}_seed${s}.txt
14+
$1 -a 0.001 -b 0.01 $f > input_m5/cluster_${p}_seed${s}.tsv 2> input_m5/cluster_${p}_seed${s}.txt
1515
done
1616
done

‎result/sims/machina_sims/cluster_m7.sh

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,6 @@ do
1111
do
1212
s=$(basename $f .tsv | sed -e s/reads_seed//g)
1313
echo Clustering seed $s pattern $p...
14-
$1 -a 0.0001 $f > input_m7/cluster_${p}_seed${s}.tsv 2> input_m7/cluster_${p}_seed${s}.txt
14+
$1 -a 0.001 -b 0.01 $f > input_m7/cluster_${p}_seed${s}.tsv 2> input_m7/cluster_${p}_seed${s}.txt
1515
done
1616
done

‎result/sims/machina_sims/input_m5/cluster_M_seed15.tsv

Lines changed: 101 additions & 91 deletions
Original file line numberDiff line numberDiff line change
@@ -1,154 +1,164 @@
11
5 #anatomical sites
22
10 #samples
3-
15 #characters
3+
16 #characters
44
#sample_index sample_label anatomical_site_index anatomical_site_label character_index character_label f- f+
55
0 P_0 0 P 0 33_35_40 0 0
6-
0 P_0 0 P 1 39 0 0
7-
0 P_0 0 P 2 37_38 0 0
8-
0 P_0 0 P 3 32_34_36 0 0
6+
0 P_0 0 P 1 37_38 0 0
7+
0 P_0 0 P 2 36 0 0
8+
0 P_0 0 P 3 32_34 0 0
99
0 P_0 0 P 4 27_31 0 0
1010
0 P_0 0 P 5 30 0 0
1111
0 P_0 0 P 6 6_11_14_19_22_26_28_29 0 0
1212
0 P_0 0 P 7 25 0 0
1313
0 P_0 0 P 8 8_9_15_23_24 0 0
14-
0 P_0 0 P 9 16_17_18_20_21 0 0
15-
0 P_0 0 P 10 7_10_12_13 0 0
16-
0 P_0 0 P 11 5 0.0309101 0.120603
17-
0 P_0 0 P 12 4 0.00704162 0.062991
18-
0 P_0 0 P 13 2_3 0.31955 0.447159
19-
0 P_0 0 P 14 0_1 0.361089 0.48237
14+
0 P_0 0 P 9 17_20_21 0 0
15+
0 P_0 0 P 10 16_18 0 0
16+
0 P_0 0 P 11 7_10_12_13 0 0
17+
0 P_0 0 P 12 5 0.0309101 0.120603
18+
0 P_0 0 P 13 4 0.00704162 0.062991
19+
0 P_0 0 P 14 2_3 0.31955 0.447159
20+
0 P_0 0 P 15 0_1 0.361089 0.48237
2021
1 P_1 0 P 0 33_35_40 0 0
21-
1 P_1 0 P 1 39 0 0
22-
1 P_1 0 P 2 37_38 0 0
23-
1 P_1 0 P 3 32_34_36 0 0
22+
1 P_1 0 P 1 37_38 0 0
23+
1 P_1 0 P 2 36 0 0
24+
1 P_1 0 P 3 32_34 0 0
2425
1 P_1 0 P 4 27_31 0 0
2526
1 P_1 0 P 5 30 0 0
2627
1 P_1 0 P 6 6_11_14_19_22_26_28_29 0 0
2728
1 P_1 0 P 7 25 0 0
2829
1 P_1 0 P 8 8_9_15_23_24 0 0
29-
1 P_1 0 P 9 16_17_18_20_21 0 0
30-
1 P_1 0 P 10 7_10_12_13 0 0
31-
1 P_1 0 P 11 5 0.0286366 0.112123
32-
1 P_1 0 P 12 4 0 0
33-
1 P_1 0 P 13 2_3 0.286698 0.410106
34-
1 P_1 0 P 14 0_1 0.38561 0.509442
30+
1 P_1 0 P 9 17_20_21 0 0
31+
1 P_1 0 P 10 16_18 0 0
32+
1 P_1 0 P 11 7_10_12_13 0 0
33+
1 P_1 0 P 12 5 0.0286366 0.112123
34+
1 P_1 0 P 13 4 0 0
35+
1 P_1 0 P 14 2_3 0.286698 0.410106
36+
1 P_1 0 P 15 0_1 0.38561 0.509442
3537
2 M1_0 1 M1 0 33_35_40 0 0
36-
2 M1_0 1 M1 1 39 0 0
37-
2 M1_0 1 M1 2 37_38 0 0
38-
2 M1_0 1 M1 3 32_34_36 0 0
38+
2 M1_0 1 M1 1 37_38 0 0
39+
2 M1_0 1 M1 2 36 0 0
40+
2 M1_0 1 M1 3 32_34 0 0
3941
2 M1_0 1 M1 4 27_31 0 0
4042
2 M1_0 1 M1 5 30 0 0
4143
2 M1_0 1 M1 6 6_11_14_19_22_26_28_29 0 0
4244
2 M1_0 1 M1 7 25 0 0
4345
2 M1_0 1 M1 8 8_9_15_23_24 0 0
44-
2 M1_0 1 M1 9 16_17_18_20_21 0.102041 0.15656
45-
2 M1_0 1 M1 10 7_10_12_13 0.475712 0.567338
46-
2 M1_0 1 M1 11 5 0 0
47-
2 M1_0 1 M1 12 4 0 0
48-
2 M1_0 1 M1 13 2_3 0.490455 0.614006
49-
2 M1_0 1 M1 14 0_1 0.394685 0.521938
46+
2 M1_0 1 M1 9 17_20_21 0.0187454 0.0575475
47+
2 M1_0 1 M1 10 16_18 0.213423 0.327272
48+
2 M1_0 1 M1 11 7_10_12_13 0.475712 0.567338
49+
2 M1_0 1 M1 12 5 0 0
50+
2 M1_0 1 M1 13 4 0 0
51+
2 M1_0 1 M1 14 2_3 0.490455 0.614006
52+
2 M1_0 1 M1 15 0_1 0.394685 0.521938
5053
3 M1_1 1 M1 0 33_35_40 0 0
51-
3 M1_1 1 M1 1 39 0 0
52-
3 M1_1 1 M1 2 37_38 0 0
53-
3 M1_1 1 M1 3 32_34_36 0 0
54+
3 M1_1 1 M1 1 37_38 0 0
55+
3 M1_1 1 M1 2 36 0 0
56+
3 M1_1 1 M1 3 32_34 0 0
5457
3 M1_1 1 M1 4 27_31 0 0
5558
3 M1_1 1 M1 5 30 0 0
5659
3 M1_1 1 M1 6 6_11_14_19_22_26_28_29 0 0
5760
3 M1_1 1 M1 7 25 0 0
5861
3 M1_1 1 M1 8 8_9_15_23_24 0 0
59-
3 M1_1 1 M1 9 16_17_18_20_21 0.0704975 0.118141
60-
3 M1_1 1 M1 10 7_10_12_13 0.407254 0.495188
61-
3 M1_1 1 M1 11 5 0 0
62-
3 M1_1 1 M1 12 4 0 0
63-
3 M1_1 1 M1 13 2_3 0.405151 0.538516
64-
3 M1_1 1 M1 14 0_1 0.413874 0.541767
62+
3 M1_1 1 M1 9 17_20_21 0.0305633 0.0771882
63+
3 M1_1 1 M1 10 16_18 0.11324 0.207188
64+
3 M1_1 1 M1 11 7_10_12_13 0.407254 0.495188
65+
3 M1_1 1 M1 12 5 0 0
66+
3 M1_1 1 M1 13 4 0 0
67+
3 M1_1 1 M1 14 2_3 0.405151 0.538516
68+
3 M1_1 1 M1 15 0_1 0.413874 0.541767
6569
4 M2_0 2 M2 0 33_35_40 0 0
66-
4 M2_0 2 M2 1 39 0 0
67-
4 M2_0 2 M2 2 37_38 0 0
68-
4 M2_0 2 M2 3 32_34_36 0 0
70+
4 M2_0 2 M2 1 37_38 0 0
71+
4 M2_0 2 M2 2 36 0 0
72+
4 M2_0 2 M2 3 32_34 0 0
6973
4 M2_0 2 M2 4 27_31 0.0329987 0.0972486
7074
4 M2_0 2 M2 5 30 0 0
7175
4 M2_0 2 M2 6 6_11_14_19_22_26_28_29 0.0675529 0.10336
7276
4 M2_0 2 M2 7 25 0.349137 0.532801
7377
4 M2_0 2 M2 8 8_9_15_23_24 0.331766 0.410858
74-
4 M2_0 2 M2 9 16_17_18_20_21 0 0
75-
4 M2_0 2 M2 10 7_10_12_13 0 0
76-
4 M2_0 2 M2 11 5 0 0
77-
4 M2_0 2 M2 12 4 0.259167 0.429867
78-
4 M2_0 2 M2 13 2_3 0 0
79-
4 M2_0 2 M2 14 0_1 0.527857 0.647394
78+
4 M2_0 2 M2 9 17_20_21 0 0
79+
4 M2_0 2 M2 10 16_18 0 0
80+
4 M2_0 2 M2 11 7_10_12_13 0 0
81+
4 M2_0 2 M2 12 5 0 0
82+
4 M2_0 2 M2 13 4 0.259167 0.429867
83+
4 M2_0 2 M2 14 2_3 0 0
84+
4 M2_0 2 M2 15 0_1 0.527857 0.647394
8085
5 M2_1 2 M2 0 33_35_40 0 0
81-
5 M2_1 2 M2 1 39 0 0
82-
5 M2_1 2 M2 2 37_38 0 0
83-
5 M2_1 2 M2 3 32_34_36 0 0
86+
5 M2_1 2 M2 1 37_38 0 0
87+
5 M2_1 2 M2 2 36 0 0
88+
5 M2_1 2 M2 3 32_34 0 0
8489
5 M2_1 2 M2 4 27_31 0 0
8590
5 M2_1 2 M2 5 30 0 0
8691
5 M2_1 2 M2 6 6_11_14_19_22_26_28_29 0.120677 0.165828
8792
5 M2_1 2 M2 7 25 0.164175 0.316111
8893
5 M2_1 2 M2 8 8_9_15_23_24 0.274961 0.34853
89-
5 M2_1 2 M2 9 16_17_18_20_21 0 0
90-
5 M2_1 2 M2 10 7_10_12_13 0 0
91-
5 M2_1 2 M2 11 5 0 0
92-
5 M2_1 2 M2 12 4 0.221692 0.384585
93-
5 M2_1 2 M2 13 2_3 0 0
94-
5 M2_1 2 M2 14 0_1 0.468193 0.590659
94+
5 M2_1 2 M2 9 17_20_21 0 0
95+
5 M2_1 2 M2 10 16_18 0 0
96+
5 M2_1 2 M2 11 7_10_12_13 0 0
97+
5 M2_1 2 M2 12 5 0 0
98+
5 M2_1 2 M2 13 4 0.221692 0.384585
99+
5 M2_1 2 M2 14 2_3 0 0
100+
5 M2_1 2 M2 15 0_1 0.468193 0.590659
95101
6 M3_0 3 M3 0 33_35_40 0 0
96-
6 M3_0 3 M3 1 39 0 0
97-
6 M3_0 3 M3 2 37_38 0.0402696 0.106073
98-
6 M3_0 3 M3 3 32_34_36 0 0
102+
6 M3_0 3 M3 1 37_38 0.0402696 0.106073
103+
6 M3_0 3 M3 2 36 0 0
104+
6 M3_0 3 M3 3 32_34 0 0
99105
6 M3_0 3 M3 4 27_31 0 0
100106
6 M3_0 3 M3 5 30 0.388873 0.558909
101107
6 M3_0 3 M3 6 6_11_14_19_22_26_28_29 0 0
102108
6 M3_0 3 M3 7 25 0 0
103109
6 M3_0 3 M3 8 8_9_15_23_24 0.4675 0.548189
104-
6 M3_0 3 M3 9 16_17_18_20_21 0 0
105-
6 M3_0 3 M3 10 7_10_12_13 0 0
106-
6 M3_0 3 M3 11 5 0 0
107-
6 M3_0 3 M3 12 4 0.46419 0.644822
108-
6 M3_0 3 M3 13 2_3 0 0
109-
6 M3_0 3 M3 14 0_1 0.509391 0.634224
110+
6 M3_0 3 M3 9 17_20_21 0 0
111+
6 M3_0 3 M3 10 16_18 0 0
112+
6 M3_0 3 M3 11 7_10_12_13 0 0
113+
6 M3_0 3 M3 12 5 0 0
114+
6 M3_0 3 M3 13 4 0.46419 0.644822
115+
6 M3_0 3 M3 14 2_3 0 0
116+
6 M3_0 3 M3 15 0_1 0.509391 0.634224
110117
7 M3_1 3 M3 0 33_35_40 0 0
111-
7 M3_1 3 M3 1 39 0 0
112-
7 M3_1 3 M3 2 37_38 0 0
113-
7 M3_1 3 M3 3 32_34_36 0 0
118+
7 M3_1 3 M3 1 37_38 0 0
119+
7 M3_1 3 M3 2 36 0 0
120+
7 M3_1 3 M3 3 32_34 0 0
114121
7 M3_1 3 M3 4 27_31 0 0
115122
7 M3_1 3 M3 5 30 0.401337 0.575812
116123
7 M3_1 3 M3 6 6_11_14_19_22_26_28_29 0 0
117124
7 M3_1 3 M3 7 25 0 0
118125
7 M3_1 3 M3 8 8_9_15_23_24 0.456342 0.537681
119-
7 M3_1 3 M3 9 16_17_18_20_21 0 0
120-
7 M3_1 3 M3 10 7_10_12_13 0 0
121-
7 M3_1 3 M3 11 5 0 0
122-
7 M3_1 3 M3 12 4 0.36469 0.543439
123-
7 M3_1 3 M3 13 2_3 0 0
124-
7 M3_1 3 M3 14 0_1 0.488726 0.617932
126+
7 M3_1 3 M3 9 17_20_21 0 0
127+
7 M3_1 3 M3 10 16_18 0 0
128+
7 M3_1 3 M3 11 7_10_12_13 0 0
129+
7 M3_1 3 M3 12 5 0 0
130+
7 M3_1 3 M3 13 4 0.36469 0.543439
131+
7 M3_1 3 M3 14 2_3 0 0
132+
7 M3_1 3 M3 15 0_1 0.488726 0.617932
125133
8 M4_0 4 M4 0 33_35_40 0.0262687 0.0700388
126-
8 M4_0 4 M4 1 39 0 0
127-
8 M4_0 4 M4 2 37_38 0 0
128-
8 M4_0 4 M4 3 32_34_36 0.0884412 0.158646
134+
8 M4_0 4 M4 1 37_38 0 0
135+
8 M4_0 4 M4 2 36 0.166733 0.314623
136+
8 M4_0 4 M4 3 32_34 0.0274943 0.0886042
129137
8 M4_0 4 M4 4 27_31 0 0
130138
8 M4_0 4 M4 5 30 0 0
131139
8 M4_0 4 M4 6 6_11_14_19_22_26_28_29 0 0
132140
8 M4_0 4 M4 7 25 0.014807 0.0846849
133141
8 M4_0 4 M4 8 8_9_15_23_24 0.4428 0.521612
134-
8 M4_0 4 M4 9 16_17_18_20_21 0 0
135-
8 M4_0 4 M4 10 7_10_12_13 0 0
136-
8 M4_0 4 M4 11 5 0 0
137-
8 M4_0 4 M4 12 4 0.420919 0.592308
138-
8 M4_0 4 M4 13 2_3 0 0
139-
8 M4_0 4 M4 14 0_1 0.468173 0.59752
142+
8 M4_0 4 M4 9 17_20_21 0 0
143+
8 M4_0 4 M4 10 16_18 0 0
144+
8 M4_0 4 M4 11 7_10_12_13 0 0
145+
8 M4_0 4 M4 12 5 0 0
146+
8 M4_0 4 M4 13 4 0.420919 0.592308
147+
8 M4_0 4 M4 14 2_3 0 0
148+
8 M4_0 4 M4 15 0_1 0.468173 0.59752
140149
9 M4_1 4 M4 0 33_35_40 0 0
141-
9 M4_1 4 M4 1 39 0 0
142-
9 M4_1 4 M4 2 37_38 0 0
143-
9 M4_1 4 M4 3 32_34_36 0.00454435 0.0298965
150+
9 M4_1 4 M4 1 37_38 0 0
151+
9 M4_1 4 M4 2 36 0.00354105 0.0562858
152+
9 M4_1 4 M4 3 32_34 0.00286275 0.0329409
144153
9 M4_1 4 M4 4 27_31 0 0
145154
9 M4_1 4 M4 5 30 0 0
146155
9 M4_1 4 M4 6 6_11_14_19_22_26_28_29 0 0
147156
9 M4_1 4 M4 7 25 0.00388936 0.061659
148157
9 M4_1 4 M4 8 8_9_15_23_24 0.482292 0.563627
149-
9 M4_1 4 M4 9 16_17_18_20_21 0 0
150-
9 M4_1 4 M4 10 7_10_12_13 0 0
151-
9 M4_1 4 M4 11 5 0 0
152-
9 M4_1 4 M4 12 4 0.476981 0.657473
153-
9 M4_1 4 M4 13 2_3 0 0
154-
9 M4_1 4 M4 14 0_1 0.445969 0.57365
158+
9 M4_1 4 M4 9 17_20_21 0 0
159+
9 M4_1 4 M4 10 16_18 0 0
160+
9 M4_1 4 M4 11 7_10_12_13 0 0
161+
9 M4_1 4 M4 12 5 0 0
162+
9 M4_1 4 M4 13 4 0.476981 0.657473
163+
9 M4_1 4 M4 14 2_3 0 0
164+
9 M4_1 4 M4 15 0_1 0.445969 0.57365

‎result/sims/machina_sims/input_m5/cluster_M_seed15.txt

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,14 @@
11
33;35;40
2-
39
32
37;38
4-
32;34;36
3+
36
4+
32;34
55
27;31
66
30
77
6;11;14;19;22;26;28;29
88
25
99
8;9;15;23;24
10-
16;17;18;20;21
10+
17;20;21
11+
16;18
1112
7;10;12;13
1213
5
1314
4

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