In [ ]:
import pandas as pd
In [6]:
import os
In [9]:
cwd = os.getcwd()
cwd
Out[9]:
'/Users/otvisitor/Documents/proj/pycharm_projects/postgap/qaqc'
In [15]:
filename = cwd + "/../tests/sample_data/qaqc_data/postgap.20180209.gold_standard_snps.txt"
filename
Out[15]:
'/Users/otvisitor/Documents/proj/pycharm_projects/postgap/qaqc/../tests/sample_data/qaqc_data/postgap.20180209.gold_standard_snps.txt'
In [16]:
df = pd.read_csv(filename, sep='\t', na_values=['None'])
In [18]:
df.head()
Out[18]:
ld_snp_rsID
chrom
pos
GRCh38_chrom
GRCh38_pos
afr_maf
amr_maf
eas_maf
eur_maf
sas_maf
...
vep_sum
vep_mean
GTEx
VEP
Fantom5
DHS
PCHiC
Nearest
Regulome
VEP_reg
0
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.000000
0.0
0
0.0
0.024005
0.0
0
0
1
rs3751812
16
53818460
16
53784548
0.0545
0.2277
0.1667
0.4135
0.2914
...
0.0
0.0
0.000000
0.0
0
0.0
0.009325
0.0
0
0
2
rs3751812
16
53818460
16
53784548
0.0545
0.2277
0.1667
0.4135
0.2914
...
0.0
0.0
0.028039
0.0
0
0.0
0.000000
0.0
0
0
3
rs1421085
16
53800954
16
53767042
0.0560
0.2392
0.1687
0.4324
0.3067
...
0.0
0.0
0.000000
0.0
0
0.0
0.013251
0.0
0
0
4
rs9939609
16
53820527
16
53786615
0.4939
0.2622
0.1687
0.4135
0.2883
...
0.0
0.0
0.093748
0.0
0
0.0
0.000000
0.0
0
0
5 rows × 44 columns
In [19]:
df.loc[df['ld_snp_rsID'] == 'rs17817449']
Out[19]:
ld_snp_rsID
chrom
pos
GRCh38_chrom
GRCh38_pos
afr_maf
amr_maf
eas_maf
eur_maf
sas_maf
...
vep_sum
vep_mean
GTEx
VEP
Fantom5
DHS
PCHiC
Nearest
Regulome
VEP_reg
0
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.000000
0.0
0
0.0
0.024005
0.0
0
0
5
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.104672
0.0
0
0.0
0.000000
0.0
0
0
10
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.291158
0.0
0
0.0
0.000000
0.0
0
0
13
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.395961
0.0
0
0.0
0.000000
0.0
0
0
17
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.515353
0.0
0
0.0
0.000000
0.0
0
0
22
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.823969
0.0
0
0.0
0.000000
0.0
0
0
29
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
4.0
1.0
0.080767
1.0
0
0.0
0.000000
1.0
0
0
33
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.000000
0.0
0
0.0
0.024005
0.0
0
0
42
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.104672
0.0
0
0.0
0.000000
0.0
0
0
66
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.291158
0.0
0
0.0
0.000000
0.0
0
0
78
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.395961
0.0
0
0.0
0.000000
0.0
0
0
101
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.515353
0.0
0
0.0
0.000000
0.0
0
0
145
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.823969
0.0
0
0.0
0.000000
0.0
0
0
190
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
4.0
1.0
0.080767
1.0
0
0.0
0.000000
1.0
0
0
216
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.000000
0.0
0
0.0
0.024005
0.0
0
0
217
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.000000
0.0
0
0.0
0.024005
0.0
0
0
297
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.104672
0.0
0
0.0
0.000000
0.0
0
0
298
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.104672
0.0
0
0.0
0.000000
0.0
0
0
442
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.291158
0.0
0
0.0
0.000000
0.0
0
0
443
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.291158
0.0
0
0.0
0.000000
0.0
0
0
539
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.395961
0.0
0
0.0
0.000000
0.0
0
0
540
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.395961
0.0
0
0.0
0.000000
0.0
0
0
680
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.515353
0.0
0
0.0
0.000000
0.0
0
0
681
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.515353
0.0
0
0.0
0.000000
0.0
0
0
1136
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.823969
0.0
0
0.0
0.000000
0.0
0
0
1137
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.823969
0.0
0
0.0
0.000000
0.0
0
0
1370
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
4.0
1.0
0.080767
1.0
0
0.0
0.000000
1.0
0
0
1371
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
4.0
1.0
0.080767
1.0
0
0.0
0.000000
1.0
0
0
1501
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.000000
0.0
0
0.0
0.024005
0.0
0
0
1510
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.104672
0.0
0
0.0
0.000000
0.0
0
0
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
11923
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.823969
0.0
0
0.0
0.000000
0.0
0
0
11968
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
4.0
1.0
0.080767
1.0
0
0.0
0.000000
1.0
0
0
12008
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.000000
0.0
0
0.0
0.024005
0.0
0
0
12009
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.000000
0.0
0
0.0
0.024005
0.0
0
0
12010
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.000000
0.0
0
0.0
0.024005
0.0
0
0
12026
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.104672
0.0
0
0.0
0.000000
0.0
0
0
12027
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.104672
0.0
0
0.0
0.000000
0.0
0
0
12028
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.104672
0.0
0
0.0
0.000000
0.0
0
0
12041
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.291158
0.0
0
0.0
0.000000
0.0
0
0
12042
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.291158
0.0
0
0.0
0.000000
0.0
0
0
12043
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.291158
0.0
0
0.0
0.000000
0.0
0
0
12050
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.395961
0.0
0
0.0
0.000000
0.0
0
0
12051
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.395961
0.0
0
0.0
0.000000
0.0
0
0
12052
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.395961
0.0
0
0.0
0.000000
0.0
0
0
12059
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.515353
0.0
0
0.0
0.000000
0.0
0
0
12060
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.515353
0.0
0
0.0
0.000000
0.0
0
0
12061
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.515353
0.0
0
0.0
0.000000
0.0
0
0
12074
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.823969
0.0
0
0.0
0.000000
0.0
0
0
12075
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.823969
0.0
0
0.0
0.000000
0.0
0
0
12076
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.823969
0.0
0
0.0
0.000000
0.0
0
0
12098
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
4.0
1.0
0.080767
1.0
0
0.0
0.000000
1.0
0
0
12099
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
4.0
1.0
0.080767
1.0
0
0.0
0.000000
1.0
0
0
12100
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
4.0
1.0
0.080767
1.0
0
0.0
0.000000
1.0
0
0
12836
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.000000
0.0
0
0.0
0.024005
0.0
0
0
12904
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.104672
0.0
0
0.0
0.000000
0.0
0
0
13034
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.291158
0.0
0
0.0
0.000000
0.0
0
0
13119
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.395961
0.0
0
0.0
0.000000
0.0
0
0
13241
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.515353
0.0
0
0.0
0.000000
0.0
0
0
13669
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
0.0
0.0
0.823969
0.0
0
0.0
0.000000
0.0
0
0
13866
rs17817449
16
53813367
16
53779455
0.3759
0.2493
0.1696
0.4145
0.2894
...
4.0
1.0
0.080767
1.0
0
0.0
0.000000
1.0
0
0
525 rows × 44 columns
In [ ]:
Content source: Ensembl/cttv024
Similar notebooks: