-
Notifications
You must be signed in to change notification settings - Fork 0
/
path_configure.py
63 lines (47 loc) · 2.46 KB
/
path_configure.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
base_path='data/'
gwas_path='/data01/ch6845/UKB_gwas_neale/'
#ukb_sub_bim_path=base_path+'ukb_imp_plink/ukb_imp_chr{}_v3.bim'
bim_path=base_path+'1000G_plink_EUR/EUR_phase3_chr{}.bim'
bfile_path=base_path+'1000G_plink_EUR/EUR_phase3_chr{}'
"""
phenotypes_both_sexes_file_path=gwas_path+'phenotypes.both_sexes.tsv.gz'
phenotypes_male_file_path=gwas_path+'phenotypes.male.tsv.gz'
phenotypes_female_file_path=gwas_path+'phenotypes.female.tsv.gz'
biomarkers_both_sexes_file_path=gwas_path+'biomarkers.both_sexes.tsv.bgz'
biomarkers_male_file_path=gwas_path+'biomarkers.male.tsv.bgz'
biomarkers_female_file_path=gwas_path+'biomarkers.female.tsv.bgz'
"""
phenotypes_both_sexes_v2_file_path=gwas_path+'phenotypes.both_sexes.v2.tsv.bgz'
phenotypes_male_v2_file_path=gwas_path+'phenotypes.male.v2.tsv.bgz'
phenotypes_female_v2_file_path=gwas_path+'phenotypes.female.v2.tsv.bgz'
variants_file_path=gwas_path+'variants.tsv.bgz'
h2_path=base_path+'ukbb_all_h2univar_results.txt'
h2_par_path=base_path+'ukbb_all_h2part_results.txt'
h2_v2_path=base_path+'ukb31063_h2_topline.02Oct2019.tsv'
variants_wo_cm_path=base_path+'variants_wo_cm.bim'
variants_w_cm_path=base_path+'variants_w_cm.bim'
filter_index_path=base_path+'filter.index'
filter_rsid_path=base_path+'filter.rsid'
ukbb_table_path=base_path+'UKBB GWAS Imputed v3 - File Manifest Release 20180731 - Manifest 201807.csv'
ukbb_table_filtered_path=base_path+'UKBB_sumstats_filtered.csv'
phenotypes_filtered_path=base_path+'phenotypes_filtered.csv'
phenotypes_uni_filtered_path=base_path+'phenotypes_uni_filtered.csv'
phenotypes_par_filtered_path=base_path+'phenotypes_par_filtered.csv'
h2_total_par_filtered_path=base_path+'h2_total_par_filtered.csv'
"""
phenotypes_par_filtered_description_dict_path=base_path+'phenotypes_par_filtered_description_dict.tsv'
pleiotropic_loci_description_dict_path=base_path+'pleiotropic_loci_description_dict.tsv'
correlation_description_dict_path=base_path+'correlation_description_dict.tsv'
"""
description_dict_merge_path=base_path+'description_dict_merge.tsv'
annot_path=base_path+'out_annot/{}.{}.annot'
#premunge_path=base_path+'out_sumstats/{}.premunge'
premunge_path='/home/ch6845/premunge/{}.premunge'
print_snps_path=base_path+'hapmap3_snps/hm.{}.snp'
snplist_path=base_path+'w_hm3.snplist'
sumstats_path=base_path+'out_sumstats/{}'
#LDscore regression
wld_path=base_path+'1000G_Phase3_weights_hm3_no_MHC/weights.hm3_noMHC.'
ldsc_path=base_path+'out_final/{}.ldsc'
#estimating LD score
ld_path=base_path+'out_annot/{}.{}'