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
|
import re
with open("./addiction_gwas.tsv", "r") as f:
for line in f:
try:
(pmid, trait0, gene0, gene1, snp, pval, trait1)=line.strip().split("\t")
except:
next
key1="unassigned"
key2="unassigned"
trait=trait0+"; "+trait1
genes=gene0+";"+gene1
if re.search('cocaine', trait, flags=re.I):
key1="addiction"
key2="cocaine"
elif re.search('smoking|congestive|nicotine|obstructive', trait, flags=re.I):
key1="addiction"
key2="nicotine"
elif re.search('opioid|morphin|heroin|methadone', trait, flags=re.I):
key1="addiction"
key2="opioid"
elif re.search('amphetam', trait, flags=re.I):
key1="addiction"
key2="amphetamine"
elif re.search('cannabis', trait, flags=re.I):
key1="addiction"
key2="cannabis"
elif re.search('food', trait, flags=re.I):
key1="addiction"
key2="food"
elif re.search('alcohol', trait, flags=re.I):
key1="addiction"
key2="alcohol"
elif re.search('addiction|abuse|dependence', trait, flags=re.I):
key1="addiction"
key2="addiction"
else:
key1="behavior"
key2="psychiatric"
genes=genes.replace(" - ", ";")
genes=genes.replace(",", ";")
printed=dict()
for gene in genes.split(";"):
gene=gene.replace(" ","")
if gene !="NR" and gene not in printed:
text="SNP:<b>"+snp+"</b>, P value: <b>"+pval+"</b>, Disease/trait:<b> "+trait0+"</b>, Mapped trait:<b> "+trait1+"</b>"
print (gene+"\t"+"GWAS"+"\t"+key2+"_GWAS\t"+pmid+"\t"+text)
printed[gene]=1
|
