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', 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('canabis', trait, flags=re.I): key1="addiction" key2="canabis" 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', 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:"+snp+", P value: "+pval+", Disease/trait: "+trait0+", Mapped trait: "+trait1+"" print (gene+"\t"+"GWAS"+"\t"+key2+"_GWAS\t"+pmid+"\t"+text) printed[gene]=1