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import os
## save all pmids for the top genes so that I don't have to search for these.
def getPMID(query):
print (query)
pmids=os.popen("esearch -db pubmed -query \"" + query + "\" | efetch -format uid").read()
return(pmids)
def collectTerms():
pmids_f=open("topGene_all.pmid","w+")
with open("./topGene_symb_alias.txt", "r") as top:
q=str()
cnt=0
for one in top:
cnt+=1
(symb, alias)=one.split("\t")
q+="|"+symb+"|"+alias.strip()
if (cnt==5):
print ("\n")
q=q[1:]
q=q.replace(";", "[tiab] OR ")+"[tiab]"
pmids=getPMID(q)
pmids_f.write(pmids)
cnt=0
q=str()
print("there should be nothing following the word empty"+q)
collectTerms()
os.system("sort topGene_all.pmid |uniq > topGene_uniq.pmid" )
os.system("rm topGene_all.pmid")
print ("results are in topGen_uniq.pmid")
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