Example #1
0
def execute(link):
    queryDict, objective, linkToHealthy = parser.getPubMedQuery(link)

    counter = 0
    for query in queryDict:


        handle = Entrez.egquery(term=queryDict[query])
        record = Entrez.read(handle)

        tempQ = queryDict[query]
        handle1=Entrez.esearch(db="pubmed", term=tempQ, retmax=retcount, usehistory='y')
        results=Entrez.read(handle1)
        handle1.close()

        env1=results["WebEnv"]
        key1=results["QueryKey"]
        medlFormat = Entrez.efetch(db="pubmed", rettype="MEDLINE", retmode="text", retmax=retcount, WebEnv=env1, query_key=key1)
        
            

        record_list = Medline.parse(medlFormat)
        
        count=0
        for rec in record_list:
                if "AB" in rec:
                    count = count+1
                    g = open( query +"_" + rec["PMID"] +".txt", 'w')
                    g.write("Title: " + rec["TI"]+"\n"+"Abstract: "+rec["AB"])
                    g.close()
                else:
                    count = count+1
                    g = open( query + "_" + rec["PMID"] + ".txt", 'w')
                    g.write("Title: " + rec["TI"])
                    g.close()
                break
                count += 1
	counter += 1
    print counter
Example #2
0
import csv
from Bio import Entrez
from Bio import Medline

Entrez.email = "*****@*****.**"
import parser

retcount = 20000


link = "http://phpartners.org/hp2020/adolescent_health.html"

queryDict, objective, linkToHealthy = parser.getPubMedQuery(link)

for query in queryDict:
    print query

    handle1 = Entrez.esearch(db="pubmed", term=queryDict[query])
    results = Entrez.read(handle1)
    handle1.close()
    env1 = results["WebEnv"]
    key1 = results["QueryKey"]
    medlFormat = Entrez.efetch(
        db="pubmed", rettype="MEDLINE", retmode="text", retmax=retcount, WebEnv=env1, query_key=key1
    )

    record_list = Medline.parse(medlFormat)
    count = 0
    for rec in record_list:
        if "AB" in rec:
            count = count + 1