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#!/usr/bin/env python3
import ncbiutils
from lxml import etree
"""
Finds all rsids that are explicitly cited in pubmed
and returns a list
"""
def get_complete_rsids():
results = ncbiutils.esearch(db="snp", retmode="json", retmax=200000, retstart=0, term='snp_pubmed_cited[sb]')
rsidlist = results["esearchresult"]["idlist"]
for x in range(0, len(rsidlist)):
rsidlist[x] = "rs" + rsidlist[x]
return(rsidlist)
"""
Generates a list of PMIDs that are explicitly cite a given rsid
"""
def get_pmids(rsid):
searchterm = rsid + "+AND+pubmed_snp_cited[sb]"
print(searchterm)
results = ncbiutils.esearch(db="pubmed", retmode="json", retmax=200000, restart=0, term=searchterm, api_key="7c0213f7c513fa71fe2cb65b4dfefa76fb09")
pmidlist = results["esearchresult"]["idlist"]
print(pmidlist)
return(pmidlist)
"""
Takes a pmid and returns the abstract text
"""
def get_abstract(pmid):
raw = ncbiutils.efetch(db="pubmed", id=pmid, rettype="abstract")
xml = etree.fromstring(raw)
abstracts = []
for a in xml.xpath('//AbstractText'):
abstracts.append(a.text)
print(abstracts)
return()
def main():
rsids = get_complete_rsids()
for rsid in rsids:
pmids = get_pmids(rsid)
for pmid in pmids:
get_abstract(pmid)
return()
if __name__ == '__main__':
main()
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