PubmedSpreadsheet Generation Code
From GersteinInfo
parse_pmids.py:
#!/usr/bin/python
import os, sys
from GoogleSpreadsheet import GoogleSpreadsheet
from datetime import datetime
master_spreadsheet_id = "thsIyYg12E8Px0zGJQsAopg" worksheet_id = "od6" master_spreadsheet = GoogleSpreadsheet(master_spreadsheet_id, worksheet_id)
ncbiquery = "/home/mpw6/new_papers/ncbiquery.txt" ncbiFile = open(ncbiquery,'w')
def buildQuery(master_spreadsheet, ncbiFile):
start = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id="
pmids =
end = "&rettype=xml&retmode=file"
for row in master_spreadsheet:
if row['pmid']:
pmids += row['pmid'].lstrip('\) + ','
pmids = pmids[:-1]
out = start + pmids + end + '\n'
ncbiFile.write(out)
buildQuery(master_spreadsheet, ncbiFile)
