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pubmedQuery.py
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pubmedQuery.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# pubmedQuery.py
#
# Copyright 2016 Hugh Shanahan <upac004@STF-MC246-001L.local>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
# MA 02110-1301, USA.
#
#
# Note - we are using the NCBI entrez direct command line scripts esearch, efetch and xtract
# these can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/
import os, tempfile
def abstracts(queryString):
# First call pubmed to pull out abstracts - one line per abstract
temp_name = "./"+next(tempfile._get_candidate_names())
efetchCommand = "esearch -db pubmed -query \""+queryString+"\" | efetch -mode xml -format abstract | xtract -pattern PubmedArticle -block Abstract -element AbstractText>"+temp_name
os.system(efetchCommand)
# Now call Normalizr (Python 3 - oi vey) to normalise text.
# Normalised text will overwrite original text.
normalizeCommand = "/Users/upac004/Python/GOFind-master/normText.py "+ temp_name
os.system(normalizeCommand)
# Now read in file to get each abstract and return a list
theAbstracts = []
fd = open(temp_name)
for line in fd:
# Remove any special non-ASCII characters
line = ''.join([i if ord(i) < 128 else '' for i in line])
theAbstracts.append(line)
fd.close()
os.remove(temp_name)
return theAbstracts
def main(args):
myAbstracts = abstracts("SATB2 gene function")
# for abstract in myAbstracts :
# print abstract
if __name__ == '__main__':
import sys
sys.exit(main(sys.argv))