Mercurial > repos > bgruening > chemical_data_sources

comparison get_pubchem/get_pubchem_as_smiles.py @ 0:f653fd06f055 draft

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author bgruening
date Thu, 15 Aug 2013 03:23:17 -0400
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children b65518a007fa
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-1:000000000000 0:f653fd06f055
1 #!/usr/bin/env python
2
3 __author__ = 'Bjoern Gruening'
4 __version__ = '0.1'
5 __date__ = '2012'
6 __license__ = 'GLP3+'
7
8 import ftplib
9 import os, sys
10 import argparse
11 import subprocess
12 from multiprocessing import Pool
13 import tempfile
14 import shutil
15
16 def main(output, processors = 10):
17 output_handle = open(output,'w+')
18
19 td = tempfile.mkdtemp()
20 ftp = ftplib.FTP('ftp.ncbi.nih.gov')
21 ftp.login()
22 ftp.cwd('/pubchem/Compound/CURRENT-Full/SDF/')
23 filelist = ftp.nlst()
24
25 pool = Pool(processes = processors)
26 filenames = zip(filelist, [td]*len(filelist))
27
28 result = pool.map_async(fetch_convert, filenames)
29 result.get()
30
31 for filename in os.listdir(td):
32 path = os.path.join(td, filename)
33 shutil.copyfileobj(open(path, 'rb'), output_handle)
34
35 output_handle.close()
36 shutil.rmtree( td )
37
38 def fetch_convert(args):
39 (filename, td) = args
40
41 tmp_name = os.path.join( tempfile.gettempdir(), filename)
42 subprocess.call( ['wget', '-O', tmp_name, os.path.join('ftp://ftp.ncbi.nih.gov/pubchem/Compound/CURRENT-Full/SDF/', filename)] )
43 output = os.path.join(td, filename)
44 subprocess.call(["obabel", "-isdf", tmp_name, "-ocan", '-O', output])
45 os.remove(tmp_name)
46
47
48 if __name__ == '__main__':
49 parser = argparse.ArgumentParser(description='Download the whole PubChem and converts it to canonical SMILES on the fly.')
50 parser.add_argument("-o", "--output", dest="output",
51 required=True,
52 help="Path to the output file.")
53 parser.add_argument("-p", "--processors", dest="processors",
54 type=int, default=10,
55 help="How many processors you want to use.")
56
57 options = parser.parse_args()
58 main( options.output, options.processors )
59