Mercurial > repos > bgruening > get_pubchem

annotate get_pubchem_assays.py @ 0:cd19c3fab3a6 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
author bgruening
date Wed, 22 May 2019 07:44:03 -0400
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cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
bgruening
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1 #!/usr/bin/env python
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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2
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3 __author__ = 'Bjoern Gruening'
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4 __version__ = '0.1'
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5 __date__ = '2014'
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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6 __license__ = 'GLP3+'
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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7
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8 import ftplib
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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9 import os, sys
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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10 import argparse
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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11 import subprocess
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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12 from multiprocessing import Pool
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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13 import tempfile
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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14 import shutil
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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15 import urllib
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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16 import zipfile
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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17 import gzip
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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19
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20 PUBCHEM_URL = "ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/CSV/Data/"
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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22 def main(output, processors = 4, white_list = ['Active','Inconclusive', 'Inactive']):
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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23 """
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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24 Starting multiple processes to download and extract PubChem Assay data.
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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25 """
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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26 td = tempfile.mkdtemp()
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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27 ftp = ftplib.FTP('ftp.ncbi.nih.gov')
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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28 ftp.login()
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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29 ftp.cwd( PUBCHEM_URL )
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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30 filelist = ftp.nlst()
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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31
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32 pool = Pool(processes = processors)
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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33 triplestore = zip(filelist, [td]*len(filelist), [white_list]*len(filelist))
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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34
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35 result = pool.map_async(fetch_convert, triplestore)
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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36 result.get()
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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37
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38 with open(output,'w+') as output_handle:
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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39 for filename in os.listdir( td ):
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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40 path = os.path.join( td, filename )
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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41 shutil.copyfileobj(open(path, 'rb'), output_handle)
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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43 shutil.rmtree( td )
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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44
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45 def fetch_convert(args):
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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46 (filename, td, white_list) = args
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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47 tmp_name = os.path.join( td, filename)
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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48 urllib.urlretrieve(os.path.join(PUBCHEM_URL, filename), tmp_name)
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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49
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50 temp_dir = tempfile.mkdtemp()
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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51 with zipfile.ZipFile(tmp_name, "r") as z:
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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52 z.extractall(temp_dir)
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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53
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54 output = os.path.join(td, filename) + '.tsv'
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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55 with open(output, 'w+') as out_handle:
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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56 for root, dirs, files in os.walk( temp_dir ):
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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57 for filename in files:
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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58 # filename encodes the assay_id, it looks like 1.csv.gz
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59 # extract the assay id and insert it as column one
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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60 assay_id = filename.split('.', 1)
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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61 gzfile_path = os.path.join( root, filename )
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62 with gzip.open(gzfile_path, 'rb') as gzfile:
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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63 gzfile.readline() # skip first line
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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64 for line in gzfile:
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65 cols = line.split(',')
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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66 PUBCHEM_ACTIVITY_OUTCOME = cols[2]
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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67 cols = line.pop(4) # removing the URL column
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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68 cols.insert(0, assay_id) # insert assay_id as first column
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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69 if PUBCHEM_ACTIVITY_OUTCOME in white_list:
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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70 out_handle.write( '%s' % line.replace(',', '\t') )
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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71 os.remove(tmp_name)
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72
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73
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74 if __name__ == '__main__':
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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75 parser = argparse.ArgumentParser(description='Download the whole PubChem and converts it to canonical SMILES on the fly.')
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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76 parser.add_argument("-o", "--output", dest="output",
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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77 required=True,
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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78 help="Path to the output file.")
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79 parser.add_argument("-p", "--processors", dest="processors",
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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80 type=int, default=10,
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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81 help="How many processors you want to use.")
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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82 parser.add_argument("-w", "--white-list", dest="white_list",
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
bgruening
parents:
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83 default="Active,Inconclusive,Inactive",
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
bgruening
parents:
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84 help="List of comma separated PUBCHEM_ACTIVITY_OUTCOME values that should be fetched.")
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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85
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
bgruening
parents:
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86 options = parser.parse_args()
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
bgruening
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87 main( options.output, options.processors, options.white_list.split(',') )
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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88