annotate get_pubchem_assays.py @ 1:4d966d5bdd17 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"

#!/usr/bin/env python

__author__ = 'Bjoern Gruening'
__version__ = '0.1'
__date__ = '2014'
__license__ = 'GLP3+'

import ftplib
import os, sys
import argparse
import subprocess
from multiprocessing import Pool
import tempfile
import shutil
import urllib
import zipfile
import gzip


PUBCHEM_URL = "ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/CSV/Data/"

def main(output, processors = 4, white_list = ['Active','Inconclusive', 'Inactive']):
    """
        Starting multiple processes to download and extract PubChem Assay data.
    """
    td = tempfile.mkdtemp()
    ftp = ftplib.FTP('ftp.ncbi.nih.gov')
    ftp.login()
    ftp.cwd( PUBCHEM_URL )
    filelist = ftp.nlst()

    pool = Pool(processes = processors)
    triplestore = zip(filelist, [td]*len(filelist), [white_list]*len(filelist))

    result = pool.map_async(fetch_convert, triplestore)
    result.get()

    with open(output,'w+') as output_handle:
        for filename in os.listdir( td ):
            path = os.path.join( td, filename )
            shutil.copyfileobj(open(path, 'rb'), output_handle)

    shutil.rmtree( td )

def fetch_convert(args):
    (filename, td, white_list) = args
    tmp_name = os.path.join( td, filename)
    urllib.urlretrieve(os.path.join(PUBCHEM_URL, filename), tmp_name)

    temp_dir = tempfile.mkdtemp()
    with zipfile.ZipFile(tmp_name, "r") as z:
        z.extractall(temp_dir)

    output = os.path.join(td, filename) + '.tsv'
    with open(output, 'w+') as out_handle:
        for root, dirs, files in os.walk( temp_dir ):
            for filename in files:
                # filename encodes the assay_id, it looks like 1.csv.gz
                # extract the assay id and insert it as column one
                assay_id = filename.split('.', 1)
                gzfile_path = os.path.join( root, filename )
                with gzip.open(gzfile_path, 'rb') as gzfile:
                    gzfile.readline() # skip first line
                    for line in gzfile:
                        cols = line.split(',')
                        PUBCHEM_ACTIVITY_OUTCOME = cols[2]
                        cols = line.pop(4) # removing the URL column
                        cols.insert(0, assay_id) # insert assay_id as first column
                        if PUBCHEM_ACTIVITY_OUTCOME in white_list:
                            out_handle.write( '%s' % line.replace(',', '\t') )
    os.remove(tmp_name)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Download the whole PubChem and converts it to canonical SMILES on the fly.')
    parser.add_argument("-o", "--output", dest="output",
                    required=True,
                    help="Path to the output file.")
    parser.add_argument("-p", "--processors", dest="processors",
                    type=int, default=10,
                    help="How many processors you want to use.")
    parser.add_argument("-w", "--white-list", dest="white_list",
                    default="Active,Inconclusive,Inactive",
                    help="List of comma separated PUBCHEM_ACTIVITY_OUTCOME values that should be fetched.")

    options = parser.parse_args()
    main( options.output, options.processors, options.white_list.split(',') )