diff subsearch.py @ 0:98e12cc1f3a8 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/subsearch.py	Sat May 20 08:40:52 2017 -0400
@@ -0,0 +1,116 @@
+#!/usr/bin/env python
+"""
+    Input: Molecules in SDF, SMILES ...
+    Output: Moleculs filtered with specified substructures.
+    Copyright 2013, Bjoern Gruening and Xavier Lucas
+"""
+import sys, os
+import argparse
+import openbabel
+openbabel.obErrorLog.StopLogging()
+import pybel
+import multiprocessing
+import tempfile
+import subprocess
+import shutil
+
+def parse_command_line():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i', '--infile', required=True, help='Molecule file.')
+    parser.add_argument('--iformat', help='Input format.')
+    parser.add_argument('--fastsearch-index', dest="fastsearch_index", 
+        required=True, help='Path to the openbabel fastsearch index.')
+    parser.add_argument('-o', '--outfile', required=True, help='Path to the output file.')
+    parser.add_argument('--oformat', 
+        default='smi', help='Output file format')
+    parser.add_argument("--max-candidates", dest="max_candidates", type=int,
+                    default=4000, help="The maximum number of candidates.")
+    parser.add_argument('-p', '--processors', type=int, 
+        default=multiprocessing.cpu_count())
+    return parser.parse_args()
+
+results = list()
+def mp_callback(res):
+    results.append(res)
+
+def mp_helper( query, args ):
+    """
+        Helper function for multiprocessing.
+        That function is a wrapper around the following command:
+        obabel file.fs -s"smarts" -Ooutfile.smi -al 999999999
+    """
+
+    if args.oformat == 'names':
+        opts = '-osmi -xt'
+    else:
+        opts = '-o%s' % args.oformat
+
+    tmp = tempfile.NamedTemporaryFile(delete=False)
+    cmd = 'obabel -ifs %s -O %s %s -s%s -al %s' % (args.fastsearch_index, tmp.name, opts, query, args.max_candidates)
+
+    child = subprocess.Popen(cmd.split(),
+        stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+
+    stdout, stderr = child.communicate()
+    return_code = child.returncode
+
+    if return_code:
+        sys.stdout.write(stdout)
+        sys.stderr.write(stderr)
+        sys.stderr.write("Return error code %i from command:\n" % return_code)
+        sys.stderr.write("%s\n" % cmd)
+    else:
+        sys.stdout.write(stdout)
+        sys.stdout.write(stderr)
+    return (tmp.name, query)
+
+
+def get_smiles_or_smarts( args ):
+    """
+    Wrapper to retrieve a striped SMILES or SMARTS string from different input formats.
+    """
+    if args.iformat in ['smi', 'text', 'tabular']:
+        with open( args.infile ) as text_file:
+            for line in text_file:
+                yield line.split('\t')[0].strip()
+    else:
+        # inchi or sdf files
+        for mol in pybel.readfile( args.iformat, args.infile ):
+            yield mol.write('smiles').split('\t')[0]
+
+def substructure_search( args ):
+
+    pool = multiprocessing.Pool( args.processors )
+    for query in get_smiles_or_smarts( args ):
+        pool.apply_async(mp_helper, args=(query, args), callback=mp_callback)
+        #mp_callback( mp_helper(query, args) )
+    pool.close()
+    pool.join()
+
+    if args.oformat == 'names':
+        out_handle = open( args.outfile, 'w' )
+        for result_file, query in results:
+            with open(result_file) as res_handle:
+                for line in res_handle:
+                    out_handle.write('%s\t%s\n' % ( line.strip(), query ))
+            os.remove( result_file )
+        out_handle.close()
+    else:
+        out_handle = open( args.outfile, 'wb' )
+        for result_file, query in results:
+            res_handle = open(result_file,'rb')
+            shutil.copyfileobj( res_handle, out_handle )
+            res_handle.close()
+            os.remove( result_file )
+        out_handle.close()
+
+
+def __main__():
+    """
+        Multiprocessing Open Babel Substructure Search.
+    """
+    args = parse_command_line()
+    substructure_search( args )
+
+if __name__ == "__main__" :
+    __main__()