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8
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1 #!/usr/bin/env python
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2
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3 import sys, os
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4 import argparse
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5
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6 import readfile
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7
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8 #dicitionary for the output format
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9
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9
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10 dict_output={"cids" :"txt", "aids" : "txt", "sids" : "txt", "description": "xml", "summary" : "xml", "record" : "csv", "classification": "xml", "targets" : "txt", "xrefs" : "txt", "synonyms" : "txt", "property": "csv", "doseresponse" : "csv" }
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8
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11
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12 #alles andere ist xml
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13 check_for_id_type=["cids", "aids", "sids"]
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14
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15 post_id_types=["inchi", "sdf", "smiles"]
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16
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17 id_dict={"compound": "cid", "assay": "aid", "substance" : "sid" }
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18
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19 def getListString(args):
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20 if args.id_type_ff == "file":
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21 #build comma list
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22 list_string=",".join(getListFromFile(open(args.id_value,"r")))
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23 else:
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24 print (args.id_value)
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25 list_string=args.id_value.strip().replace("__cr____cn__", ",")
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26 return list_string
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27
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28
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8
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29 def main(args):
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30 url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/"
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31 url+=args.id_type+"/"
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9
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32 # check if we are post then skip this part otherwise put the ids in the url
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33 if not args.id_type in post_id_types:
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34 if args.id_type ==id_dict[args.type]:
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35 url+=getListString(args)+"/"
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36 else:
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37 url+=args.id_value+"/"
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38
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39 url+=args.operation+"/"
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40 if args.operation == "target" or args.operation == "property" or args.operation == "xrefs":
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41 url+=args.operation_value+"/"
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42
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43 if args.operation == "xrefs":
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44 if "," in args.operation_value:
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45 url+="xml"
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46 else:
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47 url+="txt"
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48 else:
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49 url+=dict_output[args.operation]
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50 if args.operation in check_for_id_type and args.id_type not in post_id_types:
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51 url+="?%s_type=%s" % (args.operation, args.ids_operation_type)
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52 print(url)
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53 if args.id_type in post_id_types:
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54 postfile=open(args.id_value,"r")
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55 post_value=postfile.read()
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56 post_dict={args.id_type : post_value}
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57 print(post_dict)
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58 readfile.store_result_post(url, post_dict, args.outfile)
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59 else:
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60 readfile.store_result_get(url, args.outfile)
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8
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61 if __name__ == "__main__":
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62 parser = argparse.ArgumentParser()
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63 parser.add_argument('--type', type=str, required=True,
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64 help="That you want BioAssay Compund ...")
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65 parser.add_argument('--id-type', type=str,
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66 help="Specify the ID type")
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67 parser.add_argument('--operation', type=str, required=True,
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68 help="Specify the operation")
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69 parser.add_argument('--operation-value', dest="operation_value", type=str, required=False,
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70 help="Specify the additional operation value")
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71 parser.add_argument('--xref-operation-value', dest="xref_operation_value", type=str, required=False,
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72 help="Specify the xref operation ")
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73 parser.add_argument('--ids-operation-type', dest="ids_operation_type", type=str, required=False,
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74 help="all inactive ...")
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75 parser.add_argument('--xref', dest="xref", type=str,
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76 help="use xref to identify the searched thing")
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77 parser.add_argument('--xref-value', dest="xref_value", type=str,
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78 help="Specify the xref")
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79 parser.add_argument('--property-value', dest="property_value", type=str,
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80 help="Specify the property value")
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81 parser.add_argument('--id-type-ff', dest="id_type_ff", type=str,
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82 help="file or field")
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83 parser.add_argument('--id-value', dest="id_value", type=str, required=True,
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84 help="Specify the id")
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85 parser.add_argument('--outfile', type=argparse.FileType('w'), required=True,
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86 help="Specify the output file")
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87
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88
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89 if len(sys.argv) < 8:
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90 print "Too few arguments..."
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91 parser.print_help()
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92 exit(1)
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93 args = parser.parse_args()
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94 main( args )
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