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1 #!/usr/bin/env python
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2
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3 import json
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4 import optparse
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5 import os.path
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6
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7 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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8 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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9 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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10 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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11 return data_manager_dict
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12
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13
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14 def get_param(name, params, default=None, check_tab=True):
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15 value = params.get(name)
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16 print name, value
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17 return check_param(name, value, default=default, check_tab=check_tab)
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18
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19
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20 def check_param(name, value, default=None, check_tab=True):
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21 if value in [ None, '', '?' ]:
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22 if default:
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23 print "Using {0} for {1} as no value provided".format( default, name )
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24 value = default
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25 else:
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26 raise Exception( '{0} is not a valid {1}. You must specify a valid {1}.'.format( value, name ) )
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27 if check_tab and "\t" in value:
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28 raise Exception( '{0} is not a valid {1}. It may not contain a tab because these are used as seperators by galaxy .'.format( value, name ) )
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29 return value
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30
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31
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32 def createFileBasedOnHmm(hmms):
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33 file_name = ""
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34 bar_code = "no"
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35 for hmm in hmms:
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36 block = hmm["block"].strip()
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37 if not (block[0] in ['R','O','G','B','F','S','P']):
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38 raise Exception( "hmm block {0} is not a valid. It must start with one of ['R','O','G','B','F','S','P'].".format( block ) )
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39 if block[0] == 'B':
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40 bar_code = "yes"
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41 if block[1] != ':':
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42 raise Exception( "hmm block {0} is not a valid. The second character must be ':'".format( block ) )
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43 if "\t" in hmm:
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44 raise Exception( "hmm block {0} is not a valid. It may not contain a tab, due to galaxy using tabs as seperators".format( block ) )
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45 file_name = file_name + block + "_"
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46 file_name = file_name[:-1] + ".txt"
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47 return bar_code, file_name
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48
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49
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50 def get_path(galaxy_tool_dir, file_name):
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51 file_path = os.path.join(galaxy_tool_dir, "tagdust_architecture")
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52 if os.path.exists(file_path):
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53 if os.path.isfile(file_path):
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54 raise Exception( "Found a file at {0}, but expecting a directory there".format( file_path ) )
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55 else:
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56 os.mkdir(file_path)
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57 return os.path.join(file_path, file_name)
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58
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59
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60 def writeHmm(hmms, file_path):
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61 with open( file_path, 'w' ) as output_file:
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62 output_file.write("./tagdust")
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63 for i, hmm in enumerate( hmms, 1 ):
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64 output_file.write(" ")
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65 output_file.write(str(-i))
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66 output_file.write(" ")
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67 output_file.write(hmm["block"])
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68 output_file.write("\n")
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69
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70 def main():
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71
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72 #Parse Command Line
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73 parser = optparse.OptionParser()
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74 parser.add_option( '--data_table_name', action='store', type="string", default=None, help='path' )
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75 parser.add_option( '--json_output_file', action='store', type="string", default=None, help='path' )
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76 (options, args) = parser.parse_args()
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77
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78 data_table_name = check_param("data_table_name", options.data_table_name)
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79 json_output_file = check_param("json_output_file", options.json_output_file, check_tab=False)
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80
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81 param_dict = json.loads( open( json_output_file ).read() )
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82 params = param_dict.get("param_dict")
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83 print "input params:"
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84 print params
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85
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86 hmms = get_param("hmms", params)
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87 galaxy_tool_dir = get_param("GALAXY_DATA_INDEX_DIR", params)
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88
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89 data_table_entry = {}
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90
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91 data_table_entry["barcode"], file_name = createFileBasedOnHmm(hmms)
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92 data_table_entry["path"] = get_path(galaxy_tool_dir, file_name)
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93 writeHmm(hmms, data_table_entry["path"])
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94
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95 basename = os.path.basename(data_table_entry["path"])
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96 filename = os.path.splitext(basename)[0]
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97 data_table_entry["name"] = get_param("name", params, default=filename)
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98 data_table_entry["value"] = get_param("value", params, default=data_table_entry["name"])
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99 data_table_entry["dbkey"] = get_param("dbkey", params, default=data_table_entry["value"])
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100
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101 data_manager_dict = {}
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102 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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103
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104 print "output:"
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105 print data_manager_dict
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106 # save info to json file
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107 with open( json_output_file, 'wb' ) as output_file:
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108 output_file.write( json.dumps( data_manager_dict ) )
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109 output_file.write( "\n" )
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110
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111
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112 if __name__ == "__main__":
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113 main()
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