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1 #!/usr/bin/env python
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2
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3 # https://github.com/ross/requests-futures
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4 # http://docs.python-requests.org/en/master/user/quickstart/#more-complicated-post-requests
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5
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6 import sys, os, uuid, optparse, requests, json, time
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7 #from requests_futures.sessions import FuturesSession
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8
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9 #### NN14 ####
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10 SERVICE_URL = "http://nn14.galaxyproject.org:8080/";
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11 #service_url = "http://127.0.0.1:8082/";
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4
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12 QUERY_URL = SERVICE_URL+"tree/<tree_id>/query";
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0
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13 STATUS_URL = SERVICE_URL+"status/<query_id>";
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14 ##############
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15 # query delay in seconds
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16 QUERY_DELAY = 30;
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17 ##############
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18
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19 __version__ = "1.0.0";
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20 VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
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21 # in the case of collections, exitcodes equal to 0 and 1 are not considered errors
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22 ERR_EXIT_CODE = 2;
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23 OK_EXIT_CODE = 0;
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24
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25 def raiseException( exitcode, message, output_dir_path, errorfilename ):
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26 errorfilepath = os.path.join(output_dir_path, errorfilename+"_txt");
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27 with open(errorfilepath, 'w') as out:
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28 out.write(message);
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29 sys.exit(exitcode);
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30
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31 def query_request( options, args, payload ):
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32 output_dir_path = options.outputdir;
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33 # add additional parameters to the payload
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34 #payload["tree_id"] = str(options.treeid);
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35 payload["search_mode"] = str(options.search);
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36 payload["exact_algorithm"] = int(options.exact);
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37 payload["search_threshold"] = float(options.sthreshold);
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10
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38 payload["sort"] = int(options.sortcontrol);
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0
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39 # set the content type to application/json
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40 headers = {'Content-type': 'application/json'};
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41
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42 # create a session
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43 session = requests.Session();
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44 # make a synchronous post request to the query route
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4
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45 req = session.post(QUERY_URL.replace("<tree_id>", str(options.treeid)), headers=headers, json=payload);
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0
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46 resp_code = req.status_code;
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47 #print(str(req.content)+"\n\n");
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48 if resp_code == requests.codes.ok:
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49 resp_content = str(req.content);
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50 # convert out to json
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51 json_content = json.loads(resp_content);
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52 # retrieve query id
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53 query_id = json_content['query_id'];
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54 query_processed = False;
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55 # results json content
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56 json_status_content = None;
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57 while query_processed is False:
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58 # create a new session
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59 session = requests.Session();
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60 # make a synchronous get request to the status route
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61 status_query_url = STATUS_URL.replace("<query_id>", query_id);
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62 status_req = session.get(status_query_url);
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63 status_resp_content = str(status_req.content);
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64 #print(status_resp_content+"\n\n");
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65 # convert out to json
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66 json_status_content = json.loads(status_resp_content);
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67 # take a look at the state
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68 # state attribute is always available
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69 if json_status_content['state'] == 'SUCCESS':
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70 query_processed = True;
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71 break;
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72 elif json_status_content['state'] in ['FAILURE', 'REVOKED']:
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73 return raiseException( ERR_EXIT_CODE, "Query ID: "+str(query_id)+"\nQuery status: "+str(json_status_content['state']), output_dir_path, str(options.errorfile) );
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74 else:
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75 time.sleep(QUERY_DELAY); # in seconds
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76
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77 out_file_format = "tabular";
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78 for block in json_status_content['results']:
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79 seq_id = block['sequence_id'];
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80 # put response block in the output collection
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81 output_file_path = os.path.join(output_dir_path, seq_id + "_" + out_file_format);
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82 accessions_list = "";
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83 hits_block = block['hits'];
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8
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84 accessions_dict = { };
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4
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85 is_sabutan = False;
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0
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86 for hit in hits_block:
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87 if type(hit) is dict: # sabutan
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88 #accessions_list = accessions_list + str(hit['accession_number']) + "\t" + str(hit['score']) + "\n";
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89 accession_number = hit['accession_number'];
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12
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90 #------------
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91 #score = hit['score'];
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92 #score_split = score.split("/");
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93 #accessions_dict[accession_number] = "{0:.6f}".format(float(score_split[0])/float(score_split[1]));
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94 #------------
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95 fraction = hit['fraction'];
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96 score = hit['score'];
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12
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97 accession_scores = {
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98 "fraction": str(fraction),
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99 "score": float(score)
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100 }
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101 accessions_dict[accession_number] = accession_scores;
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102 is_sabutan = True;
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103 else: # all-some
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104 accessions_list = accessions_list + str(hit) + "\n";
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105 if is_sabutan:
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12
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106 sorted_accessions = sorted(accessions_dict, key=lambda i: float(accessions_dict[i]["score"]), reverse=True);
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107 for acc in sorted_accessions:
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108 accessions_list = accessions_list + str(acc) + "\t" + str(accessions_dict[acc]["fraction"]) + "\t" + str(accessions_dict[acc]["score"]) + "\n";
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109 with open(output_file_path, 'w') as out:
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110 out.write(accessions_list.strip());
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111 return sys.exit(OK_EXIT_CODE);
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112 else:
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113 return raiseException( ERR_EXIT_CODE, "Unable to query the remote server. Please try again in a while.", output_dir_path, str(options.errorfile) );
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114
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115 def query( options, args ):
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116 output_dir_path = options.outputdir;
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117 multiple_data = {};
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118 comma_sep_file_paths = options.files;
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119 #print("files: "+str(comma_sep_file_paths)+" - "+str(type(comma_sep_file_paths)));
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120 # check if options.files contains at least one file path
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121 if comma_sep_file_paths is not None:
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122 # split file paths
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123 file_paths = comma_sep_file_paths.split(",");
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124 # split file names
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125 comma_sep_file_names = str(options.names);
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126 #print("names: "+str(comma_sep_file_names));
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127 file_names = comma_sep_file_names.split(",");
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128 for idx, file_path in enumerate(file_paths):
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129 #file_name = file_names[idx];
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130 with open(file_path, 'r') as content_file:
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131 for line in content_file:
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132 if line.strip() != "":
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133 line_split = line.strip().split("\t"); # split on tab
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134 if len(line_split) == 2: # 0:id , 1:seq , otherwise skip line
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135 seq_id = line_split[0];
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136 # fix seq_id using valid chars only
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137 seq_id = ''.join(e for e in seq_id if e in VALID_CHARS)
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138 seq_text = line_split[1];
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139 if seq_id in multiple_data:
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140 return raiseException( ERR_EXIT_CODE, "Error: the id '"+seq_id+"' is duplicated", output_dir_path, str(options.errorfile) );
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141 multiple_data[seq_id] = seq_text;
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142 if len(multiple_data) > 0:
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143 return query_request( options, args, multiple_data );
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144 #return echo( options, args );
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145 else:
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146 return raiseException( ERR_EXIT_CODE, "An error has occurred. Please be sure that your input files are valid.", output_dir_path, str(options.errorfile) );
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147 else:
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148 # try with the sequence in --sequence
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149 text_content = options.sequences;
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150 #print("sequences: "+text_content);
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151 # check if options.sequences contains a list of sequences (one for each row)
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152 if text_content is not None:
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153 text_content = str(text_content);
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154 if text_content.strip():
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155 # populate a dictionary with the files containing the sequences to query
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156 text_content = text_content.strip().split("__cn__"); # split on new line
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157 for line in text_content:
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158 if line.strip() != "":
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159 line_split = line.strip().split("__tc__"); # split on tab
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160 if len(line_split) == 2: # 0:id , 1:seq , otherwise skip line
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161 seq_id = line_split[0];
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162 # fix seq_id using valid chars only
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163 seq_id = ''.join(e for e in seq_id if e in VALID_CHARS)
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164 seq_text = line_split[1];
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165 if seq_id in multiple_data:
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166 return raiseException( ERR_EXIT_CODE, "Error: the id '"+seq_id+"' is duplicated", output_dir_path, str(options.errorfile) );
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167 multiple_data[seq_id] = seq_text;
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168 if len(multiple_data) > 0:
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169 return query_request( options, args, multiple_data );
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170 #return echo( options, args );
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171 else:
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172 return raiseException( ERR_EXIT_CODE, "An error has occurred. Please be sure that your input files are valid.", output_dir_path, str(options.errorfile) );
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173 else:
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174 return raiseException( ERR_EXIT_CODE, "You have to insert at least one row formatted as a tab delimited (ID, SEQUENCE) couple", output_dir_path, str(options.errorfile) );
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175 return ERR_EXIT_CODE;
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176
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177 def __main__():
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178 # Parse the command line options
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179 usage = "Usage: query.py --files comma_sep_file_paths --names comma_seq_file_names --sequences sequences_text --search search_mode --exact exact_alg --sthreshold threshold --outputdir output_dir_path";
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180 parser = optparse.OptionParser(usage = usage);
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181 parser.add_option("-v", "--version", action="store_true", dest="version",
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182 default=False, help="display version and exit")
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183 parser.add_option("-f", "--files", type="string",
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184 action="store", dest="files", help="comma separated files path");
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185 parser.add_option("-n", "--names", type="string",
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186 action="store", dest="names", help="comma separated names associated to the files specified in --files");
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187 parser.add_option("-s", "--sequences", type="string",
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188 action="store", dest="sequences", help="contains a list of sequences (one for each row)");
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189 parser.add_option("-a", "--fasta", type="string",
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190 action="store", dest="fasta", help="contains the content of a fasta file");
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4
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191 parser.add_option("-x", "--search", type="string", default="rrr",
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0
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192 action="store", dest="search", help="search mode");
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193 parser.add_option("-e", "--exact", type="int", default=0,
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194 action="store", dest="exact", help="exact algorithm (required if search is 1 only)");
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195 parser.add_option("-k", "--tree", type="string", default=0,
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196 action="store", dest="treeid", help="the id of the tree that will be queried");
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197 parser.add_option("-t", "--sthreshold", type="float",
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198 action="store", dest="sthreshold", help="threshold applied to the search algrithm");
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199 parser.add_option("-z", "--sort", type="int", default=1,
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200 action="store", dest="sortcontrol", help="boolean required to sort the result");
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0
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201 parser.add_option("-o", "--outputdir", type="string", default="output",
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202 action="store", dest="outputdir", help="output directory (collection) path");
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203 parser.add_option("-r", "--errorfile", type="string", default="error_txt",
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204 action="store", dest="errorfile", help="error file name containing error messages");
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205
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206 # TEST
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207 #sequences = 'NM_001169378.2__tc__atttcggatgctttggagggaggaactctagtgctgcattgattggggcgtgtgttaatgatattcccagttcgcatggcgagcatcgattcctggtacgtatgtgggccccttgactcccacttatcgcacttgtcgttcgcaatttgcatgaattccgcttcgtctgaaacgcacttgcgccagacttctccggctggtctgatctggtctgtgatccggtctggtggggcgccagttgcgtttcgagctcatcaccagtcactccgcagtcgcattctgccagaggtctccgatcaagagcgcttctccattcgagattcaaacgcagcgcggtctgacgccgccacatcgagtgaaatccatatcgatggccacattcacacaggacgagatcgacttcctgcgcagccatggcaacgagctgtgtgccaagacctggctgggattgtgggatccgaagcgggctgtgcaccagcaggagcagcgcgaactgatgatggacaagtatgagcggaagcgatactacctggagccggccagtcctcttaagtcgctggccaatgcggtcaacctgaagtcgtctgctccggcgacgaaccacactcagaatggccaccaaaatgggtatgccagcatccatttgacgcctcctgctgcccagcggacctcggccaatggattgcagaaggtggccaactcgtcgagtaactcttctggaaagacctcatcctcgatcagtaggccacactataatcaccagaacaacagccaaaacaacaatcacgatgcctttggcctgggtggcggattgagcagcctgaacagcgccggttccacatccactggagctctttccgacaccagcagttgtgctagcaatggcttcggtgcggactgcgactttgtggctgactttggctcggccaacattttcgacgccacatcggcgcgttccacaggatcgccggcggtgtcgtccgtgtcctcagtgggttccagcaatggctacgccaaggtgcagcccatccgggcagctcatctccagcagcaacagcagttgcagcagcagctgcatcagcagcagctcctcaatggcaatggtcatcagggcactgagaactttgccgacttcgatcacgctcccatctacaatgcagtggctccaccgacttttaacgattggatcagcgactggagcaggcggggcttccacgatcccttcgacgattgcgatgactcgccaccaggtgcccgccctccagcacctgcgccagctcctgctcaagttcccgcagtatcatcaccattgccaaccgtccgagaagaaccagagcttgcgtggaatttttgggaggacgagatgcgaatagaggcgcaggaaaaggagtcccaaactaaacagccggagttgggctactccttttcgattagtactactacgcccctttccccttcgaatcccttcctgccctaccttgtcagtgaggagcagcatcgaaatcatccagagaagccctccttttcgtattcgttgttcagctccatatcaaatagttcgcaagaagatcaggcggatgatcatgagatgaatgttttaaatgccaatttccatgatttctttacgtggagtgctcccttgcagaacggccatacgaccagtccgcccaagggcggaaatgcagcgatggcgcccagtgaggatcgatatgccgctcttaaggatctcgacgagcagctgcgagaactgaaggccagcgaaagcgccacagagacgcccacgcccaccagtggcaatgttcaggccacagatgcctttggtggagccctcaacaacaatccaaatcccttcaagggccagcaacagcagcagctcagcagccatgtggtgaatccattccagcagcagcaacagcagcagcaccagcagaatctctatggccagttgacgctcataccaaatgcctacggcagcagttcccagcagcagatggggcaccatctcctccagcagcagcagcagcaacagcagagcttcttcaacttcaacaacaacgggttcgccatctcgcagggtctgcccaacggctgcggcttcggcagcatgcaacccgctcctgtgatggccaacaatccctttgcagccagcggcgccatgaacaccaacaatccattcttatgagactcaacccgggagaatccgcctcgcgccacctggcagaggcgctgagccagcgaacaaagagcagacgcggaggaaccgaaccgaaattagtccattttactaacaatagcgttaatctatgtatacataatgcacgccggagagcactctttgtgtacatagcccaaatatgtacacccgaaaggctccacgctgacgctagtcctcgcggatggcggaggcggactggggcgttgatatattcttttacatggtaactctactctaacgtttacggatacggatatttgtatttgccgtttgccctagaactctatacttgtactaagcgcccatgaacacttcatccactaacatagctactaatcctcatcctagtggaggatgcagttggtccagacactctgttatttgttttatccatcctcgtacttgtctttgtcccatttagcactttcgttgcggataagaactttgtcagttattgattgtgtggccttaataagattataaaactaaatattataacgtacgactatacatatacggatacagatacagattcagacacagttagtacagatacagatatacatatacgcttttgtacctaatgaattgcttcttgtttccattgctaatcatctgcttttcgtgtgctaattttatacactagtacgtgcgatatcggccgtgcagatagattgctcagctcgcgagtcaagcctcttttggttgcacccacggcagacatttgtacatatactgtctgattgtaagcctcgtgtaatacctccattaacaccactcccccaccacccatccatcgaaccccgaatccatgactcaattcactgctcacatgtccatgcccatgccttaacgtgtcaaacattatcgaagccttaaagttatttaaaactacgaaatttcaataaaaacaaataagaacgctatc';
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208 #(options, args) = parser.parse_args(['-x', 'rrr', '-t', 0.5, '-s', sequences, '-o', 'collection_content']);
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209
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210 (options, args) = parser.parse_args();
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211 if options.version:
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212 print __version__;
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213 else:
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214 # create output dir (collection)
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215 output_dir_path = options.outputdir;
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216 if not os.path.exists(output_dir_path):
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217 os.makedirs(output_dir_path);
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218
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219 return query( options, args );
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220
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221 if __name__ == "__main__": __main__()
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