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comparison query.py @ 4:69a3505ac594 draft

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Uploaded 20180405
author fabio
date Wed, 04 Apr 2018 18:54:40 -0400
parents 315246810bfa
children 300e4932bad6
comparison
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3:557d09d81807 4:69a3505ac594
7 #from requests_futures.sessions import FuturesSession 7 #from requests_futures.sessions import FuturesSession
8 8
9 #### NN14 #### 9 #### NN14 ####
10 SERVICE_URL = "http://nn14.galaxyproject.org:8080/"; 10 SERVICE_URL = "http://nn14.galaxyproject.org:8080/";
11 #service_url = "http://127.0.0.1:8082/"; 11 #service_url = "http://127.0.0.1:8082/";
12 QUERY_URL = SERVICE_URL+"tree/1/query"; 12 QUERY_URL = SERVICE_URL+"tree/<tree_id>/query";
13 STATUS_URL = SERVICE_URL+"status/<query_id>"; 13 STATUS_URL = SERVICE_URL+"status/<query_id>";
14 ############## 14 ##############
15 # query delay in seconds 15 # query delay in seconds
16 QUERY_DELAY = 30; 16 QUERY_DELAY = 30;
17 ############## 17 ##############
39 headers = {'Content-type': 'application/json'}; 39 headers = {'Content-type': 'application/json'};
40 40
41 # create a session 41 # create a session
42 session = requests.Session(); 42 session = requests.Session();
43 # make a synchronous post request to the query route 43 # make a synchronous post request to the query route
44 req = session.post(QUERY_URL, headers=headers, json=payload); 44 QUERY_URL.replace("<tree_id>", str(options.treeid));
45 req = session.post(QUERY_URL.replace("<tree_id>", str(options.treeid)), headers=headers, json=payload);
45 resp_code = req.status_code; 46 resp_code = req.status_code;
46 #print(str(req.content)+"\n\n"); 47 #print(str(req.content)+"\n\n");
47 if resp_code == requests.codes.ok: 48 if resp_code == requests.codes.ok:
48 resp_content = str(req.content); 49 resp_content = str(req.content);
49 # convert out to json 50 # convert out to json
78 seq_id = block['sequence_id']; 79 seq_id = block['sequence_id'];
79 # put response block in the output collection 80 # put response block in the output collection
80 output_file_path = os.path.join(output_dir_path, seq_id + "_" + out_file_format); 81 output_file_path = os.path.join(output_dir_path, seq_id + "_" + out_file_format);
81 accessions_list = ""; 82 accessions_list = "";
82 hits_block = block['hits']; 83 hits_block = block['hits'];
84 accessions_dict = { };
85 is_sabutan = False;
83 for hit in hits_block: 86 for hit in hits_block:
84 if type(hit) is dict: # sabutan 87 if type(hit) is dict: # sabutan
85 accessions_list = accessions_list + hit['accession_number'] + "\t" + hit['score'] + "\n"; 88 #accessions_list = accessions_list + str(hit['accession_number']) + "\t" + str(hit['score']) + "\n";
89 accession_number = hit['accession_number'];
90 score = hit['score'];
91 score_split = score.split("/");
92 accessions_dict[accession_number] = "{0:.6f}".format(float(score_split[0])/float(score_split[1]));
93 is_sabutan = True;
86 else: # all-some 94 else: # all-some
87 accessions_list = accessions_list + str(hit) + "\n"; 95 accessions_list = accessions_list + str(hit) + "\n";
96 if is_sabutan:
97 sorted_accessions = sorted(accessions_dict, key=lambda i: float(accessions_dict[i]));
98 for acc in sorted_accessions:
99 accessions_list = accessions_list + str(acc) + "\t" + str(accessions_dict[acc]) + "\n";
88 with open(output_file_path, 'w') as out: 100 with open(output_file_path, 'w') as out:
89 out.write(accessions_list.strip()); 101 out.write(accessions_list.strip());
90 return sys.exit(OK_EXIT_CODE); 102 return sys.exit(OK_EXIT_CODE);
91 else: 103 else:
92 return raiseException( ERR_EXIT_CODE, "Unable to query the remote server. Please try again in a while.", output_dir_path, str(options.errorfile) ); 104 return raiseException( ERR_EXIT_CODE, "Unable to query the remote server. Please try again in a while.", output_dir_path, str(options.errorfile) );
165 action="store", dest="names", help="comma separated names associated to the files specified in --files"); 177 action="store", dest="names", help="comma separated names associated to the files specified in --files");
166 parser.add_option("-s", "--sequences", type="string", 178 parser.add_option("-s", "--sequences", type="string",
167 action="store", dest="sequences", help="contains a list of sequences (one for each row)"); 179 action="store", dest="sequences", help="contains a list of sequences (one for each row)");
168 parser.add_option("-a", "--fasta", type="string", 180 parser.add_option("-a", "--fasta", type="string",
169 action="store", dest="fasta", help="contains the content of a fasta file"); 181 action="store", dest="fasta", help="contains the content of a fasta file");
170 parser.add_option("-x", "--search", type="string", default=0, 182 parser.add_option("-x", "--search", type="string", default="rrr",
171 action="store", dest="search", help="search mode"); 183 action="store", dest="search", help="search mode");
172 parser.add_option("-e", "--exact", type="int", default=0, 184 parser.add_option("-e", "--exact", type="int", default=0,
173 action="store", dest="exact", help="exact algorithm (required if search is 1 only)"); 185 action="store", dest="exact", help="exact algorithm (required if search is 1 only)");
186 parser.add_option("-k", "--tree", type="int", default=0,
187 action="store", dest="treeid", help="the id of the tree that will be queried");
174 parser.add_option("-t", "--sthreshold", type="float", 188 parser.add_option("-t", "--sthreshold", type="float",
175 action="store", dest="sthreshold", help="threshold applied to the search algrithm"); 189 action="store", dest="sthreshold", help="threshold applied to the search algrithm");
176 parser.add_option("-o", "--outputdir", type="string", default="output", 190 parser.add_option("-o", "--outputdir", type="string", default="output",
177 action="store", dest="outputdir", help="output directory (collection) path"); 191 action="store", dest="outputdir", help="output directory (collection) path");
178 parser.add_option("-r", "--errorfile", type="string", default="error.log", 192 parser.add_option("-r", "--errorfile", type="string", default="error_txt",
179 action="store", dest="errorfile", help="error file name containing error messages"); 193 action="store", dest="errorfile", help="error file name containing error messages");
180 194
181 # TEST 195 # TEST
182 #sequences = 'NM_001169378.2__tc__atttcggatgctttggagggaggaactctagtgctgcattgattggggcgtgtgttaatgatattcccagttcgcatggcgagcatcgattcctggtacgtatgtgggccccttgactcccacttatcgcacttgtcgttcgcaatttgcatgaattccgcttcgtctgaaacgcacttgcgccagacttctccggctggtctgatctggtctgtgatccggtctggtggggcgccagttgcgtttcgagctcatcaccagtcactccgcagtcgcattctgccagaggtctccgatcaagagcgcttctccattcgagattcaaacgcagcgcggtctgacgccgccacatcgagtgaaatccatatcgatggccacattcacacaggacgagatcgacttcctgcgcagccatggcaacgagctgtgtgccaagacctggctgggattgtgggatccgaagcgggctgtgcaccagcaggagcagcgcgaactgatgatggacaagtatgagcggaagcgatactacctggagccggccagtcctcttaagtcgctggccaatgcggtcaacctgaagtcgtctgctccggcgacgaaccacactcagaatggccaccaaaatgggtatgccagcatccatttgacgcctcctgctgcccagcggacctcggccaatggattgcagaaggtggccaactcgtcgagtaactcttctggaaagacctcatcctcgatcagtaggccacactataatcaccagaacaacagccaaaacaacaatcacgatgcctttggcctgggtggcggattgagcagcctgaacagcgccggttccacatccactggagctctttccgacaccagcagttgtgctagcaatggcttcggtgcggactgcgactttgtggctgactttggctcggccaacattttcgacgccacatcggcgcgttccacaggatcgccggcggtgtcgtccgtgtcctcagtgggttccagcaatggctacgccaaggtgcagcccatccgggcagctcatctccagcagcaacagcagttgcagcagcagctgcatcagcagcagctcctcaatggcaatggtcatcagggcactgagaactttgccgacttcgatcacgctcccatctacaatgcagtggctccaccgacttttaacgattggatcagcgactggagcaggcggggcttccacgatcccttcgacgattgcgatgactcgccaccaggtgcccgccctccagcacctgcgccagctcctgctcaagttcccgcagtatcatcaccattgccaaccgtccgagaagaaccagagcttgcgtggaatttttgggaggacgagatgcgaatagaggcgcaggaaaaggagtcccaaactaaacagccggagttgggctactccttttcgattagtactactacgcccctttccccttcgaatcccttcctgccctaccttgtcagtgaggagcagcatcgaaatcatccagagaagccctccttttcgtattcgttgttcagctccatatcaaatagttcgcaagaagatcaggcggatgatcatgagatgaatgttttaaatgccaatttccatgatttctttacgtggagtgctcccttgcagaacggccatacgaccagtccgcccaagggcggaaatgcagcgatggcgcccagtgaggatcgatatgccgctcttaaggatctcgacgagcagctgcgagaactgaaggccagcgaaagcgccacagagacgcccacgcccaccagtggcaatgttcaggccacagatgcctttggtggagccctcaacaacaatccaaatcccttcaagggccagcaacagcagcagctcagcagccatgtggtgaatccattccagcagcagcaacagcagcagcaccagcagaatctctatggccagttgacgctcataccaaatgcctacggcagcagttcccagcagcagatggggcaccatctcctccagcagcagcagcagcaacagcagagcttcttcaacttcaacaacaacgggttcgccatctcgcagggtctgcccaacggctgcggcttcggcagcatgcaacccgctcctgtgatggccaacaatccctttgcagccagcggcgccatgaacaccaacaatccattcttatgagactcaacccgggagaatccgcctcgcgccacctggcagaggcgctgagccagcgaacaaagagcagacgcggaggaaccgaaccgaaattagtccattttactaacaatagcgttaatctatgtatacataatgcacgccggagagcactctttgtgtacatagcccaaatatgtacacccgaaaggctccacgctgacgctagtcctcgcggatggcggaggcggactggggcgttgatatattcttttacatggtaactctactctaacgtttacggatacggatatttgtatttgccgtttgccctagaactctatacttgtactaagcgcccatgaacacttcatccactaacatagctactaatcctcatcctagtggaggatgcagttggtccagacactctgttatttgttttatccatcctcgtacttgtctttgtcccatttagcactttcgttgcggataagaactttgtcagttattgattgtgtggccttaataagattataaaactaaatattataacgtacgactatacatatacggatacagatacagattcagacacagttagtacagatacagatatacatatacgcttttgtacctaatgaattgcttcttgtttccattgctaatcatctgcttttcgtgtgctaattttatacactagtacgtgcgatatcggccgtgcagatagattgctcagctcgcgagtcaagcctcttttggttgcacccacggcagacatttgtacatatactgtctgattgtaagcctcgtgtaatacctccattaacaccactcccccaccacccatccatcgaaccccgaatccatgactcaattcactgctcacatgtccatgcccatgccttaacgtgtcaaacattatcgaagccttaaagttatttaaaactacgaaatttcaataaaaacaaataagaacgctatc'; 196 #sequences = 'NM_001169378.2__tc__atttcggatgctttggagggaggaactctagtgctgcattgattggggcgtgtgttaatgatattcccagttcgcatggcgagcatcgattcctggtacgtatgtgggccccttgactcccacttatcgcacttgtcgttcgcaatttgcatgaattccgcttcgtctgaaacgcacttgcgccagacttctccggctggtctgatctggtctgtgatccggtctggtggggcgccagttgcgtttcgagctcatcaccagtcactccgcagtcgcattctgccagaggtctccgatcaagagcgcttctccattcgagattcaaacgcagcgcggtctgacgccgccacatcgagtgaaatccatatcgatggccacattcacacaggacgagatcgacttcctgcgcagccatggcaacgagctgtgtgccaagacctggctgggattgtgggatccgaagcgggctgtgcaccagcaggagcagcgcgaactgatgatggacaagtatgagcggaagcgatactacctggagccggccagtcctcttaagtcgctggccaatgcggtcaacctgaagtcgtctgctccggcgacgaaccacactcagaatggccaccaaaatgggtatgccagcatccatttgacgcctcctgctgcccagcggacctcggccaatggattgcagaaggtggccaactcgtcgagtaactcttctggaaagacctcatcctcgatcagtaggccacactataatcaccagaacaacagccaaaacaacaatcacgatgcctttggcctgggtggcggattgagcagcctgaacagcgccggttccacatccactggagctctttccgacaccagcagttgtgctagcaatggcttcggtgcggactgcgactttgtggctgactttggctcggccaacattttcgacgccacatcggcgcgttccacaggatcgccggcggtgtcgtccgtgtcctcagtgggttccagcaatggctacgccaaggtgcagcccatccgggcagctcatctccagcagcaacagcagttgcagcagcagctgcatcagcagcagctcctcaatggcaatggtcatcagggcactgagaactttgccgacttcgatcacgctcccatctacaatgcagtggctccaccgacttttaacgattggatcagcgactggagcaggcggggcttccacgatcccttcgacgattgcgatgactcgccaccaggtgcccgccctccagcacctgcgccagctcctgctcaagttcccgcagtatcatcaccattgccaaccgtccgagaagaaccagagcttgcgtggaatttttgggaggacgagatgcgaatagaggcgcaggaaaaggagtcccaaactaaacagccggagttgggctactccttttcgattagtactactacgcccctttccccttcgaatcccttcctgccctaccttgtcagtgaggagcagcatcgaaatcatccagagaagccctccttttcgtattcgttgttcagctccatatcaaatagttcgcaagaagatcaggcggatgatcatgagatgaatgttttaaatgccaatttccatgatttctttacgtggagtgctcccttgcagaacggccatacgaccagtccgcccaagggcggaaatgcagcgatggcgcccagtgaggatcgatatgccgctcttaaggatctcgacgagcagctgcgagaactgaaggccagcgaaagcgccacagagacgcccacgcccaccagtggcaatgttcaggccacagatgcctttggtggagccctcaacaacaatccaaatcccttcaagggccagcaacagcagcagctcagcagccatgtggtgaatccattccagcagcagcaacagcagcagcaccagcagaatctctatggccagttgacgctcataccaaatgcctacggcagcagttcccagcagcagatggggcaccatctcctccagcagcagcagcagcaacagcagagcttcttcaacttcaacaacaacgggttcgccatctcgcagggtctgcccaacggctgcggcttcggcagcatgcaacccgctcctgtgatggccaacaatccctttgcagccagcggcgccatgaacaccaacaatccattcttatgagactcaacccgggagaatccgcctcgcgccacctggcagaggcgctgagccagcgaacaaagagcagacgcggaggaaccgaaccgaaattagtccattttactaacaatagcgttaatctatgtatacataatgcacgccggagagcactctttgtgtacatagcccaaatatgtacacccgaaaggctccacgctgacgctagtcctcgcggatggcggaggcggactggggcgttgatatattcttttacatggtaactctactctaacgtttacggatacggatatttgtatttgccgtttgccctagaactctatacttgtactaagcgcccatgaacacttcatccactaacatagctactaatcctcatcctagtggaggatgcagttggtccagacactctgttatttgttttatccatcctcgtacttgtctttgtcccatttagcactttcgttgcggataagaactttgtcagttattgattgtgtggccttaataagattataaaactaaatattataacgtacgactatacatatacggatacagatacagattcagacacagttagtacagatacagatatacatatacgcttttgtacctaatgaattgcttcttgtttccattgctaatcatctgcttttcgtgtgctaattttatacactagtacgtgcgatatcggccgtgcagatagattgctcagctcgcgagtcaagcctcttttggttgcacccacggcagacatttgtacatatactgtctgattgtaagcctcgtgtaatacctccattaacaccactcccccaccacccatccatcgaaccccgaatccatgactcaattcactgctcacatgtccatgcccatgccttaacgtgtcaaacattatcgaagccttaaagttatttaaaactacgaaatttcaataaaaacaaataagaacgctatc';
183 #(options, args) = parser.parse_args(['-x', 'rrr', '-t', 0.5, '-s', sequences, '-o', 'collection_content']); 197 #(options, args) = parser.parse_args(['-x', 'rrr', '-t', 0.5, '-s', sequences, '-o', 'collection_content']);