Mercurial > repos > fabio > btman
changeset 4:69a3505ac594 draft
Uploaded 20180405
| author | fabio |
|---|---|
| date | Wed, 04 Apr 2018 18:54:40 -0400 |
| parents | 557d09d81807 |
| children | b43644a7a91e |
| files | ._.shed.yml ._query.xml query.py query.xml |
| diffstat | 4 files changed, 20 insertions(+), 5 deletions(-) [+] |
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--- a/query.py Tue Apr 03 20:39:33 2018 -0400 +++ b/query.py Wed Apr 04 18:54:40 2018 -0400 @@ -9,7 +9,7 @@ #### NN14 #### SERVICE_URL = "http://nn14.galaxyproject.org:8080/"; #service_url = "http://127.0.0.1:8082/"; -QUERY_URL = SERVICE_URL+"tree/1/query"; +QUERY_URL = SERVICE_URL+"tree/<tree_id>/query"; STATUS_URL = SERVICE_URL+"status/<query_id>"; ############## # query delay in seconds @@ -41,7 +41,8 @@ # create a session session = requests.Session(); # make a synchronous post request to the query route - req = session.post(QUERY_URL, headers=headers, json=payload); + QUERY_URL.replace("<tree_id>", str(options.treeid)); + req = session.post(QUERY_URL.replace("<tree_id>", str(options.treeid)), headers=headers, json=payload); resp_code = req.status_code; #print(str(req.content)+"\n\n"); if resp_code == requests.codes.ok: @@ -80,11 +81,22 @@ output_file_path = os.path.join(output_dir_path, seq_id + "_" + out_file_format); accessions_list = ""; hits_block = block['hits']; + accessions_dict = { }; + is_sabutan = False; for hit in hits_block: if type(hit) is dict: # sabutan - accessions_list = accessions_list + hit['accession_number'] + "\t" + hit['score'] + "\n"; + #accessions_list = accessions_list + str(hit['accession_number']) + "\t" + str(hit['score']) + "\n"; + accession_number = hit['accession_number']; + score = hit['score']; + score_split = score.split("/"); + accessions_dict[accession_number] = "{0:.6f}".format(float(score_split[0])/float(score_split[1])); + is_sabutan = True; else: # all-some accessions_list = accessions_list + str(hit) + "\n"; + if is_sabutan: + sorted_accessions = sorted(accessions_dict, key=lambda i: float(accessions_dict[i])); + for acc in sorted_accessions: + accessions_list = accessions_list + str(acc) + "\t" + str(accessions_dict[acc]) + "\n"; with open(output_file_path, 'w') as out: out.write(accessions_list.strip()); return sys.exit(OK_EXIT_CODE); @@ -167,15 +179,17 @@ action="store", dest="sequences", help="contains a list of sequences (one for each row)"); parser.add_option("-a", "--fasta", type="string", action="store", dest="fasta", help="contains the content of a fasta file"); - parser.add_option("-x", "--search", type="string", default=0, + parser.add_option("-x", "--search", type="string", default="rrr", action="store", dest="search", help="search mode"); parser.add_option("-e", "--exact", type="int", default=0, action="store", dest="exact", help="exact algorithm (required if search is 1 only)"); + parser.add_option("-k", "--tree", type="int", default=0, + action="store", dest="treeid", help="the id of the tree that will be queried"); parser.add_option("-t", "--sthreshold", type="float", action="store", dest="sthreshold", help="threshold applied to the search algrithm"); parser.add_option("-o", "--outputdir", type="string", default="output", action="store", dest="outputdir", help="output directory (collection) path"); - parser.add_option("-r", "--errorfile", type="string", default="error.log", + parser.add_option("-r", "--errorfile", type="string", default="error_txt", action="store", dest="errorfile", help="error file name containing error messages"); # TEST