Mercurial > repos > melissacline > ucsc_xena_platform
comparison getXenaData.py @ 50:3167c1a26101
fix
| author | jingchunzhu |
|---|---|
| date | Wed, 12 Aug 2015 16:38:12 -0700 |
| parents | 78d6e6772e30 |
| children | bb840cc2603d |
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| 49:8da6920a39ac | 50:3167c1a26101 |
|---|---|
| 4 | 4 |
| 5 if len(sys.argv[:])!=4: | 5 if len(sys.argv[:])!=4: |
| 6 print "python getXenaData.py hub datasetId outputfile\n" | 6 print "python getXenaData.py hub datasetId outputfile\n" |
| 7 sys.exit(1) | 7 sys.exit(1) |
| 8 | 8 |
| 9 url = sys.argv[1] | 9 def main(): |
| 10 dataset = sys.argv[2] | 10 url = sys.argv[1] |
| 11 output = sys.argv[3] | 11 dataset = sys.argv[2] |
| 12 output = sys.argv[3] | |
| 12 | 13 |
| 13 fout = open(output,'w') | 14 fout = open(output,'w') |
| 14 | 15 |
| 15 if string.find(url,"galaxyxena") !=-1 and string.find(url,"ucsc.edu")!=-1: | 16 contactUrl = url |
| 16 url = "https://galaxyxena.soe.ucsc.edu:443/xena" | 17 if string.find(url,"galaxyxena") !=-1 and string.find(url,"ucsc.edu")!=-1: |
| 18 contactUrl = "https://galaxyxena.soe.ucsc.edu:443/xena" | |
| 17 | 19 |
| 18 #testing if the url is reachable | 20 #testing if the url is reachable |
| 19 try: | 21 try: |
| 20 r =json.loads(xena.post(url, "(+ 1 2)")) | 22 r =json.loads(xena.post(contactUrl, "(+ 1 2)")) |
| 21 if r!=3.0: | 23 |
| 22 print "The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to you." | 24 if r!=3.0: |
| 25 print "The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to this galaxy instance." | |
| 26 print "You entered hub: %s" % (url) | |
| 27 fout.write("The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to this galaxy instance.\n") | |
| 28 fout.write("You entered hub: %s\n" % (url)) | |
| 29 fout.close() | |
| 30 sys.exit(1) | |
| 31 | |
| 32 except: | |
| 33 print "The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to this galaxy instance." | |
| 23 print "You entered hub: %s" % (url) | 34 print "You entered hub: %s" % (url) |
| 24 fout.write("The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to you.\n") | 35 fout.write("The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to this galaxy instance.\n") |
| 25 fout.write("You entered hub: %s\n" % (url)) | |
| 26 fout.close() | |
| 27 sys.exit(1) | |
| 28 except: | |
| 29 print "The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to you." | |
| 30 print "You entered hub: %s" % (url) | |
| 31 fout.write("The hub seems can not be reached, either it is not running, the url has a typo, or it is not accessible to you.\n") | |
| 32 fout.write("You entered hub: %s\n" % (url)) | 36 fout.write("You entered hub: %s\n" % (url)) |
| 33 fout.close() | 37 fout.close() |
| 34 sys.exit(1) | 38 sys.exit(1) |
| 35 | 39 |
| 36 samples = xena.dataset_samples (url, dataset) | 40 samples = xena.dataset_samples (contactUrl, dataset) |
| 37 if not samples: | 41 if not samples: |
| 38 print "Dataset does not exist" | 42 print "Dataset does not exist" |
| 39 print "You entered dataset id: %s" % (dataset) | 43 print "You entered dataset id: %s" % (dataset) |
| 40 fout.write("Dataset does not exists\n") | 44 fout.write("Dataset does not exists\n") |
| 41 fout.write("You entered dataset id: %s\n" % (dataset)) | 45 fout.write("You entered dataset id: %s\n" % (dataset)) |
| 46 fout.close() | |
| 47 sys.exit(1) | |
| 48 | |
| 49 type = xena.dataset_type(contactUrl, dataset) | |
| 50 if type[0] not in ["genomicMatrix", "clinicalMatrix"]: | |
| 51 print "The type of data is not supported" | |
| 52 print "datatype=%s" % (type[0]) | |
| 53 fout.write("The type of data is not supported\n") | |
| 54 fout.write("datatype=%s\n" % (type[0])) | |
| 55 fout.close() | |
| 56 sys.exit(1) | |
| 57 | |
| 58 writer = csv.writer(fout, delimiter='\t') | |
| 59 writer.writerow(["sample"]+samples) | |
| 60 | |
| 61 probes = xena.dataset_field(contactUrl, dataset) | |
| 62 start=0 | |
| 63 size =100 | |
| 64 N= len(probes) | |
| 65 for i in range (start, N,size): | |
| 66 results = xena.dataset_probe_values (contactUrl, dataset, samples, probes[i:i+size]) | |
| 67 print ".", | |
| 68 for j in range (0, size): | |
| 69 if i+j == N: | |
| 70 break | |
| 71 writer.writerow([probes[i+j]]+results[j]) | |
| 72 | |
| 42 fout.close() | 73 fout.close() |
| 43 sys.exit(1) | 74 print "done" |
| 75 sys.exit(0) | |
| 44 | 76 |
| 45 type = xena.dataset_type(url, dataset) | |
| 46 if type[0] not in ["genomicMatrix", "clinicalMatrix"]: | |
| 47 print "The type of data is not supported" | |
| 48 print "datatype=%s" % (type[0]) | |
| 49 fout.write("The type of data is not supported\n") | |
| 50 fout.write("datatype=%s\n" % (type[0])) | |
| 51 fout.close() | |
| 52 sys.exit(1) | |
| 53 | 77 |
| 54 writer = csv.writer(fout, delimiter='\t') | 78 if __name__ == "__main__": |
| 55 writer.writerow(["sample"]+samples) | 79 main() |
| 56 | 80 |
| 57 probes = xena.dataset_field(url, dataset) | |
| 58 start=0 | |
| 59 size =100 | |
| 60 N= len(probes) | |
| 61 for i in range (start, N,size): | |
| 62 results = xena.dataset_probe_values (url, dataset, samples, probes[i:i+size]) | |
| 63 print ".", | |
| 64 for j in range (0, size): | |
| 65 if i+j == N: | |
| 66 break | |
| 67 writer.writerow([probes[i+j]]+results[j]) | |
| 68 | |
| 69 fout.close() | |
| 70 print "done" | |
| 71 sys.exit(0) |