コード例 #1
0
    dirJob = sys.argv[1]
    N = int(sys.argv[2])
    temp_age_folder = sys.argv[3]
    temp_OS_folder = sys.argv[4]
    
    from collections import defaultdict
    
    # Running on rnuuspr66 server
    # temporary folder to store qsub job related files
    if not os.path.exists(dirJob):
        os.mkdir(dirJob)
    fusion = getallfusion()
    fusion = list(fusion)
    
    # randomly partition the fusion list into N nearly equal parts
    fusionPartition = randompartition(fusion,N)
    for i in range(N):
        name = 'Job' + str(i) + '_datafile'
        filename = os.path.join(dirJob,name)
        ofile = open(filename,'w')
        fp = fusionPartition[i]
        for f in fp:
            line = '\t'.join([f[0],f[1],f[2]])
            ofile.write(line+'\n')
        ofile.close()
    
    for i in range(N):
        name = 'Job' + str(i) + '_datafile'
        filename = os.path.join(dirJob,name)
        qsubString = '''#!/bin/sh
#PBS -N AgeOSJob%d
コード例 #2
0
 temp_OS_folder = sys.argv[4]
 
 from collections import defaultdict
 
 # Running on rnuuspr66 server
 # temporary folder to store qsub job related files
 if not os.path.exists(dirJob):
     os.mkdir(dirJob)
 fusion = getallfusion()
 fusion = list(fusion)
 
 # randomly partition the fusion list into N nearly equal parts
 fDict = defaultdict(list)
 for cancer,g5p,g3p in fusion:
     fDict[(cancer,g3p)].append(g5p)
 fusionPartition = randompartition(fDict.keys(),N)
 for i in range(N):
     name = 'Job' + str(i) + '_datafile'
     filename = os.path.join(dirJob,name)
     ofile = open(filename,'w')
     fp = fusionPartition[i]
     for f in fp:
         g5p = fDict[f]
         if len(g5p)==1:
             gene5p = g5p[0]
         else:
             gene5p = ','.join(g5p)
         line = '\t'.join([f[0],gene5p,f[1]])
         ofile.write(line+'\n')
     ofile.close()