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1 #!/usr/bin/env python
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2
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3 import errno
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4 import os
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5 import subprocess
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6 import sys
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7
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8 ################################################################################
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9
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10 def mkdir_p(path):
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11 try:
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12 os.makedirs(path)
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13 except OSError, e:
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14 if e.errno <> errno.EEXIST:
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15 raise
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16
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17 def run_program(prog, args, stdout_file=None):
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18 #print "args:", ' '.join(args)
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19 p = subprocess.Popen(args, bufsize=-1, executable=prog, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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20 (stdoutdata, stderrdata) = p.communicate()
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21 rc = p.returncode
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22
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23 if stdout_file is not None:
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24 with open(stdout_file, 'w') as ofh:
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25 print >> ofh, stdoutdata.rstrip('\r\n')
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26
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27 if rc != 0:
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28 print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
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29 print >> sys.stderr, stderrdata
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30 sys.exit(1)
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31
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32 ################################################################################
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33
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34 if len(sys.argv) != 11:
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35 print "usage"
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36 sys.exit(1)
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37
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38 input, dbkey, output, output_files_path, chrom_col, pos_col, score_col, shuffles, cutoff, report_snps = sys.argv[1:11]
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39
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40 prog = 'sweep'
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41
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42 args = [ prog ]
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43 args.append(input)
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44 args.append(chrom_col)
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45 args.append(pos_col)
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46 args.append(score_col)
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47 args.append(cutoff)
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48 args.append(shuffles)
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49 args.append(report_snps)
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50
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51 run_program(None, args, stdout_file=output)
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52
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53 if report_snps == "0":
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54 sys.exit(0)
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55
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56 ################################################################################
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57
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58 mkdir_p(output_files_path)
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59
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60 bedgraph_filename = 'bedgraph.txt'
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61 links_filename = os.path.join(output_files_path, 'links.txt')
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62
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63 data = []
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64 links_data = []
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65
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66 with open(output) as fh:
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67 chrom = None
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68 for line in fh:
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69 line = line.rstrip('\r\n')
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70 if not line:
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71 continue
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72 if line[0] != ' ':
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73 # chrom line, add a link
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74 chrom, interval_begin, interval_end, interval_value = line.split('\t')
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75 links_data.append((chrom, int(interval_begin), int(interval_end)))
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76 else:
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77 # data line, add a bedgraph line
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78 begin, value = line.split()
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79 data.append((chrom, int(begin), value))
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80
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81 with open(bedgraph_filename, 'w') as ofh:
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82 print >> ofh, 'track type=bedGraph'
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83 for chrom, begin, value in sorted(data):
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84 print >> ofh, chrom, begin, begin+1, value
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85
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86 with open(links_filename, 'w') as ofh:
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87 for chrom, begin, end in sorted(links_data):
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88 print >> ofh, chrom, begin, end
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89
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90 ################################################################################
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91
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92 chrom_sizes_filename = '{0}.chrom.sizes'.format(dbkey)
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93
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94 prog = 'fetchChromSizes'
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95
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96 args = [ prog ]
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97 args.append(dbkey)
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98
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99 run_program(None, args, stdout_file=chrom_sizes_filename)
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100
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101 ################################################################################
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102
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103 prog = 'bedGraphToBigWig'
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104
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105 args = [ prog ]
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106 args.append(bedgraph_filename)
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107 args.append(chrom_sizes_filename)
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108 args.append(output)
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109
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110 run_program(None, args)
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111
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112 ################################################################################
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113
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114 sys.exit(0)
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115
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