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39
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1 #!/usr/bin/env python
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2
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3 import sys,string
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4 sys.path.insert(0,"../CGDataNew")
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5
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6 import CGData.GenomicSegment
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7 import CGData.SegToMatrix
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8 import CGData.RefGene
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9 import CGData.GeneMap
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10 import optparse
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11
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12 class segs:
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13 def __init__(self):
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14 self.probes = []
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15
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16 def load (self, handle): #handle bed6
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17 fin =open(handle,'r')
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18 while 1:
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19 line =string.strip(fin.readline())
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20 if line =="":
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21 break
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22 if line[0]=="#":
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23 continue
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24 tmp = string.split(line,"\t")
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25 if len(tmp)== 5:
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26 p = probeseg(tmp[0], tmp[1], int(tmp[3]), int(tmp[4]),tmp[2])
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27 self.probes.append(p)
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28 fin.close()
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29
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30
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31 class probeseg:
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32 def __init__(self, name, chrom, chrom_start, chrom_end, strand):
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33 self.name = name
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58
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34 if chrom[0:3] in ["chr","CHR","Chr"]:
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35 chrom = "chr"+chrom[3:]
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36 else:
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37 chrom = "chr"+chrom
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39
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38 self.chrom = chrom
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39 self.chrom_start = chrom_start
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40 self.chrom_end = chrom_end
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41 self.strand = strand
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42
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43
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44 if __name__ == "__main__":
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45 def printUsage():
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46 print "python segToProbeMap.py segInput(name,chr,strand,start,end) refGene(eg hg18) probeMapOut --mode=cnv|exp\n"
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47
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48 if len(sys.argv) != 5:
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49 printUsage()
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50 sys.exit()
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51
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52 parser = optparse.OptionParser()
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53 parser.add_option("--mode", action="store", type="string", dest="mode")
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54 (options, args) = parser.parse_args()
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55
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56 if (not options.mode) or (options.mode not in ["cnv","exp"]):
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57 printUsage()
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58 sys.exit()
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59
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60 probes=segs()
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61 probes.load(sys.argv[1])
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62
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63 refgene = CGData.RefGene.RefGene()
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64 refgene.load(sys.argv[2])
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65
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66 handle = open(sys.argv[3], "w")
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67 if options.mode=="cnv":
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68 probeMapper = CGData.GeneMap.ProbeMapper('b')
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69 if options.mode=="exp":
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70 probeMapper = CGData.GeneMap.ProbeMapper('g')
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71
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72 handle.write("%s\t%s\t%s\t%s\t%s\t%s\n" % ("#id", "gene","chrom","chromStart","chromEnd","strand"))
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73 for probe in probes.probes:
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74 hits = []
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75 for hit in probeMapper.find_overlap( probe, refgene ):
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76 if hit.name not in hits:
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77 hits.append(hit.name)
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78 handle.write("%s\t%s\t%s\t%s\t%s\t%s\n" % (probe.name, ",".join(hits), probe.chrom, probe.chrom_start, probe.chrom_end, probe.strand))
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79 handle.close()
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80
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81
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