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31
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1 #!/usr/bin/env python
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2
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60
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3 import sys,os, string
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31
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4 import CGData.GenomicSegment
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5 import CGData.SegToMatrix
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6 import CGData.RefGene
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7 import CGData.GeneMap
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8
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9 class matrix_write:
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10 def __init__(self, handle):
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11 self.buff = ""
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12 self.handle = handle
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13 self.probes = []
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14 def write(self, s):
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15 self.buff += s
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16 if s.endswith("\n"):
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17 tmp = self.buff.split("\t")
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60
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18 if string.strip(tmp[0]) != "probe":
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19 tmp2 = tmp[0].split("_")
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20 p = probeseg(tmp[0], tmp2[0], int(tmp2[1]), int(tmp2[2]))
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21 self.probes.append(p)
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22
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23 self.handle.write(self.buff)
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24 self.buff = ""
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25
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26 class probeseg:
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27 def __init__(self, name, chrom, chrom_start, chrom_end):
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28 self.name = name
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29 self.chrom = chrom
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30 self.chrom_start = chrom_start
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31 self.chrom_end = chrom_end
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32 self.strand = "."
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33
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34 if __name__ == "__main__":
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54
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35 if len(sys.argv[:])!= 6:
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36 print "python segToMatrixGalaxy.py inputSegmentFile refGeneFile outputMatrix outputProbeMap NORMAL_CNV\n"
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31
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37 sys.exit()
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38 seg = CGData.GenomicSegment.GenomicSegment()
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39 seg.load(sys.argv[1])
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60
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40
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41 refgene = CGData.RefGene.RefGene()
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42 refgene.load(os.path.dirname(sys.argv[0])+"/"+os.path.basename(sys.argv[2]))
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43
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44 NORMAL_CNV = sys.argv[5]
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53
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45
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46 handle = open(sys.argv[3], "w")
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47 m = matrix_write(handle)
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48 CGData.SegToMatrix.seg_to_matrix(seg, m, NORMAL_CNV)
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49 handle.close()
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50
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51 handle = open(sys.argv[4], "w")
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52 probeMapper = CGData.GeneMap.ProbeMapper('b')
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54
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53 handle.write("%s\t%s\t%s\t%s\t%s\t%s\n" % ("id", "gene","chrom","chromStart","chromEnd","strand"))
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54 for probe in m.probes:
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55 hits = []
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56 for hit in probeMapper.find_overlap( probe, refgene ):
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57 if hit.name not in hits:
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58 hits.append(hit.name)
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59 handle.write("%s\t%s\t%s\t%s\t%s\t.\n" % (probe.name, ",".join(hits), probe.chrom, probe.chrom_start, probe.chrom_end))
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60 handle.close()
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61
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62
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