Mercurial > repos > melissacline > ucsc_cancer_utilities
comparison seg2matrix/mapSegToGeneMatrix.py @ 54:59dbe857f5d4
introduce normal_CNV parameter
| author | jingchunzhu |
|---|---|
| date | Thu, 17 Sep 2015 22:03:04 -0700 |
| parents | 728eda331f07 |
| children | bf57076e27b9 |
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| 53:7de3db823f90 | 54:59dbe857f5d4 |
|---|---|
| 5 import CGData.GeneMap | 5 import CGData.GeneMap |
| 6 import segToProbeMap | 6 import segToProbeMap |
| 7 | 7 |
| 8 if __name__ == "__main__": | 8 if __name__ == "__main__": |
| 9 | 9 |
| 10 if len(sys.argv[:])!=4: | 10 if len(sys.argv[:])!=5: |
| 11 print "python mapSegToGeneMatrix.py genomicsSegmentIn refGene GeneLevelMatrixOut\n" | 11 print "python mapSegToGeneMatrix.py genomicsSegmentIn refGene GeneLevelMatrixOut NORMAL_CNV\n" |
| 12 sys.exit() | 12 sys.exit() |
| 13 refgene = CGData.RefGene.RefGene() | 13 refgene = CGData.RefGene.RefGene() |
| 14 refgene.load( sys.argv[2] ) | 14 refgene.load( sys.argv[2] ) |
| 15 | |
| 16 NORMAL_CNV=sys.argv[4] | |
| 15 | 17 |
| 16 #* b for cnv | 18 #* b for cnv |
| 17 probeMapper = CGData.GeneMap.ProbeMapper('b') | 19 probeMapper = CGData.GeneMap.ProbeMapper('b') |
| 18 | 20 |
| 19 fin =open(sys.argv[1],'r') | 21 fin =open(sys.argv[1],'r') |
| 72 for gene in genes.keys(): | 74 for gene in genes.keys(): |
| 73 fout.write(gene) | 75 fout.write(gene) |
| 74 for sample in sample_list: | 76 for sample in sample_list: |
| 75 list = matrix[samples[sample]][genes[gene]] | 77 list = matrix[samples[sample]][genes[gene]] |
| 76 if len(list)==0: | 78 if len(list)==0: |
| 77 average =0 | 79 average = NORMAL_CNV |
| 78 elif len(list)==1: | 80 elif len(list)==1: |
| 79 average = list[0] | 81 average = list[0] |
| 80 average =round(average,3) | 82 average =round(average,3) |
| 81 else: | 83 else: |
| 82 total=0.0 | 84 total=0.0 |