Mercurial > repos > melissacline > ucsc_cancer_browser_stats
comparison ttest/stats.py @ 8:f55d3b781adb
check file input ignore bad lines`
| author | jingchunzhu@gmail.com |
|---|---|
| date | Thu, 30 Jul 2015 21:42:15 -0700 |
| parents | 14c406f8fca6 |
| children | fd8529cd1564 |
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| 7:14c406f8fca6 | 8:f55d3b781adb |
|---|---|
| 26 args.a, args.b) | 26 args.a, args.b) |
| 27 outfile = open(args.outfile, "w") | 27 outfile = open(args.outfile, "w") |
| 28 outfile.write("%s\tStatistic\tpValue\tMedian1\tMedian2\tDelta\n" % (headerTokens[0])) | 28 outfile.write("%s\tStatistic\tpValue\tMedian1\tMedian2\tDelta\n" % (headerTokens[0])) |
| 29 for row in genomicFp: | 29 for row in genomicFp: |
| 30 tokens = row.rstrip().split("\t") | 30 tokens = row.rstrip().split("\t") |
| 31 if len(tokens)!= len(headerTokens): | |
| 32 continue | |
| 31 symbol = tokens[0] | 33 symbol = tokens[0] |
| 32 groupATokens = [tokens[ii] for ii in columnsGroupA] | 34 groupATokens = [tokens[ii] for ii in columnsGroupA] |
| 33 groupBTokens = [tokens[ii] for ii in columnsGroupB] | 35 groupBTokens = [tokens[ii] for ii in columnsGroupB] |
| 34 groupAValues = [float(xx) for xx in groupATokens if xx != "NA"] | 36 groupAValues = [float(xx) for xx in groupATokens if xx != "NA"] |
| 35 groupBValues = [float(xx) for xx in groupBTokens if xx != "NA"] | 37 groupBValues = [float(xx) for xx in groupBTokens if xx != "NA"] |