Mercurial > repos > melissacline > ucsc_cancer_utilities
changeset 60:bf57076e27b9 default tip
change genomicSegment input data
| author | jingchunzhu@gmail.com |
|---|---|
| date | Tue, 27 Oct 2015 16:07:09 -0700 |
| parents | b88b95642f59 |
| children | |
| files | seg2matrix/CGData/GenomicSegment.py seg2matrix/mapSegToGeneMatrix.py seg2matrix/segToMatrixGalaxy.py segToGeneMatrix.xml segToMatrix.xml |
| diffstat | 5 files changed, 22 insertions(+), 24 deletions(-) [+] |
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--- a/seg2matrix/CGData/GenomicSegment.py Tue Sep 22 15:41:03 2015 -0700 +++ b/seg2matrix/CGData/GenomicSegment.py Tue Oct 27 16:07:09 2015 -0700 @@ -13,7 +13,6 @@ "chrom", "chrom_start", "chrom_end", - "strand", "value" ], "groupKey" : "id",
--- a/seg2matrix/mapSegToGeneMatrix.py Tue Sep 22 15:41:03 2015 -0700 +++ b/seg2matrix/mapSegToGeneMatrix.py Tue Oct 27 16:07:09 2015 -0700 @@ -48,11 +48,11 @@ if line[0]=="#": continue tmp = string.split(line,"\t") - if len(tmp)!= 6: + if len(tmp)!= 5: continue - seg = segToProbeMap.probeseg("", tmp[1], int(tmp[2]), int(tmp[3]),tmp[4]) + seg = segToProbeMap.probeseg("", tmp[1], int(tmp[2]), int(tmp[3]),".") sample = tmp[0] - value = float(tmp[5]) + value = float(tmp[4]) if sample not in samples: samples[sample]=len(samples) matrix.append(copy.deepcopy(oneSample))
--- a/seg2matrix/segToMatrixGalaxy.py Tue Sep 22 15:41:03 2015 -0700 +++ b/seg2matrix/segToMatrixGalaxy.py Tue Oct 27 16:07:09 2015 -0700 @@ -1,6 +1,6 @@ #!/usr/bin/env python -import sys,os +import sys,os, string import CGData.GenomicSegment import CGData.SegToMatrix import CGData.RefGene @@ -15,7 +15,7 @@ self.buff += s if s.endswith("\n"): tmp = self.buff.split("\t") - if tmp[0] != "probe": + if string.strip(tmp[0]) != "probe": tmp2 = tmp[0].split("_") p = probeseg(tmp[0], tmp2[0], int(tmp2[1]), int(tmp2[2])) self.probes.append(p) @@ -31,14 +31,13 @@ self.chrom_end = chrom_end self.strand = "." - if __name__ == "__main__": if len(sys.argv[:])!= 6: print "python segToMatrixGalaxy.py inputSegmentFile refGeneFile outputMatrix outputProbeMap NORMAL_CNV\n" sys.exit() seg = CGData.GenomicSegment.GenomicSegment() seg.load(sys.argv[1]) - + refgene = CGData.RefGene.RefGene() refgene.load(os.path.dirname(sys.argv[0])+"/"+os.path.basename(sys.argv[2]))
--- a/segToGeneMatrix.xml Tue Sep 22 15:41:03 2015 -0700 +++ b/segToGeneMatrix.xml Tue Oct 27 16:07:09 2015 -0700 @@ -30,14 +30,14 @@ 1. Input data file format: tab-deliminated - ======= ===== ======= ===== ====== ====== - sample chr start end strand value - ======= ===== ======= ===== ====== ====== - sample1 chr1 1 100 . 0.5 - sample2 chr1 101 1000 . 1.5 - sample3 chr1 1000 2000 . -0.5 - ... ... ... ... ... ... - ======= ===== ======= ===== ====== ====== + ======= ===== ======= ===== ====== + sample chr start end value + ======= ===== ======= ===== ====== + sample1 chr1 1 100 0.5 + sample2 chr1 101 1000 1.5 + sample3 chr1 1000 2000 -0.5 + ... ... ... ... ... + ======= ===== ======= ===== ====== 2. Output file: gene-level matrix file
--- a/segToMatrix.xml Tue Sep 22 15:41:03 2015 -0700 +++ b/segToMatrix.xml Tue Oct 27 16:07:09 2015 -0700 @@ -31,14 +31,14 @@ 1. Input data file format: tab-deliminated - ======= ===== ======= ===== ====== ====== - sample chr start end strand value - ======= ===== ======= ===== ====== ====== - sample1 chr1 1 100 . 0.5 - sample2 chr1 101 1000 . 1.5 - sample3 chr1 1000 2000 . -0.5 - ... ... ... ... ... ... - ======= ===== ======= ===== ====== ====== + ======= ===== ======= ===== ====== + sample chr start end value + ======= ===== ======= ===== ====== + sample1 chr1 1 100 0.5 + sample2 chr1 101 1000 1.5 + sample3 chr1 1000 2000 -0.5 + ... ... ... ... ... + ======= ===== ======= ===== ====== 2. Output File no 1. matrix file