Mercurial > repos > xuebing > sharplabtool
diff spatial_proximity.py @ 14:76e1b1b21cce default tip
Deleted selected files
author | xuebing |
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date | Tue, 13 Mar 2012 19:05:10 -0400 |
parents | 292186c14b08 |
children |
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--- a/spatial_proximity.py Sat Mar 10 08:17:36 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ - -import os,sys - -file1 = sys.argv[1] -file2 = sys.argv[2] -genome = sys.argv[3] -outplot = sys.argv[4] -outlog = sys.argv[5] -outbed = sys.argv[6] - -strandness = '' -if len(sys.argv) > 7: - strandness = sys.argv[7] - -# real distance -cmd = 'closestBed -a '+file1+' -b '+file2 + ' '+strandness + ' -d -t first > '+outbed -os.system(cmd) -# shuffle -cmd = 'shuffleBed -chrom -g '+genome+' -i '+file1+'> shuffled.bed' -os.system(cmd) -# shuffled distance -cmd = 'closestBed -a shuffled.bed -b '+file2 + ' '+strandness + ' -d -t first > shuffled.dist' -os.system(cmd) - - -# test in R -r = open('tmp.r','w') -r.write("options(warn=-1)\n") -r.write("source('/Users/xuebing/galaxy-dist/tools/mytools/cdf.r')\n") -r.write("x = read.table('"+outbed+"',sep='\t')\n") -r.write("y = read.table('shuffled.dist',sep='\t')\n") -r.write("pdf('"+outplot+"')\n") -r.write("mycdf(list(log10(1+x[,ncol(x)]),log10(1+y[,ncol(y)])),'spatial distance',c('real','shuffled'),'topleft','log10 distance','')\n") -r.write("dev.off()\n") -r.close() -os.system("R --vanilla < tmp.r >"+outlog)