comparison spatial_proximity.py @ 2:e68d35c7d3eb default tip

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author xuebing
date Sat, 31 Mar 2012 14:09:14 -0400
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1:a14cd3a3357a 2:e68d35c7d3eb
1
2 import os,sys
3
4 file1 = sys.argv[1]
5 file2 = sys.argv[2]
6 genome = sys.argv[3]
7 outplot = sys.argv[4]
8 outlog = sys.argv[5]
9 outbed = sys.argv[6]
10
11 strandness = ''
12 if len(sys.argv) > 7:
13 strandness = sys.argv[7]
14
15 # real distance
16 cmd = 'closestBed -a '+file1+' -b '+file2 + ' '+strandness + ' -d -t first > '+outbed
17 os.system(cmd)
18 # shuffle
19 cmd = 'shuffleBed -chrom -g '+genome+' -i '+file1+'> shuffled.bed'
20 os.system(cmd)
21 # shuffled distance
22 cmd = 'closestBed -a shuffled.bed -b '+file2 + ' '+strandness + ' -d -t first > shuffled.dist'
23 os.system(cmd)
24
25
26 # test in R
27 r = open('tmp.r','w')
28 r.write("options(warn=-1)\n")
29 r.write("source('/Users/xuebing/galaxy-dist/tools/mytools/cdf.r')\n")
30 r.write("x = read.table('"+outbed+"',sep='\t')\n")
31 r.write("y = read.table('shuffled.dist',sep='\t')\n")
32 r.write("pdf('"+outplot+"')\n")
33 r.write("mycdf(list(log10(1+x[,ncol(x)]),log10(1+y[,ncol(y)])),'spatial distance',c('real','shuffled'),'topleft','log10 distance','')\n")
34 r.write("dev.off()\n")
35 r.close()
36 os.system("R --vanilla < tmp.r >"+outlog)