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