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1 #!/usr/bin/env python
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2 #Guruprasad Ananda
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3 #Adapted from bx/scripts/maf_mask_cpg.py
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4 """
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5 Mask out potential CpG sites from a maf. Restricted or inclusive definition
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6 of CpG sites can be used. The total fraction masked is printed to stderr.
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7
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8 usage: %prog < input > output restricted
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9 -m, --mask=N: Character to use as mask ('?' is default)
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10 """
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11
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12 from galaxy import eggs
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13 import pkg_resources
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14 pkg_resources.require( "bx-python" )
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15 try:
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16 pkg_resources.require( "numpy" )
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17 except:
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18 pass
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19 import bx.align
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20 import bx.align.maf
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21 from bx.cookbook import doc_optparse
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22 import sys
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23 import bx.align.sitemask.cpg
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24
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25 assert sys.version_info[:2] >= ( 2, 4 )
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26
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27 def main():
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28 options, args = doc_optparse.parse( __doc__ )
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29 try:
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30 inp_file, out_file, sitetype, definition = args
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31 if options.mask:
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32 mask = int(options.mask)
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33 else:
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34 mask = 0
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35 except:
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36 print >> sys.stderr, "Tool initialization error."
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37 sys.exit()
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38
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39 reader = bx.align.maf.Reader( open(inp_file, 'r') )
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40 writer = bx.align.maf.Writer( open(out_file,'w') )
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41
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42 mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?', 5:'N'}
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43 mask = mask_chr_dict[mask]
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44
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45 if sitetype == "CpG":
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46 if int(definition) == 1:
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47 cpgfilter = bx.align.sitemask.cpg.Restricted( mask=mask )
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48 defn = "CpG-Restricted"
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49 else:
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50 cpgfilter = bx.align.sitemask.cpg.Inclusive( mask=mask )
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51 defn = "CpG-Inclusive"
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52 else:
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53 cpgfilter = bx.align.sitemask.cpg.nonCpG( mask=mask )
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54 defn = "non-CpG"
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55 cpgfilter.run( reader, writer.write )
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56
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57 print "%2.2f percent bases masked; Mask character = %s, Definition = %s" %(float(cpgfilter.masked)/float(cpgfilter.total) * 100, mask, defn)
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58
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59 if __name__ == "__main__":
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60 main()
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