/tools/regVariation/maf_cpg_filter.py
Python | 60 lines | 49 code | 3 blank | 8 comment | 5 complexity | afd02507e622ceaf2f4e5fd476453f39 MD5 | raw file
1#!/usr/bin/python
2#Guruprasad Ananda
3#Adapted from bx/scripts/maf_mask_cpg.py
4"""
5Mask out potential CpG sites from a maf. Restricted or inclusive definition
6of CpG sites can be used. The total fraction masked is printed to stderr.
7
8usage: %prog < input > output restricted
9 -m, --mask=N: Character to use as mask ('?' is default)
10"""
11
12from galaxy import eggs
13import pkg_resources
14pkg_resources.require( "bx-python" )
15try:
16 pkg_resources.require( "numpy" )
17except:
18 pass
19import bx.align
20import bx.align.maf
21from bx.cookbook import doc_optparse
22import sys
23import bx.align.sitemask.cpg
24
25assert sys.version_info[:2] >= ( 2, 4 )
26
27def main():
28 options, args = doc_optparse.parse( __doc__ )
29 try:
30 inp_file, out_file, sitetype, definition = args
31 if options.mask:
32 mask = int(options.mask)
33 else:
34 mask = 0
35 except:
36 print >> sys.stderr, "Tool initialization error."
37 sys.exit()
38
39 reader = bx.align.maf.Reader( open(inp_file, 'r') )
40 writer = bx.align.maf.Writer( open(out_file,'w') )
41
42 mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?'}
43 mask = mask_chr_dict[mask]
44
45 if sitetype == "CpG":
46 if int(definition) == 1:
47 cpgfilter = bx.align.sitemask.cpg.Restricted( mask=mask )
48 defn = "CpG-Restricted"
49 else:
50 cpgfilter = bx.align.sitemask.cpg.Inclusive( mask=mask )
51 defn = "CpG-Inclusive"
52 else:
53 cpgfilter = bx.align.sitemask.cpg.nonCpG( mask=mask )
54 defn = "non-CpG"
55 cpgfilter.run( reader, writer.write )
56
57 print "%2.2f percent bases masked; Mask character = %s, Definition = %s" %(float(cpgfilter.masked)/float(cpgfilter.total) * 100, mask, defn)
58
59if __name__ == "__main__":
60 main()