[2] | 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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