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1 #!/usr/bin/env python
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2
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3 """
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4 Condenses pileup format into ranges of bases.
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5
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6 usage: %prog [options]
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7 -i, --input=i: Input pileup file
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8 -o, --output=o: Output pileup
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9 -c, --coverage=c: Coverage
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10 -f, --format=f: Pileup format
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11 -b, --base=b: Base to select
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12 -s, --seq_column=s: Sequence column
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13 -l, --loc_column=l: Base location column
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14 -r, --base_column=r: Reference base column
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15 -C, --cvrg_column=C: Coverage column
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16 """
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17
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18 from galaxy import eggs
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19 import pkg_resources; pkg_resources.require( "bx-python" )
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20 from bx.cookbook import doc_optparse
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21 import sys
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22
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23 def stop_err( msg ):
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24 sys.stderr.write( msg )
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25 sys.exit()
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26
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27 def __main__():
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28 strout = ''
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29 #Parse Command Line
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30 options, args = doc_optparse.parse( __doc__ )
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31 coverage = int(options.coverage)
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32 fin = file(options.input, 'r')
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33 fout = file(options.output, 'w')
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34 inLine = fin.readline()
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35 if options.format == 'six':
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36 seqIndex = 0
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37 locIndex = 1
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38 baseIndex = 2
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39 covIndex = 3
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40 elif options.format == 'ten':
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41 seqIndex = 0
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42 locIndex = 1
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43 if options.base == 'first':
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44 baseIndex = 2
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45 else:
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46 baseIndex = 3
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47 covIndex = 7
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48 else:
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49 seqIndex = int(options.seq_column) - 1
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50 locIndex = int(options.loc_column) - 1
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51 baseIndex = int(options.base_column) - 1
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52 covIndex = int(options.cvrg_column) - 1
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53 lastSeq = ''
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54 lastLoc = -1
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55 locs = []
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56 startLoc = -1
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57 bases = []
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58 while inLine.strip() != '':
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59 lineParts = inLine.split('\t')
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60 try:
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61 seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex])
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62 except IndexError, ei:
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63 if options.format == 'ten':
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64 stop_err( 'It appears that you have selected 10 columns while your file has 6. Make sure that the number of columns you specify matches the number in your file.\n' + str( ei ) )
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65 else:
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66 stop_err( 'There appears to be something wrong with your column index values.\n' + str( ei ) )
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67 except ValueError, ev:
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68 if options.format == 'six':
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69 stop_err( 'It appears that you have selected 6 columns while your file has 10. Make sure that the number of columns you specify matches the number in your file.\n' + str( ev ) )
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70 else:
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71 stop_err( 'There appears to be something wrong with your column index values.\n' + str( ev ) )
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72 # strout += str(startLoc) + '\n'
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73 # strout += str(bases) + '\n'
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74 # strout += '%s\t%s\t%s\t%s\n' % (seq, loc, base, cov)
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75 if loc == lastLoc+1 or lastLoc == -1:
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76 if cov >= coverage:
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77 if seq == lastSeq or lastSeq == '':
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78 if startLoc == -1:
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79 startLoc = loc
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80 locs.append(loc)
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81 bases.append(base)
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82 else:
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83 if len(bases) > 0:
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84 fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
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85 startLoc = loc
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86 locs = [loc]
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87 bases = [base]
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88 else:
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89 if len(bases) > 0:
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90 fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
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91 startLoc = -1
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92 locs = []
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93 bases = []
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94 else:
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95 if len(bases) > 0:
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96 fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
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97 if cov >= coverage:
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98 startLoc = loc
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99 locs = [loc]
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100 bases = [base]
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101 else:
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102 startLoc = -1
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103 locs = []
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104 bases = []
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105 lastSeq = seq
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106 lastLoc = loc
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107 inLine = fin.readline()
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108 if len(bases) > 0:
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109 fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
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110 fout.close()
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111 fin.close()
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112
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113 # import sys
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114 # strout += file(fout.name,'r').read()
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115 # sys.stderr.write(strout)
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116
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117 if __name__ == "__main__" : __main__()
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