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1 #!/usr/bin/env python
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2 # Greg Von Kuster
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3
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4 """
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5 Subtract an entire query from another query
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6 usage: %prog in_file_1 in_file_2 begin_col end_col output
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7 --ignore-empty-end-cols: ignore empty end columns when subtracting
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8 """
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9 import sys, re
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10 from bx.cookbook import doc_optparse
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11
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12 # Older py compatibility
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13 try:
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14 set()
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15 except:
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16 from sets import Set as set
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17
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18 assert sys.version_info[:2] >= ( 2, 4 )
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19
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20 def get_lines(fname, begin_col='', end_col='', ignore_empty_end_cols=False):
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21 lines = set([])
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22 i = 0
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23 for i, line in enumerate(file(fname)):
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24 line = line.rstrip('\r\n')
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25 if line and not line.startswith('#'):
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26 if begin_col and end_col:
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27 """Both begin_col and end_col must be integers at this point."""
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28 try:
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29 line = line.split('\t')
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30 line = '\t'.join([line[j] for j in range(begin_col-1, end_col)])
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31 if ignore_empty_end_cols:
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32 # removing empty fields, we do not compare empty fields at the end of a line.
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33 line = line.rstrip()
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34 lines.add( line )
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35 except: pass
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36 else:
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37 if ignore_empty_end_cols:
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38 # removing empty fields, we do not compare empty fields at the end of a line.
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39 line = line.rstrip()
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40 lines.add( line )
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41 if i: return (i+1, lines)
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42 else: return (i, lines)
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43
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44 def main():
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45
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46 # Parsing Command Line here
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47 options, args = doc_optparse.parse( __doc__ )
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48
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49 try:
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50 inp1_file, inp2_file, begin_col, end_col, out_file = args
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51 except:
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52 doc_optparse.exception()
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53
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54 begin_col = begin_col.strip()
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55 end_col = end_col.strip()
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56
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57 if begin_col != 'None' or end_col != 'None':
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58 """
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59 The user selected columns for restriction. We'll allow default
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60 values for both begin_col and end_col as long as the user selected
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61 at least one of them for restriction.
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62 """
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63 if begin_col == 'None':
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64 begin_col = end_col
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65 elif end_col == 'None':
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66 end_col = begin_col
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67 begin_col = int(begin_col)
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68 end_col = int(end_col)
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69 """Make sure that begin_col <= end_col (switch if not)"""
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70 if begin_col > end_col:
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71 tmp_col = end_col
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72 end_col = begin_col
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73 begin_col = tmp_col
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74 else:
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75 begin_col = end_col = ''
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76
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77 try:
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78 fo = open(out_file,'w')
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79 except:
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80 print >> sys.stderr, "Unable to open output file"
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81 sys.exit()
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82
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83 """
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84 len1 is the number of lines in inp1_file
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85 lines1 is the set of unique lines in inp1_file
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86 diff1 is the number of duplicate lines removed from inp1_file
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87 """
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88 len1, lines1 = get_lines(inp1_file, begin_col, end_col, options.ignore_empty_end_cols)
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89 diff1 = len1 - len(lines1)
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90 len2, lines2 = get_lines(inp2_file, begin_col, end_col, options.ignore_empty_end_cols)
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91
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92 lines1.difference_update(lines2)
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93 """lines1 is now the set of unique lines in inp1_file - the set of unique lines in inp2_file"""
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94
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95 for line in lines1:
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96 print >> fo, line
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97
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98 fo.close()
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99
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100 info_msg = 'Subtracted %d lines. ' %((len1 - diff1) - len(lines1))
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101
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102 if begin_col and end_col:
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103 info_msg += 'Restricted to columns c' + str(begin_col) + ' thru c' + str(end_col) + '. '
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104
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105 if diff1 > 0:
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106 info_msg += 'Eliminated %d duplicate/blank/comment/invalid lines from first query.' %diff1
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107
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108 print info_msg
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109
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110 if __name__ == "__main__":
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111 main()
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