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1 #!/usr/bin/env python
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2 #Done by: Guru
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3
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4 """
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5 Get Flanking regions.
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6
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7 usage: %prog input out_file size direction region
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8 -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
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9 -o, --off=N: Offset
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10 """
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11
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12 import sys, re, os
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13 from bx.cookbook import doc_optparse
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14 from galaxy.tools.util.galaxyops import *
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15
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16 def stop_err( msg ):
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17 sys.stderr.write( msg )
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18 sys.exit()
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19
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20 def main():
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21 try:
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22 if int( sys.argv[3] ) < 0:
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23 raise Exception
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24 except:
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25 stop_err( "Length of flanking region(s) must be a non-negative integer." )
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26
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27 # Parsing Command Line here
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28 options, args = doc_optparse.parse( __doc__ )
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29 try:
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30 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols )
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31 inp_file, out_file, size, direction, region = args
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32 if strand_col_1 <= 0:
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33 strand = "+" #if strand is not defined, default it to +
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34 except:
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35 stop_err( "Metadata issue, correct the metadata attributes by clicking on the pencil icon in the history item." )
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36 try:
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37 offset = int(options.off)
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38 size = int(size)
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39 except:
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40 stop_err( "Invalid offset or length entered. Try again by entering valid integer values." )
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41
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42 fo = open(out_file,'w')
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43
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44 skipped_lines = 0
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45 first_invalid_line = 0
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46 invalid_line = None
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47 elems = []
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48 j=0
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49 for i, line in enumerate( file( inp_file ) ):
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50 line = line.strip()
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51 if line and (not line.startswith( '#' )) and line != '':
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52 j+=1
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53 try:
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54 elems = line.split('\t')
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55 #if the start and/or end columns are not numbers, skip that line.
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56 assert int(elems[start_col_1])
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57 assert int(elems[end_col_1])
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58 if strand_col_1 != -1:
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59 strand = elems[strand_col_1]
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60 #if the stand value is not + or -, skip that line.
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61 assert strand in ['+', '-']
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62 if direction == 'Upstream':
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63 if strand == '+':
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64 if region == 'end':
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65 elems[end_col_1] = str(int(elems[end_col_1]) + offset)
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66 elems[start_col_1] = str( int(elems[end_col_1]) - size )
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67 else:
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68 elems[end_col_1] = str(int(elems[start_col_1]) + offset)
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69 elems[start_col_1] = str( int(elems[end_col_1]) - size )
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70 elif strand == '-':
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71 if region == 'end':
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72 elems[start_col_1] = str(int(elems[start_col_1]) - offset)
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73 elems[end_col_1] = str(int(elems[start_col_1]) + size)
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74 else:
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75 elems[start_col_1] = str(int(elems[end_col_1]) - offset)
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76 elems[end_col_1] = str(int(elems[start_col_1]) + size)
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77 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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78 fo.write( "%s\n" % '\t'.join( elems ) )
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79
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80 elif direction == 'Downstream':
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81 if strand == '-':
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82 if region == 'start':
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83 elems[end_col_1] = str(int(elems[end_col_1]) - offset)
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84 elems[start_col_1] = str( int(elems[end_col_1]) - size )
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85 else:
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86 elems[end_col_1] = str(int(elems[start_col_1]) - offset)
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87 elems[start_col_1] = str( int(elems[end_col_1]) - size )
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88 elif strand == '+':
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89 if region == 'start':
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90 elems[start_col_1] = str(int(elems[start_col_1]) + offset)
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91 elems[end_col_1] = str(int(elems[start_col_1]) + size)
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92 else:
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93 elems[start_col_1] = str(int(elems[end_col_1]) + offset)
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94 elems[end_col_1] = str(int(elems[start_col_1]) + size)
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95 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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96 fo.write( "%s\n" % '\t'.join( elems ) )
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97
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98 elif direction == 'Both':
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99 if strand == '-':
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100 if region == 'start':
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101 start = str(int(elems[end_col_1]) - offset)
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102 end1 = str(int(start) + size)
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103 end2 = str(int(start) - size)
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104 elems[start_col_1]=start
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105 elems[end_col_1]=end1
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106 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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107 fo.write( "%s\n" % '\t'.join( elems ) )
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108 elems[start_col_1]=end2
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109 elems[end_col_1]=start
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110 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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111 fo.write( "%s\n" % '\t'.join( elems ) )
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112 elif region == 'end':
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113 start = str(int(elems[start_col_1]) - offset)
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114 end1 = str(int(start) + size)
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115 end2 = str(int(start) - size)
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116 elems[start_col_1]=start
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117 elems[end_col_1]=end1
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118 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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119 fo.write( "%s\n" % '\t'.join( elems ) )
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120 elems[start_col_1]=end2
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121 elems[end_col_1]=start
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122 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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123 fo.write( "%s\n" % '\t'.join( elems ) )
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124 else:
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125 start1 = str(int(elems[end_col_1]) - offset)
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126 end1 = str(int(start1) + size)
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127 start2 = str(int(elems[start_col_1]) - offset)
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128 end2 = str(int(start2) - size)
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129 elems[start_col_1]=start1
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130 elems[end_col_1]=end1
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131 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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132 fo.write( "%s\n" % '\t'.join( elems ) )
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133 elems[start_col_1]=end2
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134 elems[end_col_1]=start2
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135 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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136 fo.write( "%s\n" % '\t'.join( elems ) )
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137 elif strand == '+':
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138 if region == 'start':
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139 start = str(int(elems[start_col_1]) + offset)
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140 end1 = str(int(start) - size)
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141 end2 = str(int(start) + size)
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142 elems[start_col_1]=end1
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143 elems[end_col_1]=start
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144 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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145 fo.write( "%s\n" % '\t'.join( elems ) )
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146 elems[start_col_1]=start
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147 elems[end_col_1]=end2
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148 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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149 fo.write( "%s\n" % '\t'.join( elems ) )
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150 elif region == 'end':
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151 start = str(int(elems[end_col_1]) + offset)
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152 end1 = str(int(start) - size)
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153 end2 = str(int(start) + size)
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154 elems[start_col_1]=end1
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155 elems[end_col_1]=start
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156 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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157 fo.write( "%s\n" % '\t'.join( elems ) )
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158 elems[start_col_1]=start
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159 elems[end_col_1]=end2
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160 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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161 fo.write( "%s\n" % '\t'.join( elems ) )
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162 else:
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163 start1 = str(int(elems[start_col_1]) + offset)
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164 end1 = str(int(start1) - size)
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165 start2 = str(int(elems[end_col_1]) + offset)
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166 end2 = str(int(start2) + size)
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167 elems[start_col_1]=end1
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168 elems[end_col_1]=start1
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169 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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170 fo.write( "%s\n" % '\t'.join( elems ) )
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171 elems[start_col_1]=start2
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172 elems[end_col_1]=end2
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173 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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174 fo.write( "%s\n" % '\t'.join( elems ) )
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175 except:
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176 skipped_lines += 1
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177 if not invalid_line:
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178 first_invalid_line = i + 1
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179 invalid_line = line
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180 fo.close()
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181
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182 if skipped_lines == j:
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183 stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
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184 if skipped_lines > 0:
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185 print 'Skipped %d invalid lines starting with #%dL "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
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186 print 'Location: %s, Region: %s, Flank-length: %d, Offset: %d ' %( direction, region, size, offset )
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187
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188 if __name__ == "__main__":
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189 main()
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