Mercurial > repos > devteam > get_flanks

annotate get_flanks.py @ 4:077f404ae1bb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:41:29 -0400
parents 4cd116158aef
children
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1 #!/usr/bin/env python
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077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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2 # Done by: Guru
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3 """
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4 Get Flanking regions.
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5
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6 usage: %prog input out_file size direction region
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7 -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
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8 -o, --off=N: Offset
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9 """
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077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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10 from __future__ import print_function
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11
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12 import sys
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077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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13
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14 from bx.cookbook import doc_optparse
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15 from galaxy.tools.util.galaxyops import parse_cols_arg
4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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16
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17
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18 def stop_err( msg ):
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19 sys.stderr.write( msg )
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20 sys.exit()
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21
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22
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23 def main():
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24 try:
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25 if int( sys.argv[3] ) < 0:
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26 raise Exception
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27 except:
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28 stop_err( "Length of flanking region(s) must be a non-negative integer." )
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29
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30 # Parsing Command Line here
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31 options, args = doc_optparse.parse( __doc__ )
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32 try:
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33 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols )
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34 inp_file, out_file, size, direction, region = args
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35 if strand_col_1 <= 0:
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4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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36 strand = "+" # if strand is not defined, default it to +
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37 except:
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38 stop_err( "Metadata issue, correct the metadata attributes by clicking on the pencil icon in the history item." )
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39 try:
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40 offset = int(options.off)
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41 size = int(size)
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42 except:
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43 stop_err( "Invalid offset or length entered. Try again by entering valid integer values." )
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44
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45 fo = open(out_file, 'w')
4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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46
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47 skipped_lines = 0
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48 first_invalid_line = 0
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49 invalid_line = None
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50 elems = []
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4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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51 j = 0
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52 for i, line in enumerate( file( inp_file ) ):
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53 line = line.strip()
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54 if line and (not line.startswith( '#' )) and line != '':
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4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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55 j += 1
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56 try:
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57 elems = line.split('\t')
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077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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58 # if the start and/or end columns are not numbers, skip that line.
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59 assert int(elems[start_col_1])
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60 assert int(elems[end_col_1])
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61 if strand_col_1 != -1:
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62 strand = elems[strand_col_1]
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63 # if the stand value is not + or -, skip that line.
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64 assert strand in ['+', '-']
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65 if direction == 'Upstream':
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66 if strand == '+':
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67 if region == 'end':
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68 elems[end_col_1] = str(int(elems[end_col_1]) + offset)
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69 elems[start_col_1] = str( int(elems[end_col_1]) - size )
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70 else:
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71 elems[end_col_1] = str(int(elems[start_col_1]) + offset)
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72 elems[start_col_1] = str( int(elems[end_col_1]) - size )
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73 elif strand == '-':
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74 if region == 'end':
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75 elems[start_col_1] = str(int(elems[start_col_1]) - offset)
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76 elems[end_col_1] = str(int(elems[start_col_1]) + size)
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77 else:
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78 elems[start_col_1] = str(int(elems[end_col_1]) - offset)
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79 elems[end_col_1] = str(int(elems[start_col_1]) + size)
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80 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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81 fo.write( "%s\n" % '\t'.join( elems ) )
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82
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83 elif direction == 'Downstream':
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84 if strand == '-':
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85 if region == 'start':
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4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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86 elems[end_col_1] = str(int(elems[end_col_1]) - offset)
4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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87 elems[start_col_1] = str( int(elems[end_col_1]) - size )
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88 else:
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89 elems[end_col_1] = str(int(elems[start_col_1]) - offset)
4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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90 elems[start_col_1] = str( int(elems[end_col_1]) - size )
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91 elif strand == '+':
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92 if region == 'start':
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93 elems[start_col_1] = str(int(elems[start_col_1]) + offset)
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94 elems[end_col_1] = str(int(elems[start_col_1]) + size)
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95 else:
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96 elems[start_col_1] = str(int(elems[end_col_1]) + offset)
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97 elems[end_col_1] = str(int(elems[start_col_1]) + size)
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98 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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99 fo.write( "%s\n" % '\t'.join( elems ) )
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100
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101 elif direction == 'Both':
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102 if strand == '-':
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103 if region == 'start':
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104 start = str(int(elems[end_col_1]) - offset)
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105 end1 = str(int(start) + size)
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106 end2 = str(int(start) - size)
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107 elems[start_col_1] = start
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108 elems[end_col_1] = end1
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109 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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110 fo.write( "%s\n" % '\t'.join( elems ) )
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111 elems[start_col_1] = end2
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112 elems[end_col_1] = start
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113 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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114 fo.write( "%s\n" % '\t'.join( elems ) )
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115 elif region == 'end':
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116 start = str(int(elems[start_col_1]) - offset)
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117 end1 = str(int(start) + size)
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118 end2 = str(int(start) - size)
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119 elems[start_col_1] = start
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120 elems[end_col_1] = end1
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121 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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122 fo.write( "%s\n" % '\t'.join( elems ) )
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123 elems[start_col_1] = end2
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124 elems[end_col_1] = start
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125 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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126 fo.write( "%s\n" % '\t'.join( elems ) )
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127 else:
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128 start1 = str(int(elems[end_col_1]) - offset)
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129 end1 = str(int(start1) + size)
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130 start2 = str(int(elems[start_col_1]) - offset)
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131 end2 = str(int(start2) - size)
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132 elems[start_col_1] = start1
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133 elems[end_col_1] = end1
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134 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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135 fo.write( "%s\n" % '\t'.join( elems ) )
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136 elems[start_col_1] = end2
4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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137 elems[end_col_1] = start2
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138 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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139 fo.write( "%s\n" % '\t'.join( elems ) )
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140 elif strand == '+':
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141 if region == 'start':
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142 start = str(int(elems[start_col_1]) + offset)
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143 end1 = str(int(start) - size)
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144 end2 = str(int(start) + size)
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4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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145 elems[start_col_1] = end1
4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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146 elems[end_col_1] = start
0
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147 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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148 fo.write( "%s\n" % '\t'.join( elems ) )
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4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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149 elems[start_col_1] = start
4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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150 elems[end_col_1] = end2
0
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151 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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152 fo.write( "%s\n" % '\t'.join( elems ) )
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153 elif region == 'end':
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154 start = str(int(elems[end_col_1]) + offset)
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155 end1 = str(int(start) - size)
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156 end2 = str(int(start) + size)
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4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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157 elems[start_col_1] = end1
4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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158 elems[end_col_1] = start
0
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159 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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160 fo.write( "%s\n" % '\t'.join( elems ) )
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4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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161 elems[start_col_1] = start
4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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162 elems[end_col_1] = end2
0
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163 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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164 fo.write( "%s\n" % '\t'.join( elems ) )
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165 else:
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166 start1 = str(int(elems[start_col_1]) + offset)
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167 end1 = str(int(start1) - size)
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168 start2 = str(int(elems[end_col_1]) + offset)
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169 end2 = str(int(start2) + size)
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4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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170 elems[start_col_1] = end1
4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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171 elems[end_col_1] = start1
0
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172 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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173 fo.write( "%s\n" % '\t'.join( elems ) )
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4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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174 elems[start_col_1] = start2
4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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175 elems[end_col_1] = end2
0
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176 assert int(elems[start_col_1]) > 0 and int(elems[end_col_1]) > 0
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177 fo.write( "%s\n" % '\t'.join( elems ) )
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178 except:
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179 skipped_lines += 1
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180 if not invalid_line:
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181 first_invalid_line = i + 1
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182 invalid_line = line
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183 fo.close()
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184
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185 if skipped_lines == j:
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186 stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
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187 if skipped_lines > 0:
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077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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188 print('Skipped %d invalid lines starting with #%dL "%s"' % ( skipped_lines, first_invalid_line, invalid_line ))
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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189 print('Location: %s, Region: %s, Flank-length: %d, Offset: %d ' % ( direction, region, size, offset ))
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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190
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4cd116158aef planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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191
0
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192 if __name__ == "__main__":
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193 main()