Mercurial > repos > devteam > column_maker

annotate column_maker.py @ 5:c6fdc1118036 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 0cb87d8f454f205af021d653d7f7d5a7c14c7718"
author devteam
date Wed, 15 Jul 2020 14:38:05 +0000
parents 3335c0d583d8
children 0aeda7a81b46
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1 #!/usr/bin/env python
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2 """
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3 This tool takes a tab-delimited textfile as input and creates another column in
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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4 the file which is the result of a computation performed on every row in the
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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5 original file. The tool will skip over invalid lines within the file,
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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6 informing the user about the number of lines skipped.
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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7 """
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8 from __future__ import print_function
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9
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10 import re
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11 import sys
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12
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13 assert sys.version_info[:2] >= (2, 4)
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14
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15 inp_file = sys.argv[1]
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16 out_file = sys.argv[2]
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17 expr = sys.argv[3]
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18 round_result = sys.argv[4]
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19 try:
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20 in_columns = int(sys.argv[5])
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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21 except Exception:
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22 exit("Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data.")
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23 if in_columns < 2:
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24 # To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method.
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25 exit("Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data.")
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26 try:
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27 in_column_types = sys.argv[6].split(',')
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28 except Exception:
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29 exit("Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data.")
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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30 if len(in_column_types) != in_columns:
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31 exit("The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data.")
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32 avoid_scientific_notation = sys.argv[7]
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33
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34 # Unescape if input has been escaped
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35 mapped_str = {
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36 '__lt__': '<',
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37 '__le__': '<=',
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38 '__eq__': '==',
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39 '__ne__': '!=',
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40 '__gt__': '>',
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41 '__ge__': '>=',
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42 '__sq__': '\'',
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43 '__dq__': '"',
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44 }
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45 for key, value in mapped_str.items():
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46 expr = expr.replace(key, value)
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47
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48 operators = 'is|not|or|and'
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49 builtin_and_math_functions = 'abs|all|any|bin|chr|cmp|complex|divmod|float|bool|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|log10|exp|sqrt|ceil|floor'
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3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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50 string_and_list_methods = [name for name in dir('') + dir([]) if not name.startswith('_')]
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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51 whitelist = r"^([c0-9\+\-\*\/\(\)\.\'\"><=,:! ]|%s|%s|%s)*$" % (operators, builtin_and_math_functions, '|'.join(string_and_list_methods))
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52 if not re.compile(whitelist).match(expr):
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53 exit("Invalid expression")
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54 if avoid_scientific_notation == "yes":
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55 expr = "format_float_positional(%s)" % expr
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56
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57 # Prepare the column variable names and wrappers for column data types
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58 cols, type_casts = [], []
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59 for col in range(1, in_columns + 1):
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60 col_name = "c%d" % col
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61 cols.append(col_name)
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62 col_type = in_column_types[col - 1].strip()
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63 if round_result == 'no' and col_type == 'int':
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64 col_type = 'float'
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65 type_cast = "%s(%s)" % (col_type, col_name)
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66 type_casts.append(type_cast)
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67
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68 col_str = ', '.join(cols) # 'c1, c2, c3, c4'
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69 type_cast_str = ', '.join(type_casts) # 'str(c1), int(c2), int(c3), str(c4)'
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70 assign = "%s = line.split('\\t')" % col_str
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71 wrap = "%s = %s" % (col_str, type_cast_str)
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72 skipped_lines = 0
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73 first_invalid_line = 0
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74 invalid_line = None
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75 lines_kept = 0
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76 total_lines = 0
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77 out = open(out_file, 'wt')
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78
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79 # Read input file, skipping invalid lines, and perform computation that will result in a new column
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80 code = '''
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81 # import here since flake8 complains otherwise
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82 from math import (
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83 ceil,
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84 exp,
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85 floor,
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86 log,
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87 log10,
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88 sqrt
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89 )
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90 from numpy import format_float_positional
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91
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92 fh = open(inp_file)
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93 for i, line in enumerate(fh):
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94 total_lines += 1
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95 line = line.rstrip('\\r\\n')
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96 if not line or line.startswith('#'):
0
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97 skipped_lines += 1
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98 if not invalid_line:
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99 first_invalid_line = i + 1
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100 invalid_line = line
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101 continue
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102 try:
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103 %s
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104 %s
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105 new_val = %s
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106 if round_result == "yes":
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107 new_val = int(round(new_val))
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108 new_line = line + '\\t' + str(new_val) + "\\n"
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109 out.write(new_line)
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110 lines_kept += 1
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111 except Exception:
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112 skipped_lines += 1
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113 if not invalid_line:
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114 first_invalid_line = i + 1
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115 invalid_line = line
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116 fh.close()
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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117 ''' % (assign, wrap, expr)
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118
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119 valid_expr = True
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120 try:
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3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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121 exec(code)
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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122 except Exception as e:
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123 out.close()
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3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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124 if str(e).startswith('invalid syntax'):
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125 valid_expr = False
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126 exit('Expression "%s" likely invalid. See tool tips, syntax and examples.' % expr)
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127 else:
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3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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128 exit(str(e))
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129
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130 if valid_expr:
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131 out.close()
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132 valid_lines = total_lines - skipped_lines
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133 print('Creating column %d with expression %s' % (in_columns + 1, expr))
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134 if valid_lines > 0:
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3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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135 print('kept %4.2f%% of %d lines.' % (100.0 * lines_kept / valid_lines,
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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136 total_lines))
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137 else:
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3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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138 print('Possible invalid expression "%s" or non-existent column referenced. See tool tips, syntax and examples.' % expr)
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139 if skipped_lines > 0:
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3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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140 print('Skipped %d invalid lines starting at line #%d: "%s"' %
3335c0d583d8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
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141 (skipped_lines, first_invalid_line, invalid_line))