Mercurial > hg > numerics

annotate numerics/read.py @ 107:19a5c2fb52bb

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add transpose functionality
author Jeff Hammel <k0scist@gmail.com>
date Sun, 15 Mar 2015 10:02:48 -0700
parents 32a849b8f1f0
children 5790bcb30bd8
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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3
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4 """
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5 read CSV
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6 """
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7 # TODO: support other formats
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9
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10 # imports
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11 import argparse
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12 import csv
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13 import os
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14 import sys
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15 from .data import transpose
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16 from .write import CSVWriter
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18 # module globals
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19 __all__ = ['CSVSchema', 'read_csv', 'CSVParser', 'main']
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20 string = (str, unicode)
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22
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23 class CSVSchema(object):
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24 """read CSV with a schema"""
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25
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26 def __init__(self, columns):
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27 self.columns = columns
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29 def read(self, f):
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31 if isinstance(f, string):
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32 with open(f) as fp:
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33 return self.read(fp)
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34
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35 retval = []
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36 reader = csv.reader(f)
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37 for row in reader:
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38 retval.append(dict(zip(self.columns, row)))
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39 return retval
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40
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41 __call__ = read
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42
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44 def aggregate_columns(directory, schema):
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45
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46 # check for missing files
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47 missing = [path for path in schema
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48 if not os.path.exists(os.path.join(directory, path))]
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49 assert not missing, "Missing files: {}".format(', '.join(missing))
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50
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51 # read records
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52 records = {filename: CSVSchema(columns).read(os.path.join(directory, filename))
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53 for filename, columns in schema.items()}
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54
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55
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56 # check lengths
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57 lengths = [len(value) for value in records.values()]
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58 assert len(set(lengths)) == 1, "Differing lengths found for files"
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59
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60 # build new rows
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61 retval = []
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62 for row in zip(*records.values()):
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63 new_row = {}
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64 for record in row:
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65 for key, value in record.items():
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66 if new_row.get(key, value) != value:
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67 raise AssertionError("{} != {}".format(new_row.get(key), value))
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68 new_row[key] = value
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69 retval.append(new_row)
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70
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71 return retval
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72
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73
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74 def read_csv(*fp):
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75 """read a series of CSV files"""
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76
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77 retval = []
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78 for f in fp:
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79
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80 if isinstance(f, string):
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81 with open(f) as _f:
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82 retval.extend(read_csv(_f))
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83 continue
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84
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85 reader = csv.reader(f)
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86 retval.extend([row for row in reader])
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87
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88 return retval
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91 class CSVParser(argparse.ArgumentParser):
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92 """CLI option parser"""
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93
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94 def __init__(self, **kwargs):
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95 kwargs.setdefault('description', __doc__)
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96 argparse.ArgumentParser.__init__(self, **kwargs)
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97 self.add_argument('csv', nargs='*',
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98 help="CSV files to read, or read from stdin")
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99 self.add_argument('-+', '--add', dest='added_columns', nargs='+',
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100 help="append this column")
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101 self.add_argument('-c', '--col', '--columns', dest='columns',
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102 nargs='+', type=int,
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103 help="column numbers to output, starting with 0")
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104 self.add_argument('-o', '--output', dest='output',
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105 type=argparse.FileType('a'), default=sys.stdout,
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106 help='output destination, or stdout')
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107 self.add_argument('--index', dest='index',
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108 action='store_true', default=False,
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109 help="prepend each row with numeric index")
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110 self.options = None
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111
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112 def parse_args(self, *args, **kw):
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113 options = argparse.ArgumentParser.parse_args(self, *args, **kw)
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114 self.validate(options)
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115 self.options = options
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116 return options
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117
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118 def validate(self, options):
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119 """validate options"""
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120
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121 if not options.csv:
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122 options.csv = [sys.stdin]
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123
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124 def read(self):
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125 """read and process CSV"""
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126
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127 data = read_csv(*self.options.csv)
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128
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129 if self.options.added_columns:
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130 # add columns
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131 for row in data:
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132 row.extend(options.added_columns)
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133
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134 if self.options.columns:
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135 # filter by column
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136 data = [[row[column] for column in self.options.columns]
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137 for row in data]
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138
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139 if self.options.index:
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140 # prepend numeric index
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141 for index, row in enumerate(data):
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142 row.insert(0, index)
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143
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144 # return processed data
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145 return data
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146
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147 def columns(self):
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148 """return columns vs `data`'s rows"""
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149 return transpose(self.read())
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150
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151
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152 def main(args=sys.argv[1:]):
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153 """CLI"""
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154
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155 # parse command line options
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156 parser = CSVParser()
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157 parser.add_argument('--transpose', dest='transpose',
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158 action='store_true', default=False,
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159 help="transpose columns and rows")
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160 options = parser.parse_args(args)
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161
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162 if not options.csv:
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163 # read from stdin
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164 options.csv = [sys.stdin]
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165
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166 # read CSV
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167 if options.transpose:
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168 data = parser.columns()
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169 else:
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170 data = parser.read()
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171
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172 # write CSV
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173 writer = CSVWriter(options.output)
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174 writer.write(data)
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175
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Jeff Hammel <k0scist@gmail.com>
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176
5
d5447d401c44 serializaion; pandas probably does this
Jeff Hammel <k0scist@gmail.com>
parents:
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177 if __name__ == '__main__':
d5447d401c44 serializaion; pandas probably does this
Jeff Hammel <k0scist@gmail.com>
parents:
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178 main()
d5447d401c44 serializaion; pandas probably does this
Jeff Hammel <k0scist@gmail.com>
parents:
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179