Mercurial > repos > jjohnson > pandas_pivot_table

annotate pandas_pivot_table.py @ 0:621144f8dbe9 draft

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
author jjohnson
date Wed, 02 Dec 2020 22:59:57 +0000
parents
children c02f59711eb6
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0
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
jjohnson
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diff changeset
1 #!/usr/bin/env python
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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2
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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3 import argparse
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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4 import json
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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5 import re
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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6 import pandas as pd
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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7 import sys
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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8 from json.decoder import JSONDecodeError
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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9
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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10
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11 def __main__():
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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12 p = argparse.ArgumentParser()
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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13 p.add_argument(
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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14 '-i', '--input',
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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15 type=argparse.FileType('r'),
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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16 required=True,
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17 help='Tabular input file to pivot'
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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18 )
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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19 p.add_argument(
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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20 '-o', '--output',
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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21 type=argparse.FileType('w'),
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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22 required=True,
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23 help='Output file'
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24 )
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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25 p.add_argument(
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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26 '-S', '--skiprows',
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27 type=int,
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28 default=0,
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29 help='Input column names'
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30 )
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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31 p.add_argument(
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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32 '-H', '--header',
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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33 default=None,
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34 help='Input column names'
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35 )
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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36 p.add_argument(
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37 '-P', '--prefix',
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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38 default=None,
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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39 help='Prefix for input column names'
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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40 )
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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41 p.add_argument(
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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42 '-I', '--index',
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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43 help='index columns'
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44 )
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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45 p.add_argument(
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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46 '-C', '--columns',
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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47 help='columns values which are returned as columns'
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48 )
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49 p.add_argument(
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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50 '-V', '--values',
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51 help='values'
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52 )
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53 p.add_argument(
621144f8dbe9 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"
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54 '-F', '--aggfunc',
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55 help='aggregate functions on the values'
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56 )
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57 p.add_argument(
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58 '-N', '--fill_value',
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59 default=None,
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60 help='fill value for missing values'
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61 )
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62 args = p.parse_args()
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63
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64 def getValueType(val):
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65 if val or 0. == val:
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66 try:
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67 return int(val)
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68 except ValueError:
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69 try:
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70 return float(val)
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71 except ValueError:
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72 return val
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73 return None
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74
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75 def getColumn(name, dfcols):
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76 if name in dfcols:
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77 return name
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78 else:
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79 try:
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80 i = int(name)
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81 return dfcols[i]
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82 except:
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83 print('%s not a column in %s' % (name, dfcols), file=sys.stderr)
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84 exit(1)
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85
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86 def getColumns(val, dfcols):
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87 fields = [v.strip() for v in val.split(',')]
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88 cols = []
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89 for name in fields:
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90 cols.append(getColumn(name, dfcols))
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91 return cols
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92
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93 def getAggFunc(funcStr, dfcols):
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94 af = funcStr
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95 try:
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96 af = json.loads(funcStr)
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97 except JSONDecodeError as de:
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98 print('"%s" is not a json string: ' % funcStr, de.msg, file=sys.stderr)
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99 exit(1)
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100 if isinstance(af, dict):
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101 aggfunc = {getColumn(k, dfcols) : v for k,v in af.items()}
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102 elif isinstance(af, list):
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103 aggfunc = af
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104 else:
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105 aggfunc = af
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106 return aggfunc
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107
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108 if args.prefix:
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109 df = pd.read_table(args.input, skiprows=args.skiprows, header=None, prefix=args.prefix)
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110 elif args.header:
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111 df = pd.read_table(args.input, skiprows=args.skiprows, header=args.header)
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112 else:
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113 df = pd.read_table(args.input, skiprows=args.skiprows)
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114 df_columns = df.columns.tolist()
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115 index = getColumns(args.index, df_columns)
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116 columns = getColumns(args.columns, df_columns)
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117 values = getColumns(args.values, df_columns)
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118 fill_value = getValueType(args.fill_value)
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119 aggfunc = getAggFunc(args.aggfunc, values)
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120 pdf = df.pivot_table(index=index, columns=columns,
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121 values=values, aggfunc=aggfunc,
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122 fill_value=fill_value)
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123 pdf_cols = ['_'.join(reversed(p)) if isinstance(p, tuple) else p for p in pdf.columns.tolist()]
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124 pdf.to_csv(args.output, sep='\t', float_format='%0.6f', header=pdf_cols)
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125
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126
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127 if __name__ == "__main__":
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128 __main__()