Mercurial > repos > jjohnson > pandas_pivot_table

comparison 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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-1:000000000000 0:621144f8dbe9
1 #!/usr/bin/env python
2
3 import argparse
4 import json
5 import re
6 import pandas as pd
7 import sys
8 from json.decoder import JSONDecodeError
9
10
11 def __main__():
12 p = argparse.ArgumentParser()
13 p.add_argument(
14 '-i', '--input',
15 type=argparse.FileType('r'),
16 required=True,
17 help='Tabular input file to pivot'
18 )
19 p.add_argument(
20 '-o', '--output',
21 type=argparse.FileType('w'),
22 required=True,
23 help='Output file'
24 )
25 p.add_argument(
26 '-S', '--skiprows',
27 type=int,
28 default=0,
29 help='Input column names'
30 )
31 p.add_argument(
32 '-H', '--header',
33 default=None,
34 help='Input column names'
35 )
36 p.add_argument(
37 '-P', '--prefix',
38 default=None,
39 help='Prefix for input column names'
40 )
41 p.add_argument(
42 '-I', '--index',
43 help='index columns'
44 )
45 p.add_argument(
46 '-C', '--columns',
47 help='columns values which are returned as columns'
48 )
49 p.add_argument(
50 '-V', '--values',
51 help='values'
52 )
53 p.add_argument(
54 '-F', '--aggfunc',
55 help='aggregate functions on the values'
56 )
57 p.add_argument(
58 '-N', '--fill_value',
59 default=None,
60 help='fill value for missing values'
61 )
62 args = p.parse_args()
63
64 def getValueType(val):
65 if val or 0. == val:
66 try:
67 return int(val)
68 except ValueError:
69 try:
70 return float(val)
71 except ValueError:
72 return val
73 return None
74
75 def getColumn(name, dfcols):
76 if name in dfcols:
77 return name
78 else:
79 try:
80 i = int(name)
81 return dfcols[i]
82 except:
83 print('%s not a column in %s' % (name, dfcols), file=sys.stderr)
84 exit(1)
85
86 def getColumns(val, dfcols):
87 fields = [v.strip() for v in val.split(',')]
88 cols = []
89 for name in fields:
90 cols.append(getColumn(name, dfcols))
91 return cols
92
93 def getAggFunc(funcStr, dfcols):
94 af = funcStr
95 try:
96 af = json.loads(funcStr)
97 except JSONDecodeError as de:
98 print('"%s" is not a json string: ' % funcStr, de.msg, file=sys.stderr)
99 exit(1)
100 if isinstance(af, dict):
101 aggfunc = {getColumn(k, dfcols) : v for k,v in af.items()}
102 elif isinstance(af, list):
103 aggfunc = af
104 else:
105 aggfunc = af
106 return aggfunc
107
108 if args.prefix:
109 df = pd.read_table(args.input, skiprows=args.skiprows, header=None, prefix=args.prefix)
110 elif args.header:
111 df = pd.read_table(args.input, skiprows=args.skiprows, header=args.header)
112 else:
113 df = pd.read_table(args.input, skiprows=args.skiprows)
114 df_columns = df.columns.tolist()
115 index = getColumns(args.index, df_columns)
116 columns = getColumns(args.columns, df_columns)
117 values = getColumns(args.values, df_columns)
118 fill_value = getValueType(args.fill_value)
119 aggfunc = getAggFunc(args.aggfunc, values)
120 pdf = df.pivot_table(index=index, columns=columns,
121 values=values, aggfunc=aggfunc,
122 fill_value=fill_value)
123 pdf_cols = ['_'.join(reversed(p)) if isinstance(p, tuple) else p for p in pdf.columns.tolist()]
124 pdf.to_csv(args.output, sep='\t', float_format='%0.6f', header=pdf_cols)
125
126
127 if __name__ == "__main__":
128 __main__()