diff pandas_pivot_table.py @ 0:621144f8dbe9 draft

"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 80684939b0bf75abb5cc70a9878054c1f734b651-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pandas_pivot_table.py	Wed Dec 02 22:59:57 2020 +0000
@@ -0,0 +1,128 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import re
+import pandas as pd
+import sys
+from json.decoder import JSONDecodeError
+
+
+def __main__():
+    p = argparse.ArgumentParser()
+    p.add_argument(
+        '-i', '--input',
+        type=argparse.FileType('r'),
+        required=True,
+        help='Tabular input file to pivot'
+    )
+    p.add_argument(
+        '-o', '--output',
+        type=argparse.FileType('w'),
+        required=True,
+        help='Output file'
+    )
+    p.add_argument(
+        '-S', '--skiprows',
+        type=int,
+        default=0,
+        help='Input column names'
+    )
+    p.add_argument(
+        '-H', '--header',
+        default=None,
+        help='Input column names'
+    )
+    p.add_argument(
+        '-P', '--prefix',
+        default=None,
+        help='Prefix for input column names'
+    )
+    p.add_argument(
+        '-I', '--index',
+        help='index columns'
+    )
+    p.add_argument(
+        '-C', '--columns',
+        help='columns values which are returned as columns'
+    )
+    p.add_argument(
+        '-V', '--values',
+        help='values'
+    )
+    p.add_argument(
+        '-F', '--aggfunc',
+        help='aggregate functions on the values'
+    )
+    p.add_argument(
+        '-N', '--fill_value',
+        default=None,
+        help='fill value for missing values'
+    )
+    args = p.parse_args()
+
+    def getValueType(val):
+        if val or 0. == val:
+            try:
+                return int(val)
+            except ValueError:
+                try:
+                    return float(val)
+                except ValueError:
+                    return val
+        return None
+
+    def getColumn(name, dfcols):
+        if name in dfcols:
+            return name
+        else:
+            try:
+                i = int(name)
+                return dfcols[i]
+            except:
+                print('%s not a column in %s' % (name, dfcols), file=sys.stderr)
+                exit(1)
+
+    def getColumns(val, dfcols):
+        fields = [v.strip() for v in val.split(',')]
+        cols = []
+        for name in fields:
+            cols.append(getColumn(name, dfcols))
+        return cols
+
+    def getAggFunc(funcStr, dfcols):
+        af = funcStr
+        try:
+            af = json.loads(funcStr)
+        except JSONDecodeError as de:
+            print('"%s" is not a json string: ' % funcStr, de.msg, file=sys.stderr)
+            exit(1)
+        if isinstance(af, dict):
+            aggfunc = {getColumn(k, dfcols) : v for k,v in af.items()}
+        elif isinstance(af, list):
+            aggfunc = af
+        else:
+            aggfunc = af
+        return aggfunc
+
+    if args.prefix:
+        df = pd.read_table(args.input, skiprows=args.skiprows, header=None, prefix=args.prefix)
+    elif args.header:
+        df = pd.read_table(args.input, skiprows=args.skiprows, header=args.header)
+    else:
+        df = pd.read_table(args.input, skiprows=args.skiprows)
+    df_columns = df.columns.tolist()
+    index = getColumns(args.index, df_columns)
+    columns = getColumns(args.columns, df_columns)
+    values = getColumns(args.values, df_columns)
+    fill_value = getValueType(args.fill_value)
+    aggfunc = getAggFunc(args.aggfunc, values)
+    pdf = df.pivot_table(index=index, columns=columns,
+                         values=values, aggfunc=aggfunc,
+                         fill_value=fill_value)
+    pdf_cols = ['_'.join(reversed(p)) if isinstance(p, tuple) else p for p in pdf.columns.tolist()]
+    pdf.to_csv(args.output, sep='\t', float_format='%0.6f', header=pdf_cols)
+
+
+if __name__ == "__main__":
+    __main__()