Mercurial > repos > jjohnson > pandas_pivot_table
diff pandas_pivot_table.py @ 4:eaf2444a2a50 draft default tip
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit de16c12e9e27d41d7c7624d7574c51b5bb8edff1-dirty"
author | jjohnson |
---|---|
date | Fri, 18 Dec 2020 19:35:57 +0000 |
parents | 4b65133e0722 |
children |
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--- a/pandas_pivot_table.py Thu Dec 17 22:23:11 2020 +0000 +++ b/pandas_pivot_table.py Fri Dec 18 19:35:57 2020 +0000 @@ -76,17 +76,21 @@ return val return None - def getColumn(name, dfcols): + def getColumn(name, dfcols, value_cols=None): + dfname = None if name in dfcols: - return name + dfname = name else: try: - i = int(name) - return dfcols[i] - except Exception: - print('%s not a column in %s' % (name, dfcols), - file=sys.stderr) - exit(1) + i = int(name) - 1 + dfname = dfcols[i] + except IndexError: + sys.exit('%s not an index into %s' % (name, dfcols)) + except ValueError: + sys.exit('%s not a column in %s' % (name, dfcols)) + if value_cols and dfname not in value_cols: + sys.exit('%s not a value column in %s' % (name, value_cols)) + return dfname def getColumns(val, dfcols): fields = [v.strip() for v in val.split(',')] @@ -95,16 +99,15 @@ cols.append(getColumn(name, dfcols)) return cols - def getAggFunc(funcStr, dfcols): + def getAggFunc(funcStr, dfcols, value_cols): 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) + sys.exit('"%s" is not a json string: %s' % (funcStr, de.msg)) if isinstance(af, dict): - aggfunc = {getColumn(k, dfcols): v for k, v in af.items()} + aggfunc = {getColumn(k, dfcols, value_cols): v + for k, v in af.items()} elif isinstance(af, list): aggfunc = af else: @@ -127,11 +130,12 @@ columns = getColumns(args.columns, df_columns) values = getColumns(args.values, df_columns) fill_value = getValueType(args.fill_value) - aggfunc = getAggFunc(args.aggfunc.replace('\'', '"'), values) + aggfunc = getAggFunc(args.aggfunc.replace('\'', '"'), df_columns, 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 + pdf_cols = ['_'.join([str(x) for x in reversed(p)]) + if isinstance(p, tuple) else str(p) for p in pdf.columns.tolist()] pdf.to_csv(args.output, sep='\t',