comparison column_maker.py @ 10:beec6ecc7d3c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6

9:33b81f9ea109

import enum
import re
import sys
# Functions that may be used in the compute expression
from math import (  # noqa: F401
    ceil,
    exp,
    floor,
    log,
    log10,
    sqrt,
)

from numpy import format_float_positional

try:
    cast_types = eval(
        'lambda fields: [from_str(s, t) for s, t in zip(fields, [%s])]'
        % args.column_types
    )
except Exception as e:
    sys.exit(
        'While parsing column types, the following problem occured: "%s"'
        % e
    )

# Get and parse actions
if args.file:
    actions = []

# a missing COL_ADD_SPEC is interpreted as mode A (append new column at the
# end of the row).
# COL_NAME is required with the --header option and specifies the name of the
# new column; without --header, any COL_NAME gets ignored.
operators = 'is|not|or|and'
builtin_and_math_functions = (
    'abs|all|any|ascii|bin|bool|chr|complex|divmod|float|format|hex|int|len|'
    'list|map|max|min|oct|ord|pow|range|reversed|round|set|sorted|str|sum|type|'
    'log|log10|exp|sqrt|ceil|floor'
)
imported_numpy_function = 'format_float_positional'
string_and_list_methods = [
    name for name in dir('') + dir([]) if not name.startswith('_')
]
whitelist = r"^([c0-9\+\-\*\/\(\)\.\'\"><=,:! ]|%s|%s|%s|%s)*$" % (

ops = []
num_cols = in_columns
for ac in actions:
    try:
        expr_string, col_add_spec, new_col_name = ac.split(';')
    except ValueError:
        sys.exit(
            'Invalid Action: "%s".  '
            'Required format: EXPR;[COL_ADD_SPEC];[COL_NAME]' % ac
        )

10:beec6ecc7d3c

import enum
import re
import sys
# Functions that may be used in the compute expression
from math import (  # noqa: F401
    acos,
    acosh,
    asin,
    asinh,
    atan,
    atan2,
    atanh,
    cbrt,
    ceil,
    comb,
    copysign,
    cos,
    cosh,
    degrees,
    dist,
    erf,
    erfc,
    exp,
    exp2,
    expm1,
    fabs,
    factorial,
    floor,
    fmod,
    frexp,
    fsum,
    gamma,
    gcd,
    hypot,
    inf,
    isclose,
    isfinite,
    isinf,
    isnan,
    isqrt,
    ldexp,
    lgamma,
    log,
    log10,
    log1p,
    log2,
    modf,
    nextafter,
    perm,
    pi,
    pow,
    prod,
    remainder,
    sin,
    sqrt,
    tan,
    tanh,
    tau,
    trunc,
    ulp,
)

from numpy import format_float_positional

try:
    cast_types = eval(
        'lambda fields: [from_str(s, t) for s, t in zip(fields, [%s])]'
        % args.column_types
    )
except Exception as err:
    sys.exit(
        'While parsing column types, the following problem occured: "%s"'
        % err
    )

# Get and parse actions
if args.file:
    actions = []

# a missing COL_ADD_SPEC is interpreted as mode A (append new column at the
# end of the row).
# COL_NAME is required with the --header option and specifies the name of the
# new column; without --header, any COL_NAME gets ignored.
operators = 'is|not|or|and'
builtin_functions = (
    'abs|all|any|ascii|bin|bool|chr|complex|divmod|float|format|hex|int|len|'
    'list|map|max|min|oct|ord|pow|range|reversed|round|set|sorted|str|sum|type'
)

math_functions = (
    'acos|acosh|asin|asinh|atan|atan2|atanh|cbrt|ceil|comb|copysign|cos|cosh|degrees|'
    'dist|erf|erfc|exp|exp2|expm1|fabs|factorial|floor|fmod|frexp|fsum|gamma|gcd|'
    'hypot|inf|isclose|isfinite|isinf|isnan|isqrt|ldexp|lgamma|log|log10|log1p|'
    'log2|modf|nextafter|perm|pi|pow|prod|remainder|sin|'
    'sqrt|tan|tanh|tau|trunc|ulp'
)
builtin_and_math_functions = builtin_functions + '|' + math_functions
imported_numpy_function = 'format_float_positional'
string_and_list_methods = [
    name for name in dir('') + dir([]) if not name.startswith('_')
]
whitelist = r"^([c0-9\+\-\*\/\(\)\.\'\"><=,:! ]|%s|%s|%s|%s)*$" % (

ops = []
num_cols = in_columns
for ac in actions:
    try:
        expr_string, col_add_spec, new_col_name = ac.split(';')
        print(expr_string)
    except ValueError:
        sys.exit(
            'Invalid Action: "%s".  '
            'Required format: EXPR;[COL_ADD_SPEC];[COL_NAME]' % ac
        )