comparison column_maker.py @ 7:427903d47026 draft

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"

6:13b6f0007d9e

import argparse
import json
import re
import sys

parser = argparse.ArgumentParser()
parser.add_argument('input', type=argparse.FileType('r'), help="input file")
parser.add_argument('output', type=argparse.FileType('wt'), help="output file")
parser.add_argument('cond', nargs='?', type=str, help="expression")

            header_line, argparse_dict['header_new_column_name']
        )
    )
try:
    in_columns = int(argparse_dict['columns'])
    if in_columns < 2:
        # To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method.
        raise ValueError
except Exception:
    if not fh.readline():
        # empty file content is ok and should produce empty output
        out.close()

    type_casts.append(type_cast)

col_str = ', '.join(cols)    # 'c1, c2, c3, c4'
type_cast_str = ', '.join(type_casts)  # 'str(c1), int(c2), int(c3), str(c4)'
assign = "%s = line.split('\\t')" % col_str
wrap = "%s = %s" % (col_str, type_cast_str)
skipped_lines = 0
first_invalid_line = 0
invalid_line = None
lines_kept = 0
total_lines = 0

# Read input file, skipping invalid lines, and perform computation that will result in a new column
code = '''
# import here since flake8 complains otherwise
from math import (
    ceil,
    exp,
    floor,
    log,
    log10,
    sqrt
)
from numpy import format_float_positional

for i, line in enumerate(fh):
    total_lines += 1
    line = line.rstrip('\\r\\n')
    if not line or line.startswith('#'):
        skipped_lines += 1

7:427903d47026

import argparse
import json
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  # noqa: F401

parser = argparse.ArgumentParser()
parser.add_argument('input', type=argparse.FileType('r'), help="input file")
parser.add_argument('output', type=argparse.FileType('wt'), help="output file")
parser.add_argument('cond', nargs='?', type=str, help="expression")

            header_line, argparse_dict['header_new_column_name']
        )
    )
try:
    in_columns = int(argparse_dict['columns'])
    if in_columns < 1:
        # To be considered tabular, data must have at least one column.
        raise ValueError
except Exception:
    if not fh.readline():
        # empty file content is ok and should produce empty output
        out.close()

    type_casts.append(type_cast)

col_str = ', '.join(cols)    # 'c1, c2, c3, c4'
type_cast_str = ', '.join(type_casts)  # 'str(c1), int(c2), int(c3), str(c4)'
assign = "%s = line.split('\\t')" % col_str
if len(cols) == 1:
    # Single column, unpacking by assignment won't work
    assign += '[0]'
wrap = "%s = %s" % (col_str, type_cast_str)
skipped_lines = 0
first_invalid_line = 0
invalid_line = None
lines_kept = 0
total_lines = 0

# Read input file, skipping invalid lines, and perform computation that will result in a new column
code = '''
for i, line in enumerate(fh):
    total_lines += 1
    line = line.rstrip('\\r\\n')
    if not line or line.startswith('#'):
        skipped_lines += 1