annotate column_maker.py @ 4:6e8d94597139 draft

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 0cb87d8f454f205af021d653d7f7d5a7c14c7718"

#!/usr/bin/env python
"""
This tool takes a tab-delimited textfile as input and creates another column in
the file which is the result of a computation performed on every row in the
original file. The tool will skip over invalid lines within the file,
informing the user about the number of lines skipped.
"""
from __future__ import print_function

import re
import sys

assert sys.version_info[:2] >= (2, 4)

inp_file = sys.argv[1]
out_file = sys.argv[2]
expr = sys.argv[3]
round_result = sys.argv[4]
try:
    in_columns = int(sys.argv[5])
except Exception:
    exit("Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data.")
if in_columns < 2:
    # To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method.
    exit("Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data.")
try:
    in_column_types = sys.argv[6].split(',')
except Exception:
    exit("Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data.")
if len(in_column_types) != in_columns:
    exit("The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data.")
avoid_scientific_notation = sys.argv[7]

# Unescape if input has been escaped
mapped_str = {
    '__lt__': '<',
    '__le__': '<=',
    '__eq__': '==',
    '__ne__': '!=',
    '__gt__': '>',
    '__ge__': '>=',
    '__sq__': '\'',
    '__dq__': '"',
}
for key, value in mapped_str.items():
    expr = expr.replace(key, value)

operators = 'is|not|or|and'
builtin_and_math_functions = 'abs|all|any|bin|chr|cmp|complex|divmod|float|bool|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|log10|exp|sqrt|ceil|floor'
string_and_list_methods = [name for name in dir('') + dir([]) if not name.startswith('_')]
whitelist = r"^([c0-9\+\-\*\/\(\)\.\'\"><=,:! ]|%s|%s|%s)*$" % (operators, builtin_and_math_functions, '|'.join(string_and_list_methods))
if not re.compile(whitelist).match(expr):
    exit("Invalid expression")
if avoid_scientific_notation == "yes":
    expr = "format_float_positional(%s)" % expr

# Prepare the column variable names and wrappers for column data types
cols, type_casts = [], []
for col in range(1, in_columns + 1):
    col_name = "c%d" % col
    cols.append(col_name)
    col_type = in_column_types[col - 1].strip()
    if round_result == 'no' and col_type == 'int':
        col_type = 'float'
    type_cast = "%s(%s)" % (col_type, col_name)
    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
out = open(out_file, 'wt')

# 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

fh = open(inp_file)
for i, line in enumerate(fh):
    total_lines += 1
    line = line.rstrip('\\r\\n')
    if not line or line.startswith('#'):
        skipped_lines += 1
        if not invalid_line:
            first_invalid_line = i + 1
            invalid_line = line
        continue
    try:
        %s
        %s
        new_val = %s
        if round_result == "yes":
            new_val = int(round(new_val))
        new_line = line + '\\t' + str(new_val) + "\\n"
        out.write(new_line)
        lines_kept += 1
    except Exception:
        skipped_lines += 1
        if not invalid_line:
            first_invalid_line = i + 1
            invalid_line = line
fh.close()
''' % (assign, wrap, expr)

valid_expr = True
try:
    exec(code)
except Exception as e:
    out.close()
    if str(e).startswith('invalid syntax'):
        valid_expr = False
        exit('Expression "%s" likely invalid. See tool tips, syntax and examples.' % expr)
    else:
        exit(str(e))

if valid_expr:
    out.close()
    valid_lines = total_lines - skipped_lines
    print('Creating column %d with expression %s' % (in_columns + 1, expr))
    if valid_lines > 0:
        print('kept %4.2f%% of %d lines.' % (100.0 * lines_kept / valid_lines,
                                             total_lines))
    else:
        print('Possible invalid expression "%s" or non-existent column referenced. See tool tips, syntax and examples.' % expr)
    if skipped_lines > 0:
        print('Skipped %d invalid lines starting at line #%d: "%s"' %
              (skipped_lines, first_invalid_line, invalid_line))