/usr/lib/python2.7/dist-packages/cogent/parse/table.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 | #!/usr/bin/env python
import cPickle, csv
from record_finder import is_empty
from gzip import GzipFile
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
class ConvertFields(object):
"""converter for input data to Table"""
def __init__(self, conversion, by_column=True):
"""handles conversions of columns or lines
Arguments:
- by_column: conversion will by done for each column, otherwise
done by entire line
- """
super(ConvertFields, self).__init__()
self.conversion = conversion
self.by_column = by_column
self._func = self.convertByColumns
if not self.by_column:
assert callable(conversion), \
"conversion must be callable to convert by line"
self._func = self.convertByLine
def convertByColumns(self, line):
"""converts each column in a line"""
for index, cast in self.conversion:
line[index] = cast(line[index])
return line
def convertByLine(self, line):
"""converts each column in a line"""
return self.conversion(line)
def _call(self, *args, **kwargs):
return self._func(*args, **kwargs)
__call__ = _call
def SeparatorFormatParser(with_header=True, converter = None, ignore = None,
sep=",", strip_wspace=True, limit=None, **kw):
"""Returns a parser for a delimited tabular file.
Arguments:
- with_header: when True, first line is taken to be the header. Not
passed to converter.
- converter: a callable that returns a correctly formatted line.
- ignore: lines for which ignore returns True are ignored. White-space
lines are always skipped.
- sep: the delimiter deparating fields.
- strip_wspace: removes redundant white-space from strings.
- limit: exits after this many lines"""
sep = kw.get("delim", sep)
if ignore is None: # keep all lines
ignore = lambda x: False
by_column = getattr(converter, 'by_column', True)
def callable(lines):
num_lines = 0
header = None
for line in lines:
if is_empty(line):
continue
line = line.strip('\n').split(sep)
if strip_wspace and by_column:
line = [field.strip() for field in line]
if with_header and not header:
header = True
yield line
continue
if converter:
line = converter(line)
if ignore(line):
continue
yield line
num_lines += 1
if limit is not None and num_lines >= limit:
break
return callable
def autogen_reader(infile, sep, with_title, limit=None):
"""returns a SeparatorFormatParser with field convertor for numeric column
types."""
seen_title_line = False
for first_data_row in infile:
if seen_title_line:
break
if sep in first_data_row and not seen_title_line:
seen_title_line = True
infile.seek(0) # reset to start of file
numeric_fields = []
for index, value in enumerate(first_data_row.strip().split(sep)):
try:
v = float(value)
except ValueError:
try:
v = long(value)
except ValueError:
continue
numeric_fields += [(index, eval(value).__class__)]
return SeparatorFormatParser(converter=ConvertFields(numeric_fields),
sep=sep, limit=limit)
def load_delimited(filename, header = True, delimiter = ',',
with_title = False, with_legend = False, limit=None):
if limit is not None:
limit += 1 # don't count header line
if filename.endswith('gz'):
f = GzipFile(filename, 'rb')
else:
f = file(filename, "U")
reader = csv.reader(f, dialect = 'excel', delimiter = delimiter)
rows = []
num_lines = 0
for row in reader:
rows.append(row)
num_lines += 1
if limit is not None and num_lines >= limit:
break
f.close()
if with_title:
title = ''.join(rows.pop(0))
else:
title = ''
if header:
header = rows.pop(0)
else:
header = None
if with_legend:
legend = ''.join(rows.pop(-1))
else:
legend = ''
# now do type casting in the order int, float, default is string
for row in rows:
for cdex, cell in enumerate(row):
try:
cell = int(cell)
row[cdex] = cell
except ValueError:
try:
cell = float(cell)
row[cdex] = cell
except ValueError:
pass
pass
return header, rows, title, legend
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