Like cut for CSVs and TSVs and what not

csvcut

#!/usr/bin/env python2.7

# Copyright (c) 2014 Elias Ponvert
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.


from argparse import ArgumentParser
from csv import reader as csv_reader, writer as csv_writer
import re

__author__ = "Elias Ponvert"
__copyright__ = "Copyright 2014, Elias Ponvert"
__version__ = 'v1.0.2'
__license__ = "MIT"

def csvcut(fh_in, fh_out, slices, input_delim, output_delim, skip_header=False):
  """Transform CSV input

  Parses fields out of each line of the input stream, writes a subset of the
  fields to the output stream

  Args:
    fh_in: Input file stream
    fh_out: Output file stream
    slices: List of Python slice objects, to extract from the rows from the input
    input_delim: The field separator for the input stream
    output_delim: The field separator for the output stream
    skip_header: If true, skip the first line of the input stream

  Raises:
    IOError: An error occured accessing the input stream or the output stream
  """
  csv_in = csv_reader(fh_in, delimiter=input_delim)
  if skip_header:
    csv_in.next()
  csv_out = csv_writer(fh_out, delimiter=output_delim)
  for row in csv_in:
    csv_out.writerow(sum([row[slice] for slice in slices], []))


def _mkslice(s):
  s = s.strip()
  m = re.match(r'^(\d+)$', s)
  if m:
    n = int(m.group(1))
    return slice(n-1, n)

  m = re.match(r'^(\d+)-(\d+)$', s)
  if m:
    return slice(int(m.group(1))-1, int(m.group(2)))

  m = re.match(r'^-(\d+)$', s)
  if m:
    return slice(int(m.group(1)))

  m = re.match(r'^(\d+)-$', s)
  if m:
    return slice(int(m.group(1))-1, None)

  raise ValueError("Unexpected slice format: %s" % (s,))

def _parse_delim(s):
  if s == '\\t':
    return '\t'
  else:
    return s

def main(argv):
  ap = ArgumentParser(description="Like cut, for CSVs and TSVs and what not")
  ap.add_argument('--version', action='version', version='%(prog)s ' + __version__)
  ap.add_argument('-f', '--fields', metavar='LIST', default='0-',
    help="select only these fields; supported formats = comma-separated, N-M, N-, -M")
  ap.add_argument('-d', '--delimiter', metavar='DELIM', default='\t',
    help="use DELIM instead of TAB for field delimiter")
  ap.add_argument('--output-delimiter', metavar='STRING', default=None,
    help="use STRING as the output delimiter, the default is to use the input delimiter")
  ap.add_argument('--skip-header', action='store_true', help="skip first row of input")
  ap.add_argument('files', metavar='FILE', nargs='*', default=None, help="csv/tsv file input")
  args = ap.parse_args(argv)

  slices = map(_mkslice, args.fields.split(','))
  input_delim = _parse_delim(args.delimiter)
  output_delim = _parse_delim(args.output_delimiter) or input_delim

  from sys import stdout

  csvcut_args = [stdout, slices, input_delim, output_delim, args.skip_header]

  try:
    if args.files:
      for f in args.files:
        with open(f, 'rU') as f_in:
          csvcut(f_in, *csvcut_args)

    else:
      from sys import stdin
      csvcut(stdin, *csvcut_args)

  except IOError, e:
    if e.errno == 32: # Broken pipe
      pass
    else:
      raise e

if __name__ == '__main__':
  from sys import argv
  main(argv[1:])