Given a CSV or tab-delimited input file (ASCII-encoding), replace all missing values or all occurances of a specified value with a new marker. Useful for large scientific data where some values are missing (i.e. gene microarrays, etc).

replace_missing_values_in_matrix.py

#! /usr/bin/env python
###################################################################################################
# Given a CSV or tab-delimited input file (ASCII-encoding), replace all
# missing values or all occurances of a specified value with a new marker.
# Useful for large scientific data where some values are missing (i.e. gene
# microarrays, etc)
# 
# The MIT License (MIT)
#
# Copyright (c) 2016 Jason L Causey, Arkansas State University
#
# 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.
###################################################################################################

usage = """
    Usage:
        {0}  ascii_matrix_file  [--help] [--missing=MISSING-MARKER] [--fill=FILL-MARKER] [--output=OUTPUT-FILE]
    
        Fill all instances of MISSING-MARKER in an ASCII-format (CSV or tab-delimited)
        matrix or table with the value specified by MISSING-FILL

            ascii_matrix_file        - a CSV or tab-delimited file in ASCII encoding
            --help                   - show this help message and exit
            --missing=MISSING-MARKER - MISSING-MARKER is the value in input file that currently 
                                       marks "missing value" locations.
                                       Default is '' (no value at all) - literally missing.
            --fill=FILL-MARKER       - FILL-MARKER is the value to place in output file for 
                                       all missing locations.
                                       Default is 0.
            --output=OUTPUT-FILE     - direct output to OUTPUT-FILE instead of stdout
                                       Default output is to stdout
"""

import sys, csv, os

def usage(code=0):
    print(usage.format(os.path.basename(sys.argv[0])))
    if code != None:
        sys.exit(code)

if len(sys.argv) < 2:
    usage(1)

inname        = sys.argv[1]
outname       = None
missing_ch    = ''
fill_value    = '0'
ids_file      = None
ids           = None

if len(sys.argv) > 2:
    for i in range(2, 6):
        if len(sys.argv) > i and sys.argv[i][0:3]          == '--h':
            usage(0)
        if len(sys.argv) > i and sys.argv[i].split('=')[0] == '--missing':
            missing_ch    = sys.argv[i].split('=')[1]
        if len(sys.argv) > i and sys.argv[i].split('=')[0] == '--fill':
            fill_value    = sys.argv[i].split('=')[1]
        if len(sys.argv) > i and sys.argv[i].split('=')[0] == '--output':
            outname       = sys.argv[i].split('=')[1]

of = sys.stdout
with open(inname, 'rb') as csvfile:
    dialect = csv.Sniffer().sniff(csvfile.read(8*1024))
    csvfile.seek(0)
    reader  = csv.reader(csvfile, dialect)
    if outname != None:
        of = open(outname, 'wb')
    writer  = csv.writer(of, dialect)
    for line in reader:
        line = [fill_value if v == missing_ch else v for v in line]
        writer.writerow(line)
    if outname != None:
        of.close()