#!/usr/bin/env python

# Copyright Harry Mangalam <harry.mangalam@uci.edu>
# I explicitly place this work into the Public Domain
# you can do anything you like with this code.
#
# This is a tutorial skeleton python script to process STDIN line by line with some
# extras thrown in to make it easier to debug and some examples as to how to
# add commandline options etc.

# following triple quoted stanza is the __doc__ string or 'docstring' - it is the
# optional (but very useful) text associated with each function or class in python
# that describes what it does.  Many Python utilities depend on the docstring to provide
# help or at least an indication of what the associated code does.

"""
This script:
    - allows the user to assign some values to variables using commandline options
    - processes a file line by line,
    - breaks the file into values based on defined input delimiter (default <TAB>)
    - does a trivial calculation on the values extracted based on the values extracted
    - outputs the transformed data.separated by a defined delimter (defaults to <TAB>)

Usage: linebyline.py [options] < file
       or
	   some other cmd -> <stdout> | linebyline.py [options]

Options:
    -c / --comments ...Comments pass thru untouched, else they are stripped
    -h / --help .......Print this message and exit.
    -d / --debug.......Turn on debugging of script
    -i / --id='input delimiter character, string'
    -o / --od='output delimiter character, string'
    --var1=float
    --var2=float
    --var3=float
    -p / --prefix='string to add to beginning of character field'
    -s / --suffix='string to add to end of character field'
"""

import sys, string, fileinput, os, getopt, errno, time

# see the showmedo.com videos for more on iPython
# http://showmedo.com/videos/series?name=PythonIPythonSeries
# uncomment the 2 lines below to enable iPython debugging.

#from IPython.Shell import IPShellEmbed
#dbg = IPShellEmbed() # and insert 'dbg()' where you want to break.

# following function uses the docstring above as the help message
# prefixed by an optional message as dmeo'ed below and provides the
# supplied exit code on exit to test the exit condition (normal (0)
# or error (nonzero - see try/except stanza below)
def usage(code, msg=''):
    if msg:
        print >> sys.stderr, msg
    print >> sys.stderr, __doc__
    sys.exit(code)


# main function
def main():

    # Set up the defaults and variables
    ID = "\t"    # default input delim is a TAB
    OD = "\t"    # ditto output
    PREFIX = ""  # default is NO prefix
    SUFFIX = ""  # ditto suffix
    VAR1 = VAR2 = VAR3 = 1 # init all VARs to 1
    DEBUG = 0    # off by default
    COMMENTS = 0 # default it to strip comments.

    # for some explanations of what the following translates into, try:
    # http://www.linuxjournal.com/article/3946

    # the following try/except stanza processes the commandline options.
    try:
        opts, args = getopt.getopt(sys.argv[1:], 'cdhi:o:p:s:', ['comments', 'debug', 'help', 'id=', 'od=', 'var1=', 'var2=', 'var3=', 'prefix=', 'suffix='])
    except getopt.GetoptError:
        # print help information and exit:
        usage(1, "\nThere was an error specifying an option flag.  The correct usage is:")


    for opt, arg in opts:
        if opt in ('-h', '--help'):  usage(0)
        elif opt in ('-c', '--comments'):  COMMENTS = 1
        elif opt in ('-i', '--id'):  ID = arg
        elif opt in ('-o', '--od'):  OD = arg
        elif opt in ('--var1'): VAR1 = float(arg) # numeric args have to be 'floated'
        elif opt in ('--var2'): VAR2 = float(arg)
        elif opt in ('--var3'): VAR3 = float(arg)
        elif opt in ('-p', '--prefix'): PREFIX = arg
        elif opt in ('-s', '--suffix'): SUFFIX = arg
        elif opt in ('-d', '--debug'): DEBUG = 1

    linecnt = 0 # line count for debugging
    while 1:
        # read stdin effectively line by line
        line = sys.stdin.readline()[:-1] # the subscript [:-1] trims the newline character
        string.strip(line) # strip it of leading and trailing spaces
        linecnt = linecnt + 1
        if line and line[0] != "#": # if a non-comment line
            #dbg()
            ttlflds = line.split(ID)
            nbrflds = len(ttlflds) # get the number of fields detected
            if DEBUG:
                print "Line %d  %d fields: " % (linecnt, nbrflds)
            output = ""
            for fld in ttlflds:
                try:
                    fld = float(fld) * VAR1 * VAR2 * VAR3 + VAR2
                    output = output + "%f" % (fld) + OD
                except:
                    fld = PREFIX + fld + SUFFIX
                    output = output + fld + OD
            print output
            if DEBUG: time.sleep(3) # this just slows things down for debugging
        elif COMMENTS: print line # passthru comments


# now that all the code has been processed, start up main().
if __name__ == '__main__':
    main()