old_contents: #!/usr/bin/python
  
  """Usage:
      set_isoform_frequencies [{help}] [{version}] {pro_file}
  
  {help_short} {help}                 Show this message.
  {version_short} {version}              Show version.
  {pro_file}  Flux simulator gene expression profile file.
  """
  
  from docopt import docopt
  from options import validate_file_option
  from schema import SchemaError
  
  HELP_SHORT = "-h"
  HELP = "--help"
  VERSION_SHORT = "-v"
  VERSION = "--version"
  PRO_FILE = "<pro-file>"
  
  __doc__ = __doc__.format(
      help_short=HELP_SHORT,
      help=HELP,
      version_short=VERSION_SHORT,
      version=VERSION,
      pro_file=PRO_FILE)
  
  # Read in command-line options
  options = docopt(__doc__, version="set_isoform_frequencies v0.1")
  
  # Validate command-line options
  
  try:
      options[PRO_FILE] = validate_file_option(
          options[PRO_FILE], "Could not open expression profile file")
  except SchemaError as exc:
      exit(exc.code)
  
  print("Now do all the things.")
  
new_contents: #!/usr/bin/python
  
  """Usage:
      set_isoform_frequencies [{help}] [{version}] {pro_file}
  
  {help_short} {help}                 Show this message.
  {version_short} {version}              Show version.
  {pro_file}  Flux simulator gene expression profile file.
  """
  
  from docopt import docopt
  from options import validate_file_option
  from pandas import read_csv
  from schema import SchemaError
  
  HELP_SHORT = "-h"
  HELP = "--help"
  VERSION_SHORT = "-v"
  VERSION = "--version"
  PRO_FILE = "<pro-file>"
  
  LOCUS_COL = 'loc'
  TRANSCRIPT_ID_COL = 't_id'
  CODING_COL = 'c'
  LENGTH_COL = 'len'
  FRACTION_COL = 'f'
  NUM_TRANSCRIPTS_COL = 'n'
  UNKNOWN_COL_1 = 'u1'
  UNKNOWN_COL_2 = 'u2'
  
  PRO_FILE_COLUMNS = [
      LOCUS_COL,
      TRANSCRIPT_ID_COL,
      CODING_COL,
      LENGTH_COL,
      FRACTION_COL,
      NUM_TRANSCRIPTS_COL,
      UNKNOWN_COL_1,
      UNKNOWN_COL_2]
  
  __doc__ = __doc__.format(
      help_short=HELP_SHORT,
      help=HELP,
      version_short=VERSION_SHORT,
      version=VERSION,
      pro_file=PRO_FILE)
  
  # Read in command-line options
  options = docopt(__doc__, version="set_isoform_frequencies v0.1")
  
  # Validate command-line options
  
  try:
      options[PRO_FILE] = validate_file_option(
          options[PRO_FILE], "Could not open expression profile file")
  except SchemaError as exc:
      exit(exc.code)
  
  df = read_csv(options[PRO_FILE], sep='\s*',
                names=PRO_FILE_COLUMNS, index_col=TRANSCRIPT_ID_COL)
  
subject: Read in Flux Simulator expression profile with pandas.