# Selected columns
if len(user_selected) == 0:
print "No columns selected for output."
sys.exit()
print "Selected columns = %s" % ' '.join(user_selected)
# Assume user counts columns starting from one and adjust to count from zero
# Also check that the requested column exists and set up file names based on
# user input
selected = []
col_lookup = {}
file_names = {}
for col in user_selected:
try:
col0 = int(col) - 1
if col0 >= data.nColumns():
logging.error("Unable to find column %s, not enough columns in input file" % col)
sys.exit(1)
except ValueError:
# Not an integer
if col not in data.header():
logging.error("Unable to find column '%s' in input file" % col)
sys.exit(1)
col0 = data.header().index(col)
# Column lookup
col_lookup[col0] = col
# Adjusted column names
selected.append(col0)
# File names
if first_line_is_header:
file_names[col0] = str(str(data.header()[col0])+".bedGraph").replace(' ','_')
