print " each experiment."
print ""
print "For each experiment defined on the command line, a subdirectory"
print "called '<name>_<expt_type>' (e.g. 'PB_ChIP-seq' - if no <expt_type>"
print "was supplied then just the name is used) will be made, and links to"
print "each of the primary data files."
sys.exit(1)
# Solid run directory
solid_run_dir = sys.argv[-1]
if not os.path.isdir(solid_run_dir):
logging.error("Solid run directory '%s' not found" % solid_run_dir)
sys.exit(1)
# Set up experiment list
expts = Experiment.ExperimentList(solid_run_dir=solid_run_dir)
# Process command line arguments
for arg in sys.argv[1:-1]:
# Process command line arguments
if arg.startswith('--name='):
expt_name = arg.split('=')[1]
expt = expts.addExperiment(expt_name)
elif arg.startswith('--type='):
expt = expts.getLastExperiment()
if expt is None:
logging.error("No experiment defined for --type argument")
sys.exit(1)
if not expt.type:
expt.type = arg.split('=')[1]
else:
