from rSeq.utils.sitRep import start_sitrep
start_sitrep('/home/augustine/tmp/')
print "this should be stdOut!\nBut also this!\n"
raise Exception('This should be stdErr!')
help="""Include to redirect stdout and stderr to a central log file in out_dir. [useful for reproducibility and debugging] (default=%default)""")
parser.add_option('--override', dest="override", action='store_true',default=False,
help="""A switch that causes the default --bt-opts to be replaced by those provided as arguments to --bt-opts instead of adding to them. (default=%default)""")
(opts, args) = parser.parse_args()
if len(sys.argv) == 1:
parser.print_help()
exit(0)
if opts.out_dir:
mkdirp(opts.out_dir)
opts.out_dir = opts.out_dir.rstrip('/')
else:
opts.out_dir = os.getcwd()
if opts.cent_log:
start_sitrep(opts.out_dir)
if not 'BOWTIE_INDEXES' in os.environ:
raise Exception('ERROR: please set the BOWTIE_INDEXES environment variable!')
try:
opts.bt_index
opts.bam_base
opts.fastqs
except KeyError:
raise MissingArgumentError('missing at least one of the required command line arguments: --bt-index, --bam-base, --fastqs')
if not opts.override:
opts.bt_opts = "%s %s" % (defaultBtOpts,opts.bt_opts)
# Change to out_dir to make sure that any tempfiles are not droped in random
# places in the file system in case of fatal errors
os.chdir(opts.out_dir)
