exit(0) """If the user didn't give a configpath, then we at least need a dbpath (to load a prior database).""" dbpath = ap.getOptionalArg("--dbpath") if configpath == False: print "\n. Error, you need to specify a configuration path, using --configpath" exit() """Regardless of which options are being executed, the DB gets built, or rebuilt, depending on its status.""" con = build_db(dbpath=dbpath) """--make_testdb is a dev-only option""" if True == ap.getOptionalToggle("--make_testdb"): reduce_db_for_test(con) exit() """--reset_files is a dev-only option""" if True == ap.getOptionalToggle("--reset_files"): reset_files(con) exit() # # IMPORT # pillarspath = ap.getArg("--pillarspath") if False == ap.getOptionalToggle("--skip_pillars_import") and False == ap.getOptionalToggle("--skip_import"): con = import_pillars(pillarspath, con) else:
print "\t. Sorts all reads and creates BAM files (samtools)" print "\t. Finds peaks (macs2)" print "\t. Calculates fold-enrichment (macs2)" print "\t. Compares peaks and fold-enrichments across " print "\t\treplicates conditions, and species." print "" print "======================================================================" splash() """read_cli reads the command-line, the annotation file, and creates a SQLite3 database.""" con = read_cli(ap) print_settings(con) validate_configuration_import(con) if ap.getOptionalToggle("--load_db_only"): "\n. Ending" exit() """Jump allows for some steps to be skipped.""" jump = ap.getOptionalArg("--jump") stop = ap.getOptionalArg("--stop") if jump == False: jump = 0 else: jump = float(jump) if stop == False: stop = 10000000 else: stop = float(stop)
if False == validate_config(ap.params): print "\n. Error: something is wrong with your configuration file." print ". Look at previous errors for more detail." exit(0) """If the user didn't give a configpath, then we at least need a dbpath (to load a prior database).""" dbpath = ap.getOptionalArg("--dbpath") if configpath == False: print "\n. Error, you need to specify a configuration path, using --configpath" exit() """Regardless of which options are being executed, the DB gets built, or rebuilt, depending on its status.""" con = build_db(dbpath=dbpath) """--make_testdb is a dev-only option""" if True == ap.getOptionalToggle("--make_testdb"): reduce_db_for_test(con) exit() """--reset_files is a dev-only option""" if True == ap.getOptionalToggle("--reset_files"): reset_files(con) exit() # # IMPORT # pillarspath = ap.getArg("--pillarspath") if False == ap.getOptionalToggle( "--skip_pillars_import") and False == ap.getOptionalToggle( "--skip_import"): con = import_pillars(pillarspath, con)
print "\t. Sorts all reads and creates BAM files (samtools)" print "\t. Finds peaks (macs2)" print "\t. Calculates fold-enrichment (macs2)" print "\t. Compares peaks and fold-enrichments across " print "\t\treplicates conditions, and species." print "" print "======================================================================" splash() """read_cli reads the command-line, the annotation file, and creates a SQLite3 database.""" con = read_cli(ap) print_settings(con) validate_configuration_import(con) if ap.getOptionalToggle("--load_db_only"): "\n. Ending" exit() """Jump allows for some steps to be skipped.""" jump = ap.getOptionalArg("--jump") stop = ap.getOptionalArg("--stop") if jump == False: jump = 0 else: jump = float(jump) if stop == False: stop = 10000000 else: