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: