def main():
parser = argparse.ArgumentParser(
description='Determine PacBio read support for gaps in scaffolds',
usage=usage())
# Main arguments
parser.add_argument('scaffolds',
action='store',
help='The input scaffolds in Fasta format')
parser.add_argument('subreads',
action='store',
help='The PacBio subreads in BAM format')
parser.add_argument('-t', '--threads', dest='threads', type=int, \
help='Number of threads to use for multi-threaded processes, default=1', default=1)
# Arguments for Setup
setup_args = parser.add_argument_group('Setup')
setup_args.add_argument('-n', '--min_gap', dest='min_gap', type=int, default=200, \
help='Minimum number of consecutive Ns to be considered a gap, default=200')
setup_args.add_argument('-x', '--max_gap', dest='max_gap', type=int, default=1000000, \
help='Maximum number of consecutive Ns to be considered a gap, default=Inf')
setup_args.add_argument('-f', '--flank_size', dest='flank_size', type=int, default=1000, \
help='Number of extracted bases flanking gaps and scaffold ends, default=1000')
# Arguments for Support
support_args = parser.add_argument_group('Support')
support_args.add_argument('-b', '--blasr', dest='blasr', type=str, \
help='Parameters to pass to BLASR', default='')
support_args.add_argument('-d', '--min_reads', dest='min_reads', type=int, \
help='The minimum number of reads required to support a gap', default=5)
support_args.add_argument('-w', '--wiggle', dest='wiggle', type=int, \
help='The percent deviation allowed from predicted gap size', default=0.5)
# Arguments for Assembly
assembly_args = parser.add_argument_group('Assembly')
assembly_args.add_argument('-m', '--minimap', dest='minimap', \
help='Parameters to pass to Minimap', default='-Sw5 -L100 -m0')
assembly_args.add_argument('-a', '--miniasm', dest='miniasm', \
help='Parameters to pass to Miniasm', default='')
assembly_args.add_argument('-r', '--racon', dest='racon', \
help='Parameters to pass to Racon', default='')
# Parse the arguments
args = parser.parse_args()
# Initialize classes
setup = Setup()
support = Support()
assembly = Assembly()
placement = Placement()
# Check for save point
try:
save = open('jelly2.save', 'r').read()
print "Found save point:", save
except IOError:
write_save('setup')
# Run Setup
if check_save('setup'):
setup.run(args)
write_save('mapping')
# Run Support
if check_save('mapping'):
support.mapping(args)
write_save('sorting')
if check_save('sorting'):
support.sorting(args)
write_save('indexing')
if check_save('indexing'):
support.indexing(args)
write_save('support')
if check_save('support'):
support.find_support(args)
write_save('assembly')
# Run Assembly
if check_save('assembly'):
assembly.assemble_gaps(args)
write_save('placement')
# Run Placement
if check_save('placement'):
placement.load_data(args)
placement.fill_gaps()
