def main():
parser = argparse.ArgumentParser(
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, )
sub = parser.add_subparsers(
help='''Annotate consensus sequence(s). An assembled consensus sequence
can be amino acid aligned to a reference (i.e. HXB2) so the
same coordinate system can be used. Sequences can then be
extracted based on the shared coordinate systems.
''')
pairwise_align.stageparser(sub.add_parser('pairwise_align'))
extract_pairwise.stageparser(sub.add_parser('extract_pairwise'))
post_assembly.stageparser(sub.add_parser('post_assembly'))
annotate_from_ref.stageparser(sub.add_parser('annotate_from_ref'))
args = parser.parse_args()
args.func(**sysutils.args_params(args))
def console():
parser = argparse.ArgumentParser(formatter_class=HF, add_help=False)
parser.add_argument('-h', '--help', action=_BaseHelpAction)
# Exit with help if no args were given
if len(sys.argv) == 1:
parser.parse_args(['-h'])
# Subparsers
sub = parser.add_subparsers()
# Reads stages
sample_reads.stageparser(sub.add_parser('sample_reads',
formatter_class=HF))
trim_reads.stageparser(sub.add_parser('trim_reads', formatter_class=HF))
join_reads.stageparser(sub.add_parser('join_reads', formatter_class=HF))
ec_reads.stageparser(sub.add_parser('ec_reads', formatter_class=HF))
# Assemble stages
assemble_denovo.stageparser(
sub.add_parser('assemble_denovo', formatter_class=HF))
assemble_amplicons.stageparser(
sub.add_parser('assemble_amplicons', formatter_class=HF))
assemble_scaffold.stageparser(
sub.add_parser('assemble_scaffold', formatter_class=HF))
align_reads.stageparser(sub.add_parser('align_reads', formatter_class=HF))
call_variants.stageparser(
sub.add_parser('call_variants', formatter_class=HF))
vcf_to_consensus.stageparser(
sub.add_parser('vcf_to_consensus', formatter_class=HF))
refine_assembly.stageparser(
sub.add_parser('refine_assembly', formatter_class=HF))
finalize_assembly.stageparser(
sub.add_parser('finalize_assembly', formatter_class=HF))
# Haplotype
predict_haplo.stageparser(
sub.add_parser('predict_haplo', formatter_class=HF))
ph_parser.stageparser(sub.add_parser('ph_parser', formatter_class=HF))
cliquesnv.stageparser(sub.add_parser('cliquesnv', formatter_class=HF))
# Annotate/Description stages
pairwise_align.stageparser(
sub.add_parser('pairwise_align', formatter_class=HF))
extract_pairwise.stageparser(
sub.add_parser('extract_pairwise', formatter_class=HF))
annotate_from_ref.stageparser(
sub.add_parser('annotate_from_ref', formatter_class=HF))
summary_stats.stageparser(
sub.add_parser('summary_stats', formatter_class=HF))
# post_assembly.stageparser(
# sub.add_parser('post_assembly', formatter_class=HF)
# )
# Phylo
multiple_align.stageparser(
sub.add_parser('multiple_align', formatter_class=HF))
model_test.stageparser(sub.add_parser('model_test', formatter_class=HF))
build_tree_NG.stageparser(
sub.add_parser('build_tree_NG', formatter_class=HF))
# Miscellaneous
demo.stageparser(sub.add_parser('demo', formatter_class=HF))
args = parser.parse_args()
try:
args.func(**sysutils.args_params(args))
except MissingRequiredArgument as e:
sub._name_parser_map[sys.argv[1]].print_usage()
print('error: %s' % e, file=sys.stderr)