def main():
parser = argparse.ArgumentParser()
sub = parser.add_subparsers(help='Assembly stages')
predict_haplo.stageparser(sub.add_parser('predict_haplo'))
args = parser.parse_args()
args.func(**sysutils.args_params(args))
def console():
parser = argparse.ArgumentParser(
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, )
sub = parser.add_subparsers(help='''Insert descirption about phylo''')
multiple_align.stageparser(sub.add_parser('multiple_align'))
#build_tree.stageparser(sub.add_parser('build_tree'))
args = parser.parse_args()
args.func(**sysutils.args_params(args))
def console():
parser = argparse.ArgumentParser(
description='Determine best-fit evolutionary model with ModelTest-NG.',
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone,
)
stageparser(parser)
args = parser.parse_args()
try:
args.func(**sysutils.args_params(args))
except MissingRequiredArgument as e:
parser.print_usage()
print('error: %s' % e, file=sys.stderr)
def console():
parser = argparse.ArgumentParser(
description='Haplotype reconstruction with CliqueSNV.',
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone,
)
stageparser(parser)
args = parser.parse_args()
try:
args.func(**sysutils.args_params(args))
except MissingRequiredArgument as e:
parser.print_usage()
print('error: %s' % e, file=sys.stderr)
def console():
parser = argparse.ArgumentParser(
description='Generate summary statistics. Required input: dir_list and/or ph_list and ref_gtf if amplicons used.',
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone,
)
stageparser(parser)
args = parser.parse_args()
try:
args.func(**sysutils.args_params(args))
except MissingRequiredArgument as e:
parser.print_usage()
print('error: %s' % e, file=sys.stderr)
def main():
parser = argparse.ArgumentParser(
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone,
)
sub = parser.add_subparsers(
help='''setup demo directory and test data.
'''
)
demo.stageparser(sub.add_parser('demo'))
args = parser.parse_args()
args.func(**sysutils.args_params(args))
def console():
parser = argparse.ArgumentParser(
description='Build Phylogenetic Tree with RAxML-NG',
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone,
)
stageparser(parser)
args = parser.parse_args()
try:
args.func(**sysutils.args_params(args))
except MissingRequiredArgument as e:
parser.print_usage()
print('error: %s' % e, file=sys.stderr)
def console():
parser = argparse.ArgumentParser(
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, )
sub = parser.add_subparsers(
help='''Manipulate reads. Input is reads in fastq format, output is
modified reads in fastq format.''')
sample_reads.stageparser(sub.add_parser('sample_reads'))
trim_reads.stageparser(sub.add_parser('trim_reads'))
join_reads.stageparser(sub.add_parser('join_reads'))
ec_reads.stageparser(sub.add_parser('ec_reads'))
args = parser.parse_args()
args.func(**sysutils.args_params(args))
def console():
parser = argparse.ArgumentParser(
description=
'Align sequences using MAFFT. Required input: --seqs AND/OR --dir_list AND --ref_gtf (unless --alignall option included).',
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone,
)
stageparser(parser)
args = parser.parse_args()
try:
args.func(**sysutils.args_params(args))
except MissingRequiredArgument as e:
parser.print_usage()
print('error: %s' % e, file=sys.stderr)
def console():
""" Entry point
Returns:
None
"""
parser = argparse.ArgumentParser(
description='Annotate consensus from reference annotation.',
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone,
)
stageparser(parser)
args = parser.parse_args()
args.func(**sysutils.args_params(args))
def console():
""" Entry point
Returns:
None
"""
parser = argparse.ArgumentParser(
description='Parse output from PredictHaplo.',
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone,
)
stageparser(parser)
args = parser.parse_args()
args.func(**sysutils.args_params(args))
def console():
""" Entry point
Returns:
None
"""
parser = argparse.ArgumentParser(
description='Join reads using FLASh.',
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone,
)
stageparser(parser)
args = parser.parse_args()
args.func(**sysutils.args_params(args))
def console():
""" Entry point
Returns:
None
"""
parser = argparse.ArgumentParser(
description='Extract sequence regions from pairwise alignment.',
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone,
)
stageparser(parser)
args = parser.parse_args()
args.func(**sysutils.args_params(args))
def console():
parser = argparse.ArgumentParser(
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, )
sub = parser.add_subparsers(
help='''Phylogenomic stages. Includes multiple alignment, evolutionary
model testing using ModelTest-ng, and building phylogenetic trees
with RAxML.
''')
multiple_align.stageparser(sub.add_parser('multiple_align'))
model_test.stageparser(sub.add_parser('model_test'))
build_tree_NG.stageparser(sub.add_parser('build_tree'))
args = parser.parse_args()
args.func(**sysutils.args_params(args))
def console():
""" Entry point
Returns:
None
"""
parser = argparse.ArgumentParser(
description='Assemble contigs to amplicon regions.',
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone,
)
stageparser(parser)
args = parser.parse_args()
args.func(**sysutils.args_params(args))
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():
""" Entry point
Returns:
None
"""
parser = argparse.ArgumentParser(
description='''Align reads to reference.''',
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone,
)
stageparser(parser)
args = parser.parse_args()
try:
args.func(**sysutils.args_params(args))
except MissingRequiredArgument as e:
parser.print_usage()
print('error: %s' % e, file=sys.stderr)
def main():
parser = argparse.ArgumentParser(
formatter_class=sysutils.ArgumentDefaultsHelpFormatterSkipNone, )
sub = parser.add_subparsers(
help='''Assemble consensus sequence(s). Input reads (in fastq format)
are assembled using either denovo assembly or reference-based
alignment. Resulting consensus can be further refined or
annotated.
''')
# Denovo
assemble_denovo.stageparser(sub.add_parser('assemble_denovo'))
assemble_amplicons.stageparser(sub.add_parser('assemble_amplicons'))
assemble_scaffold.stageparser(sub.add_parser('assemble_scaffold'))
# Reference-based
align_reads.stageparser(sub.add_parser('align_reads'))
call_variants.stageparser(sub.add_parser('call_variants'))
vcf_to_consensus.stageparser(sub.add_parser('vcf_to_consensus'))
refine_assembly.stageparser(sub.add_parser('refine_assembly'))
finalize_assembly.stageparser(sub.add_parser('finalize_assembly'))
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)
