def get_parser():
"""Returns arg parser."""
parser = argparse.ArgumentParser(prog='tofu_wrap')
helpstr = "Input full-length non-chimeric reads in FASTA or ContigSet format " + \
"(e.g., isoseq_flnc.fasta|contigset.xml)"
parser.add_argument("flnc_fa", type=str, help=helpstr)
helpstr = "Output collapsed filtered isoforms in FASTA/FASTQ format (e.g., tofu_out.fastq)"
parser.add_argument("collapsed_filtered_fn", type=str, help=helpstr)
parser = add_nfl_fa_argument(parser, positional=False, required=True)
parser.add_argument("--nfl_reads_per_split", type=int,
dest="nfl_reads_per_split", default=60000,
help="Number of nFL reads per split file (default: 60000)")
parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True, fasta_fofn=True)
# tofu output arguments
parser = add_tofu_output_arguments(parser)
parser = add_ice_arguments(parser) # Add Ice options, including --quiver
parser = add_sge_arguments(parser, blasr_nproc=True, quiver_nproc=True, gcon_nproc=True) # Sge
parser = add_ice_post_quiver_hq_lq_qv_arguments(parser) # IceQuiver HQ/LQ QV options.
parser = add_separate_flnc_arguments(parser) # separate_flnc options
parser = add_gmap_arguments(parser) # map to gmap reference options
parser = add_post_mapping_to_genome_arguments(parser) # post mapping to genome options
misc_group = parser.add_argument_group("Misc arguments")
misc_group.add_argument("--mem_debug", default=False, action="store_true",
help=argparse.SUPPRESS)
misc_group.add_argument("--keep_tmp_files", default=False, action="store_true",
help="False: delete tmp files; True: keep tmp files (default: False).")
misc_group.add_argument("--version", action='version', version='%(prog)s ' + str(get_version()))
return parser
def get_parser():
"""Returns arg parser."""
parser = argparse.ArgumentParser(prog='tofu_wrap')
helpstr = "Input full-length non-chimeric reads in FASTA or ContigSet format " + \
"(e.g., isoseq_flnc.fasta|contigset.xml)"
parser.add_argument("flnc_fa", type=str, help=helpstr)
helpstr = "Output collapsed filtered isoforms in FASTA/FASTQ format (e.g., tofu_out.fastq)"
parser.add_argument("collapsed_filtered_fn", type=str, help=helpstr)
parser = add_nfl_fa_argument(parser, positional=False, required=True)
parser.add_argument("--nfl_reads_per_split", type=int,
dest="nfl_reads_per_split", default=60000,
help="Number of nFL reads per split file (default: 60000)")
parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True, fasta_fofn=True)
# tofu output arguments
parser = add_tofu_output_arguments(parser)
parser = add_ice_arguments(parser) # Add Ice options, including --quiver
parser = add_sge_arguments(parser, blasr_nproc=True, quiver_nproc=True, gcon_nproc=True) # Sge
parser = add_ice_post_quiver_hq_lq_qv_arguments(parser) # IceQuiver HQ/LQ QV options.
parser = add_separate_flnc_arguments(parser) # separate_flnc options
parser = add_gmap_arguments(parser) # map to gmap reference options
parser = add_post_mapping_to_genome_arguments(parser) # post mapping to genome options
misc_group = parser.add_argument_group("Misc arguments")
misc_group.add_argument("--mem_debug", default=False, action="store_true",
help=argparse.SUPPRESS)
misc_group.add_argument("--keep_tmp_files", default=False, action="store_true",
help="False: delete tmp files; True: keep tmp files (default: False).")
misc_group.add_argument("--version", action='version', version='%(prog)s ' + str(get_version()))
return parser
def add_ice_partial_split_arguments(parser):
"""Add arguments for ice_partial split."""
parser = add_cluster_root_dir_as_positional_argument(parser)
parser = add_nfl_fa_argument(parser, positional=True)
helpstr = "Split non-full-length reads into N chunks, N < 100."
parser.add_argument("N", help=helpstr, type=int)
def add_ice_partial_split_arguments(parser):
"""Add arguments for ice_partial split."""
parser = add_cluster_root_dir_as_positional_argument(parser)
parser = add_nfl_fa_argument(parser, positional=True)
helpstr = "Split non-full-length reads into N chunks, N < 100."
parser.add_argument("N", help=helpstr, type=int)
def add_ice_polish_arguments(parser):
"""Set up argument parser."""
parser = add_cluster_root_dir_as_positional_argument(parser)
parser = add_nfl_fa_argument(parser, positional=True)
parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True)
parser = add_ice_post_quiver_hq_lq_arguments(parser)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
parser = add_tmp_dir_argument(parser)
return parser
def add_ice_polish_arguments(parser):
"""Set up argument parser."""
parser = add_cluster_root_dir_as_positional_argument(parser)
parser = add_nfl_fa_argument(parser, positional=True)
parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True)
parser = add_ice_post_quiver_hq_lq_arguments(parser)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
parser = add_tmp_dir_argument(parser)
return parser