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_all_partials_arguments(parser):
"""Add IceAllPartials argument parser."""
parser.add_argument("fasta_filenames",
type=str,
help="comma delimited fasta files of " +
"splitted non-full-length reads")
parser.add_argument("ref_fasta",
type=str,
help="Reference fasta file, most likely " +
"ref_consensus.fasta from ICE output")
parser.add_argument("out_pickle",
type=str,
help="Output pickle file.")
parser.add_argument("--root_dir",
dest="root_dir",
default="",
help="A directory for saving intermediate files.")
parser = add_sge_arguments(parser, blasr_nproc=True)
parser = add_fofn_arguments(parser, ccs_fofn=True)
parser.add_argument("--done", dest="done_filename", type=str,
help="An empty file generated to indicate that " +
"out_pickle is done.")
parser = add_tmp_dir_argument(parser)
return parser
def add_ice_daligner_arguments(parser):
"""Set up argument parser."""
helpstr = "Query reads fasta file"
parser.add_argument("query_fasta", type=str, help=helpstr)
helpstr = "Target reads fasta file"
parser.add_argument("target_fasta", type=str, help=helpstr)
helpstr = "Output directory to store daligner and LA4Ice outputs"
parser.add_argument("output_dir", type=str, help=helpstr)
helpstr = "Query reads are Full-Length isoforms."
parser.add_argument("--is_FL",
default=False,
action="store_true",
help=helpstr)
helpstr = "Query and target reads are of the same strand"
parser.add_argument("--same_strand_only",
default=False,
action="store_true",
help=helpstr)
parser = add_sge_arguments(parser, blasr_nproc=True)
return parser
def add_ice_all_partials_arguments(parser):
"""Add IceAllPartials argument parser."""
parser.add_argument("fasta_filenames",
type=str,
help="comma delimited fasta files of " +
"splitted non-full-length reads")
parser.add_argument("ref_fasta",
type=str,
help="Reference fasta file, most likely " +
"ref_consensus.fasta from ICE output")
parser.add_argument("out_pickle",
type=str,
help="Output pickle file.")
parser.add_argument("--root_dir",
dest="root_dir",
default="",
help="A directory for saving intermediate files.")
parser = add_sge_arguments(parser, blasr_nproc=True)
parser = add_fofn_arguments(parser, ccs_fofn=True)
parser.add_argument("--done", dest="done_filename", type=str,
help="An empty file generated to indicate that " +
"out_pickle is done.")
parser = add_tmp_dir_argument(parser)
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_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
def add_ice_quiver_all_arguments(parser):
"""Add arguments for IceQuiverAll, including arguments for IceQuiver and
IceQuiverPostprocess."""
arg_parser = parser.arg_parser.parser
tcp = parser.tool_contract_parser
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_fofn_arguments(arg_parser, bas_fofn=True,
tool_contract_parser=parser.tool_contract_parser)
tcp_parser = add_cluster_summary_report_arguments(_wrap_parser(arg_parser))
arg_parser = add_ice_post_quiver_hq_lq_arguments(arg_parser)
arg_parser = add_sge_arguments(arg_parser, quiver_nproc=True,
blasr_nproc=True)
arg_parser = add_tmp_dir_argument(arg_parser)
return parser
def add_ice_quiver_i_arguments(parser):
"""Add IceQuiverI (ice_quiver.py i) arguments."""
parser = add_cluster_root_dir_as_positional_argument(parser)
helpstr = "Divide clusters into N chunks."
parser.add_argument("N", help=helpstr, type=int)
helpstr = "Call quiver to polish clusters in the (i / N)-th chunk."
parser.add_argument("i", nargs="+", help=helpstr, type=int)
parser = add_fofn_arguments(parser, bas_fofn=True)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
parser = add_tmp_dir_argument(parser)
return parser
def add_ice_quiver_i_arguments(parser):
"""Add IceQuiverI (ice_quiver.py i) arguments."""
parser = add_cluster_root_dir_as_positional_argument(parser)
helpstr = "Divide clusters into N chunks."
parser.add_argument("N", help=helpstr, type=int)
helpstr = "Call quiver to polish clusters in the (i / N)-th chunk."
parser.add_argument("i", nargs="+", help=helpstr, type=int)
parser = add_fofn_arguments(parser, bas_fofn=True)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
parser = add_tmp_dir_argument(parser)
return parser
def add_ice_quiver_all_arguments(parser):
"""Add arguments for IceQuiverAll, including arguments for IceQuiver and
IceQuiverPostprocess."""
arg_parser = parser.arg_parser.parser
tcp = parser.tool_contract_parser
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_fofn_arguments(
arg_parser,
bas_fofn=True,
tool_contract_parser=parser.tool_contract_parser)
tcp_parser = add_cluster_summary_report_arguments(_wrap_parser(arg_parser))
arg_parser = add_ice_post_quiver_hq_lq_arguments(arg_parser)
arg_parser = add_sge_arguments(arg_parser,
quiver_nproc=True,
blasr_nproc=True)
arg_parser = add_tmp_dir_argument(arg_parser)
return parser
def add_ice_daligner_arguments(parser):
"""Set up argument parser."""
helpstr = "Query reads fasta file"
parser.add_argument("query_fasta", type=str, help=helpstr)
helpstr = "Target reads fasta file"
parser.add_argument("target_fasta", type=str, help=helpstr)
helpstr = "Output directory to store daligner and LA4Ice outputs"
parser.add_argument("output_dir", type=str, help=helpstr)
helpstr = "Query reads are Full-Length isoforms."
parser.add_argument("--is_FL", default=False, action="store_true", help=helpstr)
helpstr = "Query and target reads are of the same strand"
parser.add_argument("--same_strand_only", default=False, action="store_true", help=helpstr)
parser = add_sge_arguments(parser, blasr_nproc=True)
return parser
def add_ice_quiver_arguments(parser):
"""Add arguments for IceQuiver, not including IceQuiverPostprocess."""
parser = add_cluster_root_dir_as_positional_argument(parser)
parser = add_fofn_arguments(parser, bas_fofn=True)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
return parser
def add_ice_quiver_arguments(parser):
"""Add arguments for IceQuiver, not including IceQuiverPostprocess."""
parser = add_cluster_root_dir_as_positional_argument(parser)
parser = add_fofn_arguments(parser, bas_fofn=True)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
return parser