def add_ice_partial_one_arguments(parser):
"""Add arguments for assigning nfl reads of a given input fasta
to unpolished isoforms."""
parser.add_input_file_type(FileTypes.DS_CONTIG, "input_fasta",
name="ContigSet",
description="ContigSet of non-full-length reads")
parser.add_input_file_type(FileTypes.DS_CONTIG, "ref_fasta",
name="Reference ContigSet",
description="Reference fasta file, most likely " +
"ref_consensus.fasta from ICE output")
arg_parser = add_fofn_arguments(parser.arg_parser.parser,
ccs_fofn=True,
tool_contract_parser=parser.tool_contract_parser)
parser.add_output_file_type(FileTypes.PICKLE, "out_pickle",
name="JSON pickle",
description="Output pickle file",
default_name="ice_partial_one")
arg_parser.add_argument("--done", dest="done_filename", type=str,
help="An empty file generated to indicate that " +
"out_pickle is done.")
arg_parser = add_use_blasr_argument(arg_parser)
arg_parser = add_tmp_dir_argument(arg_parser)
# ToDo: comment OUT BLASR-related arguments; using DALIGNER
arg_parser.add_argument("--blasr_nproc", dest="blasr_nproc",
type=int, default=12,
help="blasr --nproc, number of CPUs [default: 12]")
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_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_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_partial_one_arguments(parser):
"""Add arguments for assigning nfl reads of a given input fasta
to unpolished isoforms."""
parser.add_argument("input_fasta", help="Non full-length reads (fasta)")
parser.add_argument("--input_fastq", default=None, help="Non full-length reads (fastq). If not given, no QVs are used.")
parser.add_argument("ref_fasta", help="Reference fasta, most likely ref.consensus.fasta")
parser.add_argument("out_pickle", help="Output pickle file", default="ice_partial_one")
parser.add_argument("--done", dest="done_filename", type=str,
help="An empty file generated to indicate that " +
"out_pickle is done.")
parser = add_partial_argument(parser)
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_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_partial_i_arguments(parser):
"""Add IcePartialI arguments."""
parser = add_cluster_root_dir_as_positional_argument(parser)
helpstr = "To process the i-th chunk of non-full-length reads."
parser.add_argument("i", nargs="+", help=helpstr, type=int)
parser.add_argument("--blasr_nproc",
type=int,
dest="blasr_nproc",
action="store",
default=12,
help="Number of cores for each BLASR job.")
parser = add_fofn_arguments(parser, ccs_fofn=True)
parser = add_tmp_dir_argument(parser)
return parser
def add_ice_partial_one_arguments(parser):
"""Add arguments for assigning nfl reads of a given input fasta
to unpolished isoforms."""
parser.add_input_file_type(
FileTypes.DS_CONTIG,
"input_fasta",
name="ContigSet",
description="ContigSet of non-full-length reads")
parser.add_input_file_type(
FileTypes.DS_CONTIG,
"ref_fasta",
name="Reference ContigSet",
description="Reference fasta file, most likely " +
"ref_consensus.fasta from ICE output")
arg_parser = add_fofn_arguments(
parser.arg_parser.parser,
ccs_fofn=True,
tool_contract_parser=parser.tool_contract_parser)
parser.add_output_file_type(FileTypes.PICKLE,
"out_pickle",
name="JSON pickle",
description="Output pickle file",
default_name="ice_partial_one")
arg_parser.add_argument("--done",
dest="done_filename",
type=str,
help="An empty file generated to indicate that " +
"out_pickle is done.")
arg_parser = add_use_blasr_argument(arg_parser)
arg_parser = add_tmp_dir_argument(arg_parser)
# ToDo: comment OUT BLASR-related arguments; using DALIGNER
arg_parser.add_argument("--blasr_nproc",
dest="blasr_nproc",
type=int,
default=12,
help="blasr --nproc, number of CPUs [default: 12]")
return parser
