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="Input fasta split file")
parser.add_argument("ref_fasta",
help="Reference fasta file, most likely " +
"ref_consensus.fa from ICE output")
parser.add_argument("out_pickle", type=str, help="Output pickle files.")
parser = add_fofn_arguments(parser, ccs_fofn=True)
parser.add_argument("--sa",
dest="sa_file",
default=None,
help="Suffix array of ref_fasta")
parser.add_argument("--done",
dest="done_filename",
type=str,
help="An empty file generated to indicate that " +
"out_pickle is done.")
parser.add_argument("--blasr_nproc",
dest="blasr_nproc",
type=int,
default=12,
help="blasr -nproc, number of CPUs [default: 12]")
parser.add_argument(
"--use_finer_qv",
action="store_true",
default=False,
help="Use finer QV which uses more memory & time [default: False]")
return parser
def set_parser(parser):
"""Get 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.fa 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_options(parser, blasr_nproc=True)
parser = add_fofn_arguments(parser, ccs_fofn=True)
parser.add_argument("--sa",
dest="sa_file",
default=None,
help="saffix array of ref_fasta")
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.fa 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("--sa",
dest="sa_file",
default=None,
help="saffix array of ref_fasta")
parser.add_argument("--done", dest="done_filename", type=str,
help="An empty file generated to indicate that " +
"out_pickle is done.")
return parser
def add_ice_all_partials_arguments(parser):
"""Add IceAllPartials argument parser."""
parser.add_argument("fastq_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.fa 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("--sa",
dest="sa_file",
default=None,
help="saffix array of ref_fasta")
parser.add_argument("--done", dest="done_filename", type=str,
help="An empty file generated to indicate that " +
"out_pickle is done.")
return parser
def set_parser(parser):
"""Get arguments."""
parser.add_argument("input_fasta", help="Input fasta split file")
parser.add_argument("ref_fasta",
help="Reference fasta file, most likely " +
"ref_consensus.fa from ICE output")
parser.add_argument("out_pickle",
type=str,
default=None,
help="Output pickle file.")
from pbtools.pbtranscript.PBTranscriptOptions import add_fofn_arguments
parser = add_fofn_arguments(parser, ccs_fofn=True)
parser.add_argument("--sa",
dest="sa_file",
default=None,
help="saffix array of ref_fasta")
parser.add_argument("--done",
dest="done_filename",
help="An empty file generated to indicate that" +
"out_pickle is done.")
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_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, fasta_fofn=True)
parser = add_ice_post_quiver_hq_lq_arguments(parser)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True, sge_env_name=True, sge_queue=True)
return parser
def set_parser(parser):
"""Set argument parser."""
parser.add_argument("root_dir",
type=str,
default=None,
help="Root directory for ICE, " + \
"e.g., SMRTPortal data/clusterOutDir")
parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=True)
parser = add_sge_options(parser, quiver_nproc=True)
def add_ice_quiver_all_arguments(parser):
"""Add arguments for IceQuiverAll, including arguments for IceQuiver and
IceQuiverPostprocess."""
parser = add_cluster_root_dir_as_positional_argument(parser)
parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=True)
parser = add_cluster_summary_report_arguments(parser)
parser = add_ice_post_quiver_hq_lq_arguments(parser)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
return parser
def add_ice_quiver_all_arguments(parser):
"""Add arguments for IceQuiverAll, including arguments for IceQuiver and
IceQuiverPostprocess."""
parser = add_cluster_root_dir_as_positional_argument(parser)
parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=True)
parser = add_cluster_summary_report_arguments(parser)
parser = add_ice_post_quiver_hq_lq_arguments(parser)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
return parser
def set_parser(parser):
"""Set argument parser."""
parser.add_argument("root_dir",
type=str,
default=None,
help="Root directory for ICE, " + \
"e.g., SMRTPortal data/clusterOutDir")
parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=True)
parser = add_sge_options(parser, quiver_nproc=True)
def add_ice_quiver_i_arguments(parser):
"""Add IceQuiverI (ice_quiver.py i) arguments."""
parser = add_cluster_root_dir_as_positional_argument(parser)
helpstr = "Call quiver to polish clusters in the (i / N)-th chunk."
parser.add_argument("i", help=helpstr, type=int)
helpstr = "Divide clusters into N chunks."
parser.add_argument("N", help=helpstr, type=int)
parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=True)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
return parser
def set_parser(parser):
"""Set up argument parser."""
parser.add_argument("root_dir",
type=str,
default=None,
help="Root directory for ICE, " + \
"e.g., SMRTPortal data/clusterOutDir")
parser = add_nfl_fa_arguments(parser, positional=True)
parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True)
parser = add_polished_isoforms_arguments(parser)
parser = add_sge_options(parser, quiver_nproc=True)
def set_parser(parser):
"""Set up argument parser."""
parser.add_argument("root_dir",
type=str,
default=None,
help="Root directory for ICE, " + \
"e.g., SMRTPortal data/clusterOutDir")
parser = add_nfl_fa_arguments(parser, positional=True)
parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True)
parser = add_polished_isoforms_arguments(parser)
parser = add_sge_options(parser, quiver_nproc=True)
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", 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)
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", 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)
return parser
def set_parser(parser):
"""Get arguments."""
parser.add_argument("input_fasta", help="Input fasta split file")
parser.add_argument("ref_fasta", help="Reference fasta file, most likely " + "ref_consensus.fa from ICE output")
parser.add_argument("out_pickle", type=str, default=None, help="Output pickle file.")
from pbtools.pbtranscript.PBTranscriptOptions import add_fofn_arguments
parser = add_fofn_arguments(parser, ccs_fofn=True)
parser.add_argument("--sa", dest="sa_file", default=None, help="saffix array of ref_fasta")
parser.add_argument(
"--done", dest="done_filename", help="An empty file generated to indicate that" + "out_pickle is done."
)
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_partial_one_arguments(parser):
"""Add arguments for assigning nfl reads of a given input fasta
to unpolished isoforms."""
parser.add_argument("input_fastq", help="Input fastq split file")
parser.add_argument("ref_fasta",
help="Reference fasta file, most likely " +
"ref_consensus.fa from ICE output")
parser.add_argument("out_pickle", type=str, help="Output pickle files.")
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_argument("--use_finer_qv", action="store_true", default=False,
help="Use finer QV which uses more memory & time [default: False]")
# ToDo: comment OUT BLASR-related arguments; using DALIGNER
parser.add_argument("--sa", dest="sa_file", default=None,
help="Suffix array of ref_fasta")
parser.add_argument("--blasr_nproc", dest="blasr_nproc",
type=int, default=12,
help="blasr -nproc, number of CPUs [default: 12]")
return parser
def set_parser(parser):
"""Get 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.fa 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_options(parser, blasr_nproc=True)
parser = add_fofn_arguments(parser, ccs_fofn=True)
parser.add_argument("--sa",
dest="sa_file",
default=None,
help="saffix array of ref_fasta")
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, fasta_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, fasta_fofn=True)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
return parser
