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 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_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 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 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 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