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 " +
"final.consensus.fasta from ICE output")
parser.add_argument("out_pickle",
type=str,
help="Output pickle file.")
parser.add_argument("--fastq_filenames",
default=None,
type=str,
help="(optional) comma delimited fastq files of " +
"splitted non-full-length reads. If not given, no QVs are used.")
parser.add_argument("--root_dir",
dest="root_dir",
default="",
help="A directory for saving intermediate files.")
parser = add_partial_argument(parser)
# for running Partial, only relevant nproc is the gcon_nproc
parser = add_sge_arguments(parser, blasr_nproc=False, arrow_nproc=False, gcon_nproc=False)
# Liz: I don't think fofn (subread XML) is needed at partial step. commenting out for now.
#parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=False)
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_arrow_all_arguments(parser):
arg_parser = parser #parser.arg_parser.parser
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_fofn_arguments(arg_parser, subread_xml=True)
arg_parser = add_cluster_summary_report_arguments(arg_parser)
arg_parser = add_ice_post_arrow_hq_lq_arguments2(arg_parser)
arg_parser = add_sge_arguments(arg_parser, blasr_nproc=True, arrow_nproc=True)
arg_parser = add_tmp_dir_argument(arg_parser)
return arg_parser
def add_ice_arrow_all_arguments(parser):
arg_parser = parser #parser.arg_parser.parser
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_fofn_arguments(arg_parser, subread_xml=True)
arg_parser = add_cluster_summary_report_arguments(arg_parser)
arg_parser = add_ice_post_arrow_hq_lq_arguments2(arg_parser)
arg_parser = add_sge_arguments(arg_parser,
blasr_nproc=True,
arrow_nproc=True)
arg_parser = add_tmp_dir_argument(arg_parser)
return arg_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 " +
"final.consensus.fasta from ICE output")
parser.add_argument("out_pickle", type=str, help="Output pickle file.")
parser.add_argument(
"--fastq_filenames",
default=None,
type=str,
help="(optional) comma delimited fastq files of " +
"splitted non-full-length reads. If not given, no QVs are used.")
parser.add_argument("--root_dir",
dest="root_dir",
default="",
help="A directory for saving intermediate files.")
parser = add_partial_argument(parser)
# for running Partial, only relevant nproc is the gcon_nproc
parser = add_sge_arguments(parser,
blasr_nproc=False,
arrow_nproc=False,
gcon_nproc=False)
# Liz: I don't think fofn (subread XML) is needed at partial step. commenting out for now.
#parser = add_fofn_arguments(parser, bas_fofn=True, fasta_fofn=False)
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_arrow_arguments(parser):
"""Add arguments for IceArrow2, not including IceArrowPostprocess2."""
parser = add_cluster_root_dir_as_positional_argument(parser)
parser = add_fofn_arguments(parser, subread_xml=True)
parser = add_sge_arguments(parser, arrow_nproc=True, blasr_nproc=True)
return parser
from argparse import ArgumentParser
parser = ArgumentParser("run IceIterative2.")
parser.add_argument("fasta_filenames")
parser.add_argument("fastq_filenames")
parser.add_argument("all_fasta_filename")
parser = add_cluster_root_dir_as_positional_argument(parser)
parser.add_argument("--init_uc_pickle",
default=None,
type=str,
help="Init2 pickle (ex: init.uc.pickle)")
parser = add_ice_arguments(parser)
parser = add_sge_arguments(parser,
blasr_nproc=True,
gcon_nproc=True,
arrow_nproc=False)
args = parser.parse_args()
# currently, the user is NOT allowed to set the definition for full missed start/end
# (i.e. how much of the query must be mapped to consider it a hit)
ice_opts = IceOptions2(
ece_penalty=args.ece_penalty,
ece_min_len=args.ece_min_len,
max_missed_start=args.max_missed_start,
max_missed_end=args.max_missed_end,
full_missed_start=30,
full_missed_end=20,
aligner_choice=args.aligner_choice,
)
icec.run()
if __name__ == "__main__":
from argparse import ArgumentParser
parser = ArgumentParser("run IceIterative2.")
parser.add_argument("fasta_filenames")
parser.add_argument("fastq_filenames")
parser.add_argument("all_fasta_filename")
parser = add_cluster_root_dir_as_positional_argument(parser)
parser.add_argument("--init_uc_pickle", default=None, type=str, help="Init2 pickle (ex: init.uc.pickle)")
parser = add_ice_arguments(parser)
parser = add_sge_arguments(parser, blasr_nproc=True, gcon_nproc=True, arrow_nproc=False)
args = parser.parse_args()
# currently, the user is NOT allowed to set the definition for full missed start/end
# (i.e. how much of the query must be mapped to consider it a hit)
ice_opts = IceOptions2(ece_penalty=args.ece_penalty,
ece_min_len=args.ece_min_len,
max_missed_start=args.max_missed_start,
max_missed_end=args.max_missed_end,
full_missed_start=30,
full_missed_end=20,
aligner_choice=args.aligner_choice,
)