def human_filter_main(argv=None):
p = argparse.ArgumentParser()
# Input
p.add_argument(
"--forward-reads", required=True,
type=argparse.FileType("r"),
help="FASTQ file of forward reads")
p.add_argument(
"--reverse-reads", required=True,
type=argparse.FileType("r"),
help="FASTQ file of reverse reads")
p.add_argument(
"--config-file",
type=argparse.FileType("r"),
help="JSON configuration file")
p.add_argument(
"--organism", required=True,
help="reference organism to filter from")
p.add_argument(
"--pct", required=False,
type=float, default=0.5,
help="Percent identity Default: 0.5")
p.add_argument(
"--frac", required=False,
type=float, default=0.6,
help="Fraction of alignment length Default: 0.6")
# Output
p.add_argument(
"--summary-file", required=True,
type=argparse.FileType("w"),
help="long table of results.")
p.add_argument(
"--output-dir", required=True,
help="Path to output directory")
args = p.parse_args(argv)
config = get_config(args.config_file, args.organism)
fwd_fp = args.forward_reads.name
rev_fp = args.reverse_reads.name
args.forward_reads.close()
args.reverse_reads.close()
tool = FilteringTool(config)
if not tool.index_exists():
tool.make_index()
if not os.path.exists(args.output_dir):
os.mkdir(args.output_dir)
summary_data = tool.decontaminate(fwd_fp, rev_fp, args.output_dir,
args.organism, args.pct, args.frac)
save_summary(args.summary_file, config, summary_data)
def make_index_main(argv=None):
p = argparse.ArgumentParser()
p.add_argument(
"--config-file", required=True,
type=argparse.FileType("r"),
help="JSON configuration file")
p.add_argument(
"--organism", required=True,
help="reference organism to filter from")
args = p.parse_args(argv)
config = get_config(args.config_file, args.organism)
tool = FilteringTool(config)
if not tool.index_exists():
tool.make_index()
def make_index_main(argv=None):
p = argparse.ArgumentParser()
p.add_argument(
"--config-file", required=True,
type=argparse.FileType("r"),
help="JSON configuration file")
args = p.parse_args(argv)
config = default_config.copy()
if args.config_file:
user_config = json.load(args.config_file)
config.update(user_config)
tool = FilteringTool(config)
if not tool.index_exists():
tool.make_index()
def make_index_main(argv=None):
p = argparse.ArgumentParser()
p.add_argument("--config-file",
required=True,
type=argparse.FileType("r"),
help="JSON configuration file")
p.add_argument("--organism",
required=True,
help="reference organism to filter from")
args = p.parse_args(argv)
config = get_config(args.config_file, args.organism)
tool = FilteringTool(config)
if not tool.index_exists():
tool.make_index()
def human_filter_main(argv=None):
p = argparse.ArgumentParser()
# Input
p.add_argument("--forward-reads",
required=True,
type=argparse.FileType("r"),
help="FASTQ file of forward reads")
p.add_argument("--reverse-reads",
required=True,
type=argparse.FileType("r"),
help="FASTQ file of reverse reads")
p.add_argument("--config-file",
type=argparse.FileType("r"),
help="JSON configuration file")
p.add_argument("--organism",
required=True,
help="reference organism to filter from")
p.add_argument("--pct",
required=False,
type=float,
default=0.5,
help="Percent identity Default: 0.5")
p.add_argument("--frac",
required=False,
type=float,
default=0.6,
help="Fraction of alignment length Default: 0.6")
# Output
p.add_argument("--summary-file",
required=True,
type=argparse.FileType("w"),
help="long table of results.")
p.add_argument("--output-dir",
required=True,
help="Path to output directory")
args = p.parse_args(argv)
config = get_config(args.config_file, args.organism)
fwd_fp = args.forward_reads.name
rev_fp = args.reverse_reads.name
args.forward_reads.close()
args.reverse_reads.close()
tool = FilteringTool(config)
if not tool.index_exists():
tool.make_index()
if not os.path.exists(args.output_dir):
os.mkdir(args.output_dir)
summary_data = tool.decontaminate(fwd_fp, rev_fp, args.output_dir,
args.organism, args.pct, args.frac)
save_summary(args.summary_file, config, summary_data)
def human_filter_main(argv=None):
p = argparse.ArgumentParser()
# Input
p.add_argument(
"--forward-reads", required=True,
type=argparse.FileType("r"),
help="FASTQ file of forward reads")
p.add_argument(
"--reverse-reads", required=True,
type=argparse.FileType("r"),
help="FASTQ file of reverse reads")
p.add_argument(
"--organism", required=True,
help="reference organism to filter from",
choices=['human', 'phix'])
p.add_argument(
"--summary-file", required=True,
type=argparse.FileType("w"),
help="long table of results.")
p.add_argument(
"--output-dir", required=True,
help="Path to output directory")
p.add_argument(
"--method", default="bwa",
help="Method to use (default %(default)s)",
choices=tools_available.keys())
p.add_argument(
"--index",
help="Path to contaminant genome indexes")
p.add_argument(
"--threads", default=1,
type=int, help="Number of threads to use")
p.add_argument(
"--pct", required=False,
type=float, default=0.5,
help="Percent identity (default: %(default)s)")
p.add_argument(
"--frac", required=False,
type=float, default=0.6,
help="Fraction of alignment length (default: %(default)s)")
p.add_argument(
"--keep-sam-file", action="store_true",
help="Write SAM file to output directory.")
p.add_argument(
"--sam-file", required=False,
type=argparse.FileType("r"),
help="File of alignments to reference database (SAM format, optional)")
p.add_argument(
"--bowtie2_fp", default="bowtie2",
help="Path to bowtie2 (if using)")
p.add_argument(
"--bwa_fp", default="bwa",
help="Path to bwa (if using)")
# Output
args = p.parse_args(argv)
config = get_config(args, args.organism)
fwd_fp = args.forward_reads.name
rev_fp = args.reverse_reads.name
args.forward_reads.close()
args.reverse_reads.close()
if args.sam_file is not None:
config["method"] = "samfile"
config["sam_fp"] = args.sam_file.name
if args.keep_sam_file is True:
config["keep_sam_file"] = True
else:
config["keep_sam_file"] = False
tool = FilteringTool(config)
if not tool.index_exists():
tool.make_index()
if not os.path.exists(args.output_dir):
os.mkdir(args.output_dir)
summary_data = tool.decontaminate(fwd_fp, rev_fp, args.output_dir,
args.organism, args.pct, args.frac)
save_summary(args.summary_file, config, summary_data)
def human_filter_main(argv=None):
p = argparse.ArgumentParser()
# Input
p.add_argument("--forward-reads",
required=True,
type=argparse.FileType("r"),
help="FASTQ file of forward reads")
p.add_argument("--reverse-reads",
required=True,
type=argparse.FileType("r"),
help="FASTQ file of reverse reads")
p.add_argument("--organism",
required=True,
help="reference organism to filter from",
choices=['human', 'phix'])
p.add_argument("--summary-file",
required=True,
type=argparse.FileType("w"),
help="long table of results.")
p.add_argument("--output-dir",
required=True,
help="Path to output directory")
p.add_argument("--method",
default="bwa",
help="Method to use (default %(default)s)",
choices=tools_available.keys())
p.add_argument("--index", help="Path to contaminant genome indexes")
p.add_argument("--threads",
default=1,
type=int,
help="Number of threads to use")
p.add_argument("--pct",
required=False,
type=float,
default=0.5,
help="Percent identity (default: %(default)s)")
p.add_argument("--frac",
required=False,
type=float,
default=0.6,
help="Fraction of alignment length (default: %(default)s)")
p.add_argument("--keep-sam-file",
action="store_true",
help="Write SAM file to output directory.")
p.add_argument(
"--sam-file",
required=False,
type=argparse.FileType("r"),
help="File of alignments to reference database (SAM format, optional)")
p.add_argument("--bowtie2_fp",
default="bowtie2",
help="Path to bowtie2 (if using)")
p.add_argument("--bwa_fp", default="bwa", help="Path to bwa (if using)")
# Output
args = p.parse_args(argv)
config = get_config(args, args.organism)
fwd_fp = args.forward_reads.name
rev_fp = args.reverse_reads.name
args.forward_reads.close()
args.reverse_reads.close()
if args.sam_file is not None:
config["method"] = "samfile"
config["sam_fp"] = args.sam_file.name
if args.keep_sam_file is True:
config["keep_sam_file"] = True
else:
config["keep_sam_file"] = False
tool = FilteringTool(config)
if not tool.index_exists():
tool.make_index()
if not os.path.exists(args.output_dir):
os.mkdir(args.output_dir)
summary_data = tool.decontaminate(fwd_fp, rev_fp, args.output_dir,
args.organism, args.pct, args.frac)
save_summary(args.summary_file, config, summary_data)
