def update(args):
if args.in_place and args.strict:
raise SystemExit(
"Incompatible arguments: --strict cannot be used with --in_place "
"to prevent unexpected loss of config settings.")
old_config = ruamel.yaml.safe_load(args.config_file)
# Remove the old version number
old_config.get('all', {}).pop('version', None)
new_config = config.new(conda_fp=config._find_conda_fp(),
project_fp=old_config.get('all',
{}).get('version', ''),
template=args.template)
updated_config = config.update(new_config, old_config, args.strict)
# If strict, preserve the blast databases
if args.strict:
blastdbs = old_config.get('blastdbs', None)
updated_config['blastdbs'] = blastdbs
if args.in_place:
cfg_fp = args.config_file.name
args.config_file.close()
with open(cfg_fp, 'w') as out:
config.dump(updated_config, out)
else:
config.dump(updated_config, args.out)
def write_config(args, project_fp, samplelists):
multiple_configs = len(samplelists.values()) != 1
for layout in samplelists.keys(
): # one paired, one unpaired, or one of each
if multiple_configs:
config_file = check_existing(
project_fp /
Path(layout + "_" + str(Path(project_fp / args.output).name)),
args.force)
else:
config_file = check_existing(project_fp / args.output, args.force)
cfg = config.new(project_fp=project_fp, template=args.template)
defaults = {}
if args.defaults:
defaults = ruamel.yaml.safe_load(args.defaults)
# Override loaded config defaults (if any) for a few specific items.
paired = layout == "paired"
defaults["all"] = defaults.get("all", {})
defaults["all"]["paired_end"] = paired
defaults["all"]["samplelist_fp"] = samplelists[layout].name
if args.data_acc:
defaults["all"]["download_reads"] = True
# Convert cfg from raw text to dict, including any defaults we have
# set, and write to disk.
cfg = config.update(cfg, defaults)
with config_file.open('w') as out:
config.dump(cfg, out)
sys.stderr.write("New config file written to {}\n".format(config_file))
if multiple_configs:
raise SystemExit(
"Found both paired and unpaired reads. Wrote two sample lists "
"and config files, with '_paired' or '_single' appended.")
def main(argv=sys.argv):
"""Create a blank config file with the given name."""
try:
conda_prefix = os.environ.get("CONDA_PREFIX")
except (KeyError, IndexError):
raise SystemExit(
"Could not determine Conda prefix. Activate your Sunbeam "
"environment and try this command again.")
parser = argparse.ArgumentParser(
"init", description="Initialize a new sunbeam project")
parser.add_argument(
"-o", "--output", help="Name of config file (written to project_fp)",
default="sunbeam_config.yml", metavar="FILE")
parser.add_argument(
"-f", "--force", help="Overwrite config file if it already exists",
action="store_true")
parser.add_argument(
"-d", "--defaults", type=argparse.FileType("r"), metavar="FILE",
help="Set of default values to use to populate config file")
parser.add_argument(
"project_fp", type=Path,
help="Project directory (will be created if it does not exist)")
parser.add_argument(
"--template", default=None, metavar="FILE",
help="Custom config file template, in YAML format",
type=argparse.FileType("r"))
args = parser.parse_args(argv)
# Create project folder if it doesn't exist
if not args.project_fp.exists():
sys.stderr.write("Creating project folder at {}...\n".format(args.project_fp))
args.project_fp.mkdir(parents=True, exist_ok=True)
cfg_fp = args.project_fp/args.output
if cfg_fp.exists() and not args.force:
raise SystemExit(
"Error: config file already exists at {}. Choose a new name or use --force "
"to overwrite.".format(cfg_fp))
cfg = config.new(
conda_fp=conda_prefix,
project_fp=args.project_fp,
template=args.template)
if args.defaults:
defaults = ruamel.yaml.safe_load(args.defaults)
cfg = config.update(cfg, defaults)
with open(cfg_fp, 'w') as out:
config.dump(cfg, out)
sys.stderr.write("New config file written to {}\n".format(cfg_fp))
def modify(args):
update_src = args.str if args.str else args.file
new_values = ruamel.yaml.safe_load(update_src)
if isinstance(new_values, str) and args.str:
raise SystemExit(
"Invalid YAML in --str. Did you make sure to put spaces between "
"keys and values?")
modified_config = config.update(args.config_file, new_values, strict=False)
if args.in_place:
cfg_fp = args.config_file.name
args.config_file.close()
with open(cfg_fp, 'w') as out:
config.dump(modified_config, out)
else:
config.dump(modified_config, args.out)
def main(argv=sys.argv):
try:
conda_prefix = os.environ.get("CONDA_PREFIX")
except (KeyError, IndexError):
raise SystemExit(
"Could not determine Conda prefix. Activate your Sunbeam "
"environment and try this command again.")
description_str = (
"Initialize a new Sunbeam project in a given directory, creating "
"a new config file and sample list from SRA accessions.")
parser = argparse.ArgumentParser("get", description=description_str)
parser.add_argument(
"project_fp",
type=Path,
help="project directory (will be created if it does not exist)")
parser.add_argument("-f",
"--force",
help="overwrite files if they already exist",
action="store_true")
parser.add_argument("--output",
help=("name of config file (%(default)s)"),
default="sunbeam_config.yml",
metavar="FILE")
configs = parser.add_argument_group("config file options")
configs.add_argument(
"--defaults",
type=argparse.FileType("r"),
metavar="FILE",
help="set of default values to use to populate config file")
configs.add_argument("--template",
default=None,
metavar="FILE",
help="custom config file template, in YAML format",
type=argparse.FileType("r"))
samplelist = parser.add_argument_group("sample list options")
samplelist.add_argument("--data_acc",
metavar="PATH",
nargs="+",
help="list of SRA accession numbers")
args = parser.parse_args(argv)
### Project Directory
# Create project folder if it doesn't exist
project_fp_exists = False
project_fp = args.project_fp
try:
project_fp = args.project_fp.resolve()
project_fp_exists = project_fp.exists()
except FileNotFoundError:
pass
if not project_fp_exists:
sys.stderr.write("Creating project folder at {}...\n".format(
args.project_fp))
project_fp.mkdir(parents=True, exist_ok=True)
### Sample list(s)
# Create sample list(s). One or two depending on paired/unpaired
# situation.
samplelists = build_sample_list_sra(args.data_acc, args)
for fp in samplelists.values():
sys.stderr.write("New sample list written to {}\n".format(fp))
### Config(s)
# TODO from here on, update config-handling to handle possible mixed
# unpaired/paired case. (Append suffix to existing args.output in that
# case, between name and .yml?)
# Louis thought: gonna append for now since I don't know how to parse Path objects
multiple_configs = len(samplelists.values()) != 1
for layout in samplelists.keys(
): # one paired, one unpaired, or one of each
# Create config file
if multiple_configs:
config_file = check_existing(
project_fp /
Path(layout + "_" + str(Path(project_fp / args.output).name)),
args.force)
# config_file = check_existing(Path(str(project_fp/args.output)+"_"+layout), args.force)
else:
config_file = check_existing(project_fp / args.output, args.force)
cfg = config.new(conda_fp=conda_prefix,
project_fp=project_fp,
template=args.template)
if args.defaults:
defaults = ruamel.yaml.safe_load(args.defaults)
cfg = config.update(cfg, defaults)
paired = layout == "paired"
sample_file = samplelists[layout].name
cfg = config.update(
cfg, {"all": {
"paired_end": paired,
"download_reads": True
}})
with config_file.open('w') as out:
config.dump(cfg, out)
sys.stderr.write("New config file written to {}\n".format(config_file))
if multiple_configs:
raise Exception(
"Found both paired and unpaired reads. Wrote two sample lists "
"and config files, with '_paired' or '_single' appended.")
def main(argv=sys.argv):
"""Create a blank config file with the given name."""
try:
conda_prefix = os.environ.get("CONDA_PREFIX")
except (KeyError, IndexError):
raise SystemExit(
"Could not determine Conda prefix. Activate your Sunbeam "
"environment and try this command again.")
description_str = (
"Initialize a new Sunbeam project in a given directory, creating "
"a new config file and (optionally) a sample list.")
parser = argparse.ArgumentParser("init", description=description_str)
parser.add_argument(
"project_fp",
type=Path,
help="project directory (will be created if it does not exist)")
parser.add_argument("-f",
"--force",
help="overwrite files if they already exist",
action="store_true")
parser.add_argument("--output",
help=("name of config file (%(default)s)"),
default="sunbeam_config.yml",
metavar="FILE")
configs = parser.add_argument_group("config file options")
configs.add_argument(
"--defaults",
type=argparse.FileType("r"),
metavar="FILE",
help="set of default values to use to populate config file")
configs.add_argument("--template",
default=None,
metavar="FILE",
help="custom config file template, in YAML format",
type=argparse.FileType("r"))
samplelist = parser.add_argument_group("sample list options")
samplelist.add_argument("--data_fp",
type=Path,
metavar="PATH",
help="path to folder containing fastq.gz files")
samplelist.add_argument("--format",
type=str,
metavar="STR",
help="filename format (default: guessed)")
samplelist.add_argument(
"--single_end",
action="store_true",
help="fastq files are in single-end, not paired-end, format")
args = parser.parse_args(argv)
# Create project folder if it doesn't exist
project_fp_exists = False
project_fp = args.project_fp
try:
project_fp = args.project_fp.resolve()
project_fp_exists = project_fp.exists()
except FileNotFoundError:
pass
if not project_fp_exists:
sys.stderr.write("Creating project folder at {}...\n".format(
args.project_fp))
project_fp.mkdir(parents=True, exist_ok=True)
# Check if files already exist
config_file = check_existing(project_fp / args.output, args.force)
samplelist_file = check_existing(project_fp / "samples.csv", args.force)
# Create config file
cfg = config.new(conda_fp=conda_prefix,
project_fp=project_fp,
template=args.template)
if args.defaults:
defaults = ruamel.yaml.safe_load(args.defaults)
cfg = config.update(cfg, defaults)
with config_file.open('w') as out:
config.dump(cfg, out)
sys.stderr.write("New config file written to {}\n".format(config_file))
# Create sample list (if given data_fp)
if args.data_fp:
try:
with samplelist_file.open('w') as out:
build_sample_list(data_fp=args.data_fp,
format_str=args.format,
output_file=out,
is_single_end=args.single_end)
sys.stderr.write(
"New sample list written to {}\n".format(samplelist_file))
except SampleFormatError as e:
raise SystemExit(
"Error: could not create sample list. Specify correct sample filename"
" format using --format.\n Reason: {}".format(e))
except MissingMatePairError as e:
raise SystemExit(
"Error: assuming paired-end reads, but could not find mates. Specify "
"--single-end if not paired-end, or provide sample name format "
"using --format."
"\n Reason: {}".format(e))