def main(sysargs=sys.argv[1:]):
parser = argparse.ArgumentParser(
prog=_program,
description=
'pangolin: Phylogenetic Assignment of Named Global Outbreak LINeages',
usage='''pangolin <query> [options]''')
parser.add_argument('query',
nargs="*",
help='Query fasta file of sequences to analyse.')
parser.add_argument(
'-o',
'--outdir',
action="store",
help="Output directory. Default: current working directory")
parser.add_argument(
'--outfile',
action="store",
help="Optional output file name. Default: lineage_report.csv")
parser.add_argument('--alignment',
action="store_true",
help="Optional alignment output.")
parser.add_argument(
'-d',
'--datadir',
action='store',
dest="datadir",
help=
"Data directory minimally containing a fasta alignment and guide tree")
parser.add_argument(
'--tempdir',
action="store",
help="Specify where you want the temp stuff to go. Default: $TMPDIR")
parser.add_argument(
"--no-temp",
action="store_true",
help="Output all intermediate files, for dev purposes.")
parser.add_argument(
'--decompress-model',
action="store_true",
dest="decompress",
help=
"Permanently decompress the model file to save time running pangolin.")
parser.add_argument(
'--max-ambig',
action="store",
default=0.5,
type=float,
help=
"Maximum proportion of Ns allowed for pangolin to attempt assignment. Default: 0.5",
dest="maxambig")
parser.add_argument(
'--min-length',
action="store",
default=10000,
type=int,
help=
"Minimum query length allowed for pangolin to attempt assignment. Default: 10000",
dest="minlen")
parser.add_argument('--panGUIlin',
action='store_true',
help="Run web-app version of pangolin",
dest="panGUIlin")
parser.add_argument("--verbose",
action="store_true",
help="Print lots of stuff to screen")
parser.add_argument("-t",
"--threads",
action="store",
help="Number of threads")
parser.add_argument("-v",
"--version",
action='version',
version=f"pangolin {__version__}")
parser.add_argument("-pv",
"--pangoLEARN-version",
action='version',
version=f"pangoLEARN {pangoLEARN.__version__}",
help="show pangoLEARN's version number and exit")
parser.add_argument(
"--update",
action='store_true',
default=False,
help=
"Automatically updates to latest release of pangolin and pangoLEARN, then exits"
)
if len(sysargs) < 1:
parser.print_help()
sys.exit(-1)
else:
args = parser.parse_args(sysargs)
args = parser.parse_args()
if args.update:
update(__version__, pangoLEARN.__version__)
snakefile = os.path.join(thisdir, 'scripts', 'pangolearn.smk')
if not os.path.exists(snakefile):
sys.stderr.write(
'Error: cannot find Snakefile at {}\n'.format(snakefile))
sys.exit(-1)
else:
print(pfunk.green("Found the snakefile"))
# to enable not having to pass a query if running update
# by allowing query to accept 0 to many arguments
if len(args.query) > 1:
print(
pfunk.cyan(
f"Error: Too many query (input) fasta files supplied: {args.query}\nPlease supply one only"
))
parser.print_help()
sys.exit(-1)
else:
# find the query fasta
query = os.path.join(cwd, args.query[0])
if not os.path.exists(query):
sys.stderr.write(
'Error: cannot find query (input) fasta file at {}\nPlease enter your fasta sequence file and refer to pangolin usage at:\nhttps://github.com/hCoV-2019/pangolin#usage\n for detailed instructions\n'
.format(query))
sys.exit(-1)
else:
print(pfunk.green(f"The query file is:") + f"{query}")
# default output dir
outdir = ''
if args.outdir:
outdir = os.path.join(cwd, args.outdir)
if not os.path.exists(outdir):
try:
os.mkdir(outdir)
except:
sys.stderr.write(
pfunk.cyan(f'Error: cannot create directory:') +
f"{outdir}")
sys.exit(-1)
else:
outdir = cwd
outfile = ""
if args.outfile:
outfile = os.path.join(outdir, args.outfile)
else:
outfile = os.path.join(outdir, "lineage_report.csv")
tempdir = ''
if args.tempdir:
to_be_dir = os.path.join(cwd, args.tempdir)
if not os.path.exists(to_be_dir):
os.mkdir(to_be_dir)
temporary_directory = tempfile.TemporaryDirectory(suffix=None,
prefix=None,
dir=to_be_dir)
tempdir = temporary_directory.name
else:
temporary_directory = tempfile.TemporaryDirectory(suffix=None,
prefix=None,
dir=None)
tempdir = temporary_directory.name
if args.no_temp:
print(
pfunk.green(f"--no-temp:") +
"all intermediate files will be written to {outdir}")
tempdir = outdir
if args.alignment:
align_dir = outdir
alignment_out = True
else:
align_dir = tempdir
alignment_out = False
if args.threads:
print(
pfunk.cyan(
f"\n--threads flag used, but threading not currently supported. Continuing with one thread."
))
"""
QC steps:
1) check no empty seqs
2) check N content
3) write a file that contains just the seqs to run
"""
do_not_run = []
run = []
for record in SeqIO.parse(query, "fasta"):
# replace spaces in sequence headers with underscores
record.id = record.description.replace(' ', '_')
if "," in record.id:
record.id = record.id.replace(",", "_")
if len(record) < args.minlen:
record.description = record.description + f" fail=seq_len:{len(record)}"
do_not_run.append(record)
print(record.id, "\tsequence too short")
else:
num_N = str(record.seq).upper().count("N")
prop_N = round((num_N) / len(record.seq), 2)
if prop_N > args.maxambig:
record.description = record.description + f" fail=N_content:{prop_N}"
do_not_run.append(record)
print(f"{record.id}\thas an N content of {prop_N}")
else:
run.append(record)
if run == []:
with open(outfile, "w") as fw:
fw.write(
"taxon,lineage,probability,pangoLEARN_version,status,note\n")
for record in do_not_run:
desc = record.description.split(" ")
reason = ""
for item in desc:
if item.startswith("fail="):
reason = item.split("=")[1]
fw.write(
f"{record.id},None,0,{pangoLEARN.__version__},fail,{reason}\n"
)
print(pfunk.cyan(f'Note: no query sequences have passed the qc\n'))
sys.exit(0)
post_qc_query = os.path.join(tempdir, 'query.post_qc.fasta')
with open(post_qc_query, "w") as fw:
SeqIO.write(run, fw, "fasta")
qc_fail = os.path.join(tempdir, 'query.failed_qc.fasta')
with open(qc_fail, "w") as fw:
SeqIO.write(do_not_run, fw, "fasta")
config = {
"query_fasta": post_qc_query,
"outdir": outdir,
"outfile": outfile,
"tempdir": tempdir,
"aligndir": align_dir,
"alignment_out": alignment_out,
"trim_start": 265, # where to pad to using datafunk
"trim_end": 29674, # where to pad after using datafunk
"qc_fail": qc_fail,
"pangoLEARN_version": pangoLEARN.__version__
}
# find the data
data_dir = ""
if args.datadir:
data_dir = os.path.join(cwd, args.datadir)
version = "Unknown"
for r, d, f in os.walk(data_dir):
for fn in f:
if fn == "__init__.py":
print("Found __init__.py")
with open(os.path.join(r, fn), "r") as fr:
for l in fr:
if l.startswith("__version__"):
l = l.rstrip("\n")
version = l.split('=')[1]
version = version.replace('"',
"").replace(" ", "")
print("pangoLEARN version", version)
config["pangoLEARN_version"] = version
if not args.datadir:
pangoLEARN_dir = pangoLEARN.__path__[0]
data_dir = os.path.join(pangoLEARN_dir, "data")
print(f"Looking in {data_dir} for data files...")
trained_model = ""
header_file = ""
lineages_csv = ""
for r, d, f in os.walk(data_dir):
for fn in f:
if fn == "decisionTreeHeaders_v1.joblib":
header_file = os.path.join(r, fn)
elif fn == "decisionTree_v1.joblib":
trained_model = os.path.join(r, fn)
elif fn == "lineages.metadata.csv":
lineages_csv = os.path.join(r, fn)
if trained_model == "" or header_file == "" or lineages_csv == "":
print(
pfunk.cyan(
"""Check your environment, didn't find appropriate files from the pangoLEARN repo.\n Trained model must be installed, please see https://cov-lineages.org/pangolin.html for installation instructions."""
))
exit(1)
else:
if args.decompress:
prev_size = os.path.getsize(trained_model)
print("Decompressing model and header files")
model = joblib.load(trained_model)
joblib.dump(model, trained_model, compress=0)
headers = joblib.load(header_file)
joblib.dump(headers, header_file, compress=0)
if os.path.getsize(trained_model) >= prev_size:
print(
pfunk.green(
f'Success! Decompressed the model file. Exiting\n'))
sys.exit(0)
else:
print(
pfunk.cyan(
f'Error: failed to decompress model. Exiting\n'))
sys.exit(0)
print(pfunk.green("\nData files found"))
print(f"Trained model:\t{trained_model}")
print(f"Header file:\t{header_file}")
print(f"Lineages csv:\t{lineages_csv}")
config["trained_model"] = trained_model
config["header_file"] = header_file
reference_fasta = pkg_resources.resource_filename('pangolin',
'data/reference.fasta')
config["reference_fasta"] = reference_fasta
variants_file = pkg_resources.resource_filename('pangolin',
'data/config_b.1.1.7.csv')
config["b117_variants"] = variants_file
variants_file = pkg_resources.resource_filename('pangolin',
'data/config_b.1.351.csv')
config["b1351_variants"] = variants_file
variants_file = pkg_resources.resource_filename('pangolin',
'data/config_p.1.csv')
config["p1_variants"] = variants_file
variants_file = pkg_resources.resource_filename('pangolin',
'data/config_p.2.csv')
config["p2_variants"] = variants_file
if args.panGUIlin:
config["lineages_csv"] = lineages_csv
if args.verbose:
quiet_mode = False
config["log_string"] = ""
else:
quiet_mode = True
lh_path = os.path.realpath(lh.__file__)
config["log_string"] = f"--quiet --log-handler-script {lh_path} "
if args.verbose:
print(pfunk.green("\n**** CONFIG ****"))
for k in sorted(config):
print(pfunk.green(k), config[k])
status = snakemake.snakemake(snakefile,
printshellcmds=True,
forceall=True,
force_incomplete=True,
workdir=tempdir,
config=config,
cores=1,
lock=False)
else:
logger = custom_logger.Logger()
status = snakemake.snakemake(snakefile,
printshellcmds=False,
forceall=True,
force_incomplete=True,
workdir=tempdir,
config=config,
cores=1,
lock=False,
quiet=True,
log_handler=logger.log_handler)
if status: # translate "success" into shell exit code of 0
return 0
return 1
def main(sysargs = sys.argv[1:]):
parser = argparse.ArgumentParser(prog = _program,
description=qcfunk.preamble(__version__),
usage='''apollo -i <path/to/reads> [options]
apollo -c <config.yaml>''')
io_group = parser.add_argument_group('input output options')
io_group.add_argument('-c',"--configfile",help="Config file with apollo run settings",dest="configfile")
io_group.add_argument('-i','--read-path',help="Path to the directory containing fastq files",dest="read_path")
io_group.add_argument('-o','--output-prefix', action="store",help="Output prefix. Default: apollo_<species>_<date>")
io_group.add_argument('--outdir', action="store",help="Output directory. Default: current working directory")
io_group.add_argument('--tempdir',action="store",help="Specify where you want the temp stuff to go. Default: $TMPDIR")
barcode_group = parser.add_argument_group('barcode options')
barcode_group.add_argument('-b','--barcodes-csv',help="CSV file describing which barcodes were used on which sample",dest="barcodes_csv")
barcode_group.add_argument('-k','--barcode-kit',help="Indicates which barcode kit was used. Default: native. Options: native, rapid, pcr, all",dest="barcode_kit")
demux_group = parser.add_argument_group('demultiplexing options')
demux_group.add_argument('--demultiplex',action="store_true",help="Indicates that your reads have not been demultiplexed and will run guppy demultiplex on your provided read directory",dest="demultiplex")
demux_group.add_argument('--path-to-guppy',action="store",help="Path to guppy_barcoder executable",dest="path_to_guppy")
run_group = parser.add_argument_group('run options')
run_group.add_argument('-s',"--species", action="store",help="Indicate which species is being sequenced. Options: mus, apodemus", dest="species")
run_group.add_argument("-r","--report",action="store_true",help="Generate markdown report of estimated age")
misc_group = parser.add_argument_group('misc options')
misc_group.add_argument('-t', '--threads', action='store',type=int,help="Number of threads")
misc_group.add_argument("--no-temp",action="store_true",help="Output all intermediate files, for dev purposes.")
misc_group.add_argument("--verbose",action="store_true",help="Print lots of stuff to screen")
misc_group.add_argument("-v","--version", action='version', version=f"apollo {__version__}")
"""
Exit with help menu if no args supplied
"""
args = parser.parse_args(sysargs)
"""
Initialising dicts
"""
config = qcfunk.get_defaults()
configfile = qcfunk.look_for_config(args.configfile,cwd,config)
# if a yaml file is detected, add everything in it to the config dict
if configfile:
qcfunk.parse_yaml_file(configfile, config)
else:
if len(sysargs)<1:
parser.print_help()
sys.exit(0)
"""
Get outdir, tempdir and the data
"""
# default output dir
qcfunk.get_outdir(args.outdir,args.output_prefix,cwd,config)
# specifying temp directory, outdir if no_temp (tempdir becomes working dir)
tempdir = qcfunk.get_temp_dir(args.tempdir, args.no_temp,cwd,config)
# get data for a particular species, and get species
qcfunk.get_package_data(thisdir, args.species, config)
config["cpg_header"] = qcfunk.make_cpg_header(config["cpg_sites"])
# add min and max read lengths to the config
qcfunk.get_read_length_filter(config)
# looks for basecalled directory
qcfunk.look_for_basecalled_reads(args.read_path,cwd,config)
# looks for the csv file saying which barcodes in sample
qcfunk.look_for_barcodes_csv(args.barcodes_csv,cwd,config)
"""
Configure whether guppy barcoder needs to be run
"""
qcfunk.look_for_guppy_barcoder(args.demultiplex,args.path_to_guppy,cwd,config)
# don't run in quiet mode if verbose specified
if args.verbose:
quiet_mode = False
config["log_string"] = ""
else:
quiet_mode = True
lh_path = os.path.realpath(lh.__file__)
config["log_string"] = f"--quiet --log-handler-script {lh_path} "
qcfunk.add_arg_to_config("threads",args.threads,config)
try:
config["threads"]= int(config["threads"])
except:
sys.stderr.write(qcfunk.cyan('Error: Please specifiy an integer for variable `threads`.\n'))
sys.exit(-1)
threads = config["threads"]
print(f"Number of threads: {threads}\n")
# find the master Snakefile
snakefile = qcfunk.get_snakefile(thisdir)
if args.verbose:
print("\n**** CONFIG ****")
for k in sorted(config):
print(qcfunk.green(k), config[k])
status = snakemake.snakemake(snakefile, printshellcmds=True, forceall=True, force_incomplete=True,
workdir=tempdir,config=config, cores=threads,lock=False
)
else:
logger = custom_logger.Logger()
status = snakemake.snakemake(snakefile, printshellcmds=False, forceall=True,force_incomplete=True,workdir=tempdir,
config=config, cores=threads,lock=False,quiet=True,log_handler=logger.log_handler
)
if status: # translate "success" into shell exit code of 0
return 0
return 1
def log_handler(msg):
logger = custom_logger.Logger()
return logger.log_handler
