def __init__(self, config, log, sampleinfo={}, input=""):
self.config = config
self.logger = log
self.db_pusher = DB_Manipulator(config, log)
self.referencer = Referencer(config, log)
self.job_fallback = Job_Creator(config=config,
log=log,
sampleinfo=sampleinfo)
self.infolder = os.path.abspath(input)
self.sampledir = ""
# Since all scraped folders are generated by Job_Creator, datestring is automatically provided in last folder
last_folder = self.infolder.split("/")[-1]
self.name = last_folder.split("_")[0]
self.sampleinfo = sampleinfo
self.sample = None
if isinstance(self.sampleinfo, list) and len(self.sampleinfo) > 1:
self.name = self.sampleinfo[0].get("CG_ID_project")
self.sample = self.sampleinfo[0]
for entry in self.sampleinfo:
if entry.get("CG_ID_sample") == self.name:
raise Exception(
"Mixed projects in samples_info file. Do not know how to proceed"
)
else:
if isinstance(self.sampleinfo, list):
self.sampleinfo = self.sampleinfo[0]
self.name = self.sampleinfo.get("CG_ID_sample")
self.sample = self.sampleinfo
self.gene2resistance = self.load_resistances()
def add(ctx, organism, force):
""" Adds a new internal organism from pubMLST """
referee = Referencer(config=ctx.obj["config"], log=ctx.obj["log"], force=force)
try:
referee.add_pubmlst(organism)
except Exception as e:
click.echo(e.args[0])
ctx.abort()
click.echo("INFO - Checking versions of all references..")
referee = Referencer(config=ctx.obj["config"], log=ctx.obj["log"], force=force)
referee.update_refs()
def analyse(ctx, sampleinfo_file, input, config, dry, email, skip_update,
force_update, untrimmed, uncareful):
"""Sequence analysis, typing and resistance identification"""
# Run section
pool = []
trimmed = not untrimmed
careful = not uncareful
set_cli_config(config)
ctx.obj["config"]["regex"]["mail_recipient"] = email
ctx.obj["config"]["dry"] = dry
if not os.path.isdir(input):
click.echo(
"ERROR - Sequence data folder {} does not exist.".format(input))
ctx.abort()
for subfolder in os.listdir(input):
if os.path.isdir("{}/{}".format(input, subfolder)):
pool.append(subfolder)
run_settings = {
"input": input,
"dry": dry,
"email": email,
"skip_update": skip_update,
"trimmed": not untrimmed,
"careful": not uncareful,
"pool": pool,
}
# Samples section
sampleinfo = review_sampleinfo(sampleinfo_file)
run_creator = Job_Creator(
config=ctx.obj["config"],
log=ctx.obj["log"],
sampleinfo=sampleinfo,
run_settings=run_settings,
)
ext_refs = Referencer(config=ctx.obj["config"],
log=ctx.obj["log"],
sampleinfo=sampleinfo,
force=force_update)
click.echo("INFO - Checking versions of references..")
try:
if not skip_update:
ext_refs.identify_new(project=True)
ext_refs.update_refs()
click.echo("INFO - Version check done. Creating sbatch jobs")
else:
click.echo("INFO - Skipping version check.")
except Exception as e:
click.echo("{}".format(e))
if len(sampleinfo) > 1:
run_creator.project_job()
elif len(sampleinfo) == 1:
run_creator.project_job(single_sample=True)
else:
ctx.abort()
done()
def review(ctx, type, customer, skip_update, email, output):
"""Generates information about novel ST"""
# Trace exists by some samples having pubMLST_ST filled in. Make trace function later
ctx.obj["config"]["regex"]["mail_recipient"] = email
ext_refs = Referencer(config=ctx.obj["config"], log=ctx.obj["log"])
if not skip_update:
ext_refs.update_refs()
ext_refs.resync()
click.echo("INFO - Version check done. Generating output")
if type == "report":
codemonkey = Reporter(config=ctx.obj["config"],
log=ctx.obj["log"],
output=output)
codemonkey.report(type="st_update", customer=customer)
elif type == "list":
ext_refs.resync(type=type)
done()
def autobatch(ctx, dry, skip_update, email):
"""Analyses all currently unanalysed projects in the seqdata folder"""
# Trace exists by some samples having pubMLST_ST filled in. Make trace function later
ctx.obj["config"]["regex"]["mail_recipient"] = email
ext_refs = Referencer(config=ctx.obj["config"], log=ctx.obj["log"])
if not skip_update:
ext_refs.identify_new(project=True)
ext_refs.update_refs()
process = subprocess.Popen(
'squeue --format="%50j" -h -r'.split(), stdout=subprocess.PIPE
)
run_jobs, error = process.communicate()
run_jobs = run_jobs.splitlines()
run_jobs = [
re.search('"(.+)"', str(jobname)).group(1).replace(" ", "")
for jobname in run_jobs
]
old_jobs = os.listdir(ctx.obj["config"]["folders"]["results"])
for foldah in os.listdir(ctx.obj["config"]["folders"]["seqdata"]):
# Project name not found in slurm list
if len([job for job in run_jobs if foldah in job]) == 0:
# Project name not found in results directories
if len([job for job in old_jobs if foldah in job]) == 0:
if dry:
click.echo(
"DRY - microSALT analyse {} --skip_update".format(foldah)
)
else:
process = subprocess.Popen(
"microSALT analyse project {} --skip_update".format(
foldah
).split(),
stdout=subprocess.PIPE,
)
output, error = process.communicate()
elif dry:
click.echo(
"INFO - Skipping {} due to existing analysis in results folder".format(
foldah
)
)
elif dry:
click.echo("INFO - Skipping {} due to concurrent SLURM run".format(foldah))
done()
def init_references(testdata):
ref_obj = Referencer(config=preset_config, log=logger, sampleinfo=testdata)
ref_obj.identify_new(testdata[0].get('CG_ID_project'), project=True)
ref_obj.update_refs()
def references():
ref_obj = Referencer(config=preset_config, log=logger)
fixer.identify_new(project_id, project=True)
fixer.update_refs()
def overwrite(ctx, sample_name, force):
"""Flags sample as resolved"""
ext_refs = Referencer(config=ctx.obj["config"], log=ctx.obj["log"])
ext_refs.resync(type="overwrite", sample=sample_name, ignore=force)
done()
def observe(ctx):
""" Lists all stored organisms """
refe = Referencer(config=ctx.obj["config"], log=ctx.obj["log"])
click.echo("INFO - Currently stored organisms:")
for org in sorted(refe.existing_organisms()):
click.echo(org.replace("_", " ").capitalize())
def finish(ctx, sampleinfo_file, input, track, config, dry, email, skip_update,
report, output):
"""Sequence analysis, typing and resistance identification"""
# Run section
pool = []
set_cli_config(config)
ctx.obj["config"]["regex"]["mail_recipient"] = email
ctx.obj["config"]["dry"] = dry
if not os.path.isdir(input):
click.echo(
"ERROR - Sequence data folder {} does not exist.".format(input))
ctx.abort()
if output == "":
output = input
for subfolder in os.listdir(input):
if os.path.isdir("{}/{}".format(input, subfolder)):
pool.append(subfolder)
run_settings = {
"input": input,
"track": track,
"dry": dry,
"email": email,
"skip_update": skip_update,
}
# Samples section
sampleinfo = review_sampleinfo(sampleinfo_file)
ext_refs = Referencer(config=ctx.obj["config"],
log=ctx.obj["log"],
sampleinfo=sampleinfo)
click.echo("INFO - Checking versions of references..")
try:
if not skip_update:
ext_refs.identify_new(project=True)
ext_refs.update_refs()
click.echo("INFO - Version check done. Creating sbatch jobs")
else:
click.echo("INFO - Skipping version check.")
except Exception as e:
click.echo("{}".format(e))
res_scraper = Scraper(config=ctx.obj["config"],
log=ctx.obj["log"],
sampleinfo=sampleinfo,
input=input)
if isinstance(sampleinfo, list) and len(sampleinfo) > 1:
res_scraper.scrape_project()
# for subfolder in pool:
# res_scraper.scrape_sample()
else:
res_scraper.scrape_sample()
codemonkey = Reporter(
config=ctx.obj["config"],
log=ctx.obj["log"],
sampleinfo=sampleinfo,
output=output,
collection=True,
)
codemonkey.report(report)
done()
def __init__(self, config, log, sampleinfo={}, run_settings={}):
self.config = config
self.logger = log
self.batchfile = "/tmp/batchfile.sbatch"
self.filelist = list()
if isinstance(run_settings.get("input"), list):
self.filelist = run_settings.get("input")
run_settings["input"] = "/tmp/"
self.run_settings = run_settings
self.indir = os.path.abspath(run_settings.get("input", "/tmp/"))
self.trimmed = run_settings.get("trimmed", True)
self.qc_only = run_settings.get("qc_only", False)
self.careful = run_settings.get("careful", True)
self.pool = run_settings.get("pool", [])
self.finishdir = run_settings.get("finishdir", "")
self.sampleinfo = sampleinfo
self.sample = None
if isinstance(self.sampleinfo, list) and len(self.sampleinfo) > 1:
self.name = self.sampleinfo[0].get("CG_ID_project")
self.sample = self.sampleinfo[0]
for entry in self.sampleinfo:
if entry.get("CG_ID_sample") == self.name:
raise Exception(
"Mixed projects in samples_info file. Do not know how to proceed"
)
else:
if isinstance(self.sampleinfo, list):
self.sampleinfo = self.sampleinfo[0]
self.name = self.sampleinfo.get("CG_ID_sample")
self.sample = self.sampleinfo
# If timestamp is provided. Use it as analysis time. Else use current time
if run_settings.get("timestamp") is not None:
self.now = run_settings.get("timestamp")
temp = run_settings.get("timestamp").replace("_", ".").split(".")
self.dt = datetime(
int(temp[0]),
int(temp[1]),
int(temp[2]),
int(temp[3]),
int(temp[4]),
int(temp[5]),
)
else:
self.dt = datetime.now()
self.now = time.strftime("{}.{}.{}_{}.{}.{}".format(
self.dt.year,
self.dt.month,
self.dt.day,
self.dt.hour,
self.dt.minute,
self.dt.second,
))
if run_settings.get("finishdir") is None:
self.finishdir = "{}/{}_{}".format(config["folders"]["results"],
self.name, self.now)
self.db_pusher = DB_Manipulator(config, log)
self.concat_files = dict()
self.ref_resolver = Referencer(config, log)
class Job_Creator:
def __init__(self, config, log, sampleinfo={}, run_settings={}):
self.config = config
self.logger = log
self.batchfile = "/tmp/batchfile.sbatch"
self.filelist = list()
if isinstance(run_settings.get("input"), list):
self.filelist = run_settings.get("input")
run_settings["input"] = "/tmp/"
self.run_settings = run_settings
self.indir = os.path.abspath(run_settings.get("input", "/tmp/"))
self.trimmed = run_settings.get("trimmed", True)
self.qc_only = run_settings.get("qc_only", False)
self.careful = run_settings.get("careful", True)
self.pool = run_settings.get("pool", [])
self.finishdir = run_settings.get("finishdir", "")
self.sampleinfo = sampleinfo
self.sample = None
if isinstance(self.sampleinfo, list) and len(self.sampleinfo) > 1:
self.name = self.sampleinfo[0].get("CG_ID_project")
self.sample = self.sampleinfo[0]
for entry in self.sampleinfo:
if entry.get("CG_ID_sample") == self.name:
raise Exception(
"Mixed projects in samples_info file. Do not know how to proceed"
)
else:
if isinstance(self.sampleinfo, list):
self.sampleinfo = self.sampleinfo[0]
self.name = self.sampleinfo.get("CG_ID_sample")
self.sample = self.sampleinfo
# If timestamp is provided. Use it as analysis time. Else use current time
if run_settings.get("timestamp") is not None:
self.now = run_settings.get("timestamp")
temp = run_settings.get("timestamp").replace("_", ".").split(".")
self.dt = datetime(
int(temp[0]),
int(temp[1]),
int(temp[2]),
int(temp[3]),
int(temp[4]),
int(temp[5]),
)
else:
self.dt = datetime.now()
self.now = time.strftime("{}.{}.{}_{}.{}.{}".format(
self.dt.year,
self.dt.month,
self.dt.day,
self.dt.hour,
self.dt.minute,
self.dt.second,
))
if run_settings.get("finishdir") is None:
self.finishdir = "{}/{}_{}".format(config["folders"]["results"],
self.name, self.now)
self.db_pusher = DB_Manipulator(config, log)
self.concat_files = dict()
self.ref_resolver = Referencer(config, log)
def get_sbatch(self):
""" Returns sbatchfile, slightly superflous"""
return self.batchfile
def get_headerargs(self):
headerline = "-A {} -p {} -n {} -t {} -J {}_{} --qos {} --output {}/slurm_{}.log".format(
self.config["slurm_header"]["project"],
self.config["slurm_header"]["type"],
self.config["slurm_header"]["threads"],
self.config["slurm_header"]["time"],
self.config["slurm_header"]["job_prefix"],
self.name,
self.config["slurm_header"]["qos"],
self.finishdir,
self.name,
)
return headerline
def verify_fastq(self):
""" Uses arg indir to return a dict of PE fastq tuples fulfilling naming convention """
verified_files = list()
files = os.listdir(self.indir)
if files == []:
raise Exception("Directory {} lacks fastq files.".format(
self.indir))
for file in files:
file_match = re.match(self.config["regex"]["file_pattern"], file)
if file_match:
# Check that symlinks resolve
path = "{}/{}".format(self.indir, file)
if os.path.islink(path):
if not os.path.exists(os.readlink(path)):
raise Exception(
"Some fastq files are unresolved symlinks in directory {}."
.format(self.indir))
# Make sure both mates exist
if (file_match[1] == "1" or file_match[1] == "2"
or file_match[1] == "forward"
or file_match[1] == "reverse"):
if file_match[1] == "forward" or file_match[1] == "reverse":
pairno = "forward"
if "forward" in file_match[1]:
pairno = "reverse"
pairname = file_match[0].replace(file_match[1], pairno)
else:
pairno = 2 - 1 % int(file_match[1]) # 1->2, 2->1
# Construct mate name
pairname = "{}{}{}".format(
file_match.string[:file_match.end(1) - 1],
pairno,
file_match.string[file_match.end(1):file_match.end(
)],
)
if pairname in files:
files.pop(files.index(pairname))
verified_files.append(file_match[0])
verified_files.append(pairname)
else:
raise Exception(
"Some fastq files have no mate in directory {}.".
format(self.indir))
if verified_files == []:
raise Exception(
"No files in directory {} match file_pattern '{}'.".format(
self.indir, self.config["regex"]["file_pattern"]))
# Warn about file sizes
for vfile in verified_files:
try:
bsize = os.stat("{}/{}".format(self.indir, vfile)).st_size
bsize = bsize >> 20
if bsize > 1000:
self.logger.warning(
"Input fastq {} exceeds 1000MB".format(vfile))
except Exception as e:
self.logger.warning(
"Unable to verify size of input file {}/{}".format(
self.indir, vfile))
# Warn about invalid fastq files
for vfile in verified_files:
f = gzip.open("{}/{}".format(self.indir, vfile), "r")
lines = f.read().splitlines()
if len(lines) < 2 or not "+" in str(lines[-2]):
self.logger.warning(
"Input fastq {} does not seem to end properly".format(
vfile))
return sorted(verified_files)
def create_assemblysection(self):
batchfile = open(self.batchfile, "a+")
# memory is actually 128 per node regardless of cores.
batchfile.write("# Spades assembly\n")
if self.trimmed:
trimline = "-s {}".format(self.concat_files["i"])
else:
trimline = ""
if self.careful:
careline = "--careful"
else:
careline = ""
batchfile.write(
"spades.py --threads {} {} --memory {} -o {}/assembly -1 {} -2 {} {}\n"
.format(
self.config["slurm_header"]["threads"],
careline,
8 * int(self.config["slurm_header"]["threads"]),
self.finishdir,
self.concat_files["f"],
self.concat_files["r"],
trimline,
))
batchfile.write(
"mv {0}/assembly/contigs.fasta {0}/assembly/{1}_contigs.fasta\n".
format(self.finishdir, self.name))
batchfile.write(
"sed -n '/NODE_1000_/q;p' {0}/assembly/{1}_contigs.fasta > {0}/assembly/{1}_trimmed_contigs.fasta\n"
.format(self.finishdir, self.name))
# batchfile.write("##Input cleanup\n")
# batchfile.write("rm -r {}/trimmed\n".format(self.finishdir))
batchfile.write("\n\n")
batchfile.close()
def blast_subset(self, name, search_string):
# Create run
file_list = glob.glob(search_string)
batchfile = open(self.batchfile, "a+")
batchfile.write("mkdir {}/blast_search/{}\n".format(
self.finishdir, name))
blast_format = '"7 stitle sstrand qaccver saccver pident evalue bitscore qstart qend sstart send length"'
if len(file_list) > 1:
for ref in file_list:
if re.search(r"(\w+(?:\-\w+)*)\.\w+",
os.path.basename(ref)) is None:
self.logger.error(
"File {} does not match typical format. Consider deleting and redownloading"
)
else:
ref_nosuf = re.search(r"(\w+(?:\-\w+)*)\.\w+",
os.path.basename(ref)).group(1)
batchfile.write("# BLAST {} search for {}, {}\n".format(
name, self.sample.get("organism"), ref_nosuf))
if name == "mlst":
batchfile.write(
"blastn -db {}/{} -query {}/assembly/{}_contigs.fasta -out {}/blast_search/{}/loci_query_{}.txt -task megablast -num_threads {} -outfmt {}\n"
.format(
os.path.dirname(ref),
ref_nosuf,
self.finishdir,
self.name,
self.finishdir,
name,
ref_nosuf,
self.config["slurm_header"]["threads"],
blast_format,
))
else:
batchfile.write(
"blastn -db {}/{} -query {}/assembly/{}_contigs.fasta -out {}/blast_search/{}/{}.txt -task megablast -num_threads {} -outfmt {}\n"
.format(
os.path.dirname(ref),
ref_nosuf,
self.finishdir,
self.name,
self.finishdir,
name,
ref_nosuf,
self.config["slurm_header"]["threads"],
blast_format,
))
elif len(file_list) == 1:
ref_nosuf = re.search(r"(\w+(?:\-\w+)*)\.\w+",
os.path.basename(file_list[0])).group(1)
batchfile.write("## BLAST {} search in {}\n".format(
name,
self.sample.get("organism").replace("_", " ").capitalize()))
batchfile.write(
"blastn -db {}/{} -query {}/assembly/{}_contigs.fasta -out {}/blast_search/{}/{}.txt -task megablast -num_threads {} -outfmt {}\n"
.format(
os.path.dirname(search_string),
ref_nosuf,
self.finishdir,
self.name,
self.finishdir,
name,
ref_nosuf,
self.config["slurm_header"]["threads"],
blast_format,
))
batchfile.write("\n")
batchfile.close()
def create_variantsection(self):
""" Creates a job for variant calling based on local alignment """
ref = "{}/{}.fasta".format(self.config["folders"]["genomes"],
self.sample.get("reference"))
localdir = "{}/alignment".format(self.finishdir)
outbase = "{}/{}_{}".format(localdir, self.name,
self.sample.get("reference"))
# Create run
batchfile = open(self.batchfile, "a+")
batchfile.write("# Variant calling based on local alignment\n")
batchfile.write("mkdir {}\n".format(localdir))
batchfile.write("## Alignment & Deduplication\n")
batchfile.write("bwa mem -M -t {} {} {} {} > {}.sam\n".format(
self.config["slurm_header"]["threads"],
ref,
self.concat_files["f"],
self.concat_files["r"],
outbase,
))
batchfile.write(
"samtools view --threads {} -b -o {}.bam -T {} {}.sam\n".format(
self.config["slurm_header"]["threads"], outbase, ref, outbase))
batchfile.write(
"samtools sort --threads {} -o {}.bam_sort {}.bam\n".format(
self.config["slurm_header"]["threads"], outbase, outbase))
batchfile.write(
"picard MarkDuplicates I={}.bam_sort O={}.bam_sort_rmdup M={}.stats.dup REMOVE_DUPLICATES=true\n"
.format(outbase, outbase, outbase))
batchfile.write("samtools index {}.bam_sort_rmdup\n".format(outbase))
batchfile.write(
"samtools idxstats {}.bam_sort_rmdup &> {}.stats.ref\n".format(
outbase, outbase))
# Removal of temp aligment files
batchfile.write("rm {}.bam {}.sam\n".format(outbase, outbase))
batchfile.write("## Primary stats generation\n")
# Insert stats, dedupped
batchfile.write(
"picard CollectInsertSizeMetrics I={}.bam_sort_rmdup O={}.stats.ins H={}.hist.ins\n"
.format(outbase, outbase, outbase))
# Coverage
batchfile.write(
"samtools stats --coverage 1,10000,1 {}.bam_sort_rmdup |grep ^COV | cut -f 2- &> {}.stats.cov\n"
.format(outbase, outbase))
# Mapped rate, no dedup,dedup in MWGS (trimming has no effect)!
batchfile.write(
"samtools flagstat {}.bam_sort &> {}.stats.map\n".format(
outbase, outbase))
# Total reads, no dedup,dedup in MWGS (trimming has no effect)!
batchfile.write(
"samtools view -c {}.bam_sort &> {}.stats.raw\n".format(
outbase, outbase))
batchfile.write("\n\n")
batchfile.close()
def create_preprocsection(self):
"""Concatinates data, possibly trims it, then makes the unstranded reads usable"""
forward = list()
reverse = list()
for root, dirs, files in os.walk(self.config["folders"]["adapters"]):
if not "NexteraPE-PE.fa" in files:
self.logger.error(
"Adapters folder at {} does not contain NexteraPE-PE.fa. Review paths.yml"
)
else:
break
trimdir = "{}/trimmed".format(self.finishdir)
files = self.verify_fastq()
batchfile = open(self.batchfile, "a+")
batchfile.write("#Trimmomatic section\n")
batchfile.write("mkdir {}\n".format(trimdir))
batchfile.write("##Pre-concatination\n")
for file in files:
fullfile = "{}/{}".format(self.indir, file)
# Even indexes = Forward
if not files.index(file) % 2:
forward.append(fullfile)
elif files.index(file) % 2:
reverse.append(fullfile)
outfile = files[0].split("_")[0]
self.concat_files["f"] = "{}/trimmed/{}_forward_reads.fastq.gz".format(
self.finishdir, self.name)
self.concat_files["r"] = "{}/trimmed/{}_reverse_reads.fastq.gz".format(
self.finishdir, self.name)
batchfile.write("cat {} > {}\n".format(" ".join(forward),
self.concat_files.get("f")))
batchfile.write("cat {} > {}\n".format(" ".join(reverse),
self.concat_files.get("r")))
if self.trimmed:
fp = "{}/{}_trim_front_pair.fastq.gz".format(trimdir, outfile)
fu = "{}/{}_trim_front_unpair.fastq.gz".format(trimdir, outfile)
rp = "{}/{}_trim_rev_pair.fastq.gz".format(trimdir, outfile)
ru = "{}/{}_trim_rev_unpair.fastq.gz".format(trimdir, outfile)
batchfile.write("##Trimming section\n")
batchfile.write(
"trimmomatic PE -threads {} -phred33 {} {} {} {} {} {}\
ILLUMINACLIP:{}/NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36\n"
.format(
self.config["slurm_header"]["threads"],
self.concat_files.get("f"),
self.concat_files.get("r"),
fp,
fu,
rp,
ru,
self.config["folders"]["adapters"],
))
batchfile.write("## Interlaced trimmed files\n")
self.concat_files["f"] = fp
self.concat_files["r"] = rp
self.concat_files["i"] = "{}/{}_trim_unpair.fastq.gz".format(
trimdir, outfile)
batchfile.write("cat {} >> {}\n".format(" ".join(
[fu, ru]), self.concat_files.get("i")))
batchfile.write("\n")
batchfile.close()
def create_assemblystats_section(self):
batchfile = open(self.batchfile, "a+")
batchfile.write("# QUAST QC metrics\n")
batchfile.write("mkdir {}/assembly/quast\n".format(self.finishdir))
batchfile.write(
"quast.py {}/assembly/{}_contigs.fasta -o {}/assembly/quast\n".
format(self.finishdir, self.name, self.finishdir))
batchfile.write(
"mv {}/assembly/quast/report.tsv {}/assembly/quast/{}_report.tsv\n\n"
.format(self.finishdir, self.finishdir, self.name))
batchfile.close()
def create_snpsection(self):
snplist = self.filelist.copy()
batchfile = open(self.batchfile, "a+")
name = ""
# VCFTools filters:
vcffilter = "--minQ 30 --thin 50 --minDP 3 --min-meanDP 20"
# BCFTools filters:
bcffilter = "GL[0]<-500 & GL[1]=0 & QR/RO>30 & QA/AO>30 & QUAL>5000 & ODDS>1100 & GQ>140 & DP>100 & MQM>59 & SAP<15 & PAIRED>0.9 & EPP>3"
for item in snplist:
if item.count("/") >= 2:
name = item.split("/")[-2]
if "_" in name:
name = name.split("_")[0]
batchfile.write("# Basecalling for sample {}\n".format(name))
ref = "{}/{}.fasta".format(self.config["folders"]["genomes"],
self.sample.get("reference"))
outbase = "{}/{}_{}".format(item, name,
self.sample.get("reference"))
batchfile.write(
"samtools view -h -q 1 -F 4 -F 256 {}.bam_sort_rmdup | grep -v XA:Z | grep -v SA:Z| samtools view -b - > {}/{}.unique\n"
.format(outbase, self.finishdir, name))
batchfile.write(
"freebayes -= --pvar 0.7 -j -J --standard-filters -C 6 --min-coverage 30 --ploidy 1 -f {} -b {}/{}.unique -v {}/{}.vcf\n"
.format(ref, self.finishdir, name, self.finishdir, name))
batchfile.write(
"bcftools view {}/{}.vcf -o {}/{}.bcf.gz -O b --exclude-uncalled --types snps\n"
.format(self.finishdir, name, self.finishdir, name))
batchfile.write("bcftools index {}/{}.bcf.gz\n".format(
self.finishdir, name))
batchfile.write("\n")
batchfile.write(
"vcftools --bcf {}/{}.bcf.gz {} --remove-filtered-all --recode-INFO-all --recode-bcf --out {}/{}\n"
.format(self.finishdir, name, vcffilter, self.finishdir, name))
batchfile.write(
'bcftools view {}/{}.recode.bcf -i "{}" -o {}/{}.recode.bcf.gz -O b --exclude-uncalled --types snps\n'
.format(self.finishdir, name, bcffilter, self.finishdir, name))
batchfile.write("bcftools index {}/{}.recode.bcf.gz\n\n".format(
self.finishdir, name))
batchfile.write("# SNP pair-wise distance\n")
batchfile.write("touch {}/stats.out\n".format(self.finishdir))
while len(snplist) > 1:
nameOne = ""
nameTwo = ""
top = snplist.pop(0)
if top.count("/") >= 2:
nameOne = top.split("/")[-2]
if "_" in nameOne:
nameOne = nameOne.split("_")[0]
for entry in snplist:
if entry.count("/") >= 2:
nameTwo = entry.split("/")[-2]
if "_" in nameTwo:
nameTwo = nameTwo.split("_")[0]
pair = "{}_{}".format(nameOne, nameTwo)
batchfile.write(
"bcftools isec {}/{}.recode.bcf.gz {}/{}.recode.bcf.gz -n=1 -c all -p {}/tmp -O b\n"
.format(self.finishdir, nameOne, self.finishdir, nameTwo,
self.finishdir))
batchfile.write(
"bcftools merge -O b -o {}/{}.bcf.gz --force-samples {}/tmp/0000.bcf {}/tmp/0001.bcf\n"
.format(self.finishdir, pair, self.finishdir,
self.finishdir))
batchfile.write("bcftools index {}/{}.bcf.gz\n".format(
self.finishdir, pair))
batchfile.write(
"echo {} $( bcftools stats {}/{}.bcf.gz |grep SNPs: | cut -d $'\\t' -f4 ) >> {}/stats.out\n"
.format(pair, self.finishdir, pair, self.finishdir))
batchfile.write("\n")
batchfile.close()
def create_collection(self):
"""Creates collection entry in database"""
if self.db_pusher.exists("Collections", {"ID_collection": self.name}):
self.db_pusher.purge_rec(name=self.name, type="Collections")
for sample in self.pool:
self.db_pusher.add_rec(
{
"ID_collection": self.name,
"CG_ID_sample": sample
}, "Collections")
addedprojs = list()
for sample in self.pool:
proj = re.search(r"(\w+)A(?:\w+)", sample).group(1)
if proj not in addedprojs:
self.create_project(proj)
addedprojs.append(proj)
def create_project(self, name):
"""Creates project in database"""
proj_col = dict()
proj_col["CG_ID_project"] = name
proj_col["Customer_ID_project"] = self.sample.get(
"Customer_ID_project")
proj_col["Customer_ID"] = self.sample.get("Customer_ID")
self.db_pusher.add_rec(proj_col, "Projects")
self.db_pusher.upd_rec({"CG_ID_project": name}, "Projects", proj_col)
def create_sample(self, name):
"""Creates sample in database"""
try:
sample_col = self.db_pusher.get_columns("Samples")
sample_col["CG_ID_sample"] = self.sample.get("CG_ID_sample")
sample_col["CG_ID_project"] = self.sample.get("CG_ID_project")
sample_col["Customer_ID_sample"] = self.sample.get(
"Customer_ID_sample")
sample_col["reference_genome"] = self.sample.get("reference")
sample_col["reference_length"] = self.sample.get(
"reference_length")
sample_col["date_analysis"] = self.dt
sample_col["organism"] = self.sample.get("organism")
sample_col["application_tag"] = self.sample.get("application_tag")
sample_col["priority"] = self.sample.get("priority")
sample_col["date_arrival"] = datetime.strptime(
self.sample.get("date_arrival"), "%Y-%m-%d %H:%M:%S")
sample_col["date_sequencing"] = datetime.strptime(
self.sample.get("date_sequencing"), "%Y-%m-%d %H:%M:%S")
sample_col["date_libprep"] = datetime.strptime(
self.sample.get("date_libprep"), "%Y-%m-%d %H:%M:%S")
sample_col["method_libprep"] = self.sample.get("method_libprep")
sample_col["method_sequencing"] = self.sample.get(
"method_sequencing")
# self.db_pusher.purge_rec(sample_col['CG_ID_sample'], 'sample')
self.db_pusher.add_rec(sample_col, "Samples")
except Exception as e:
self.logger.error("Unable to add sample {} to database".format(
self.name))
def project_job(self, single_sample=False):
if "dry" in self.config and self.config["dry"] == True:
dry = True
else:
dry = False
jobarray = list()
if not os.path.exists(self.finishdir):
os.makedirs(self.finishdir)
# Loads project level info.
try:
if single_sample:
self.create_project(self.sample.get("CG_ID_project"))
elif self.pool:
self.create_collection()
else:
self.create_project(self.name)
except Exception as e:
self.logger.error(
"LIMS interaction failed. Unable to read/write project {}".
format(self.name))
# Writes the job creation sbatch
if single_sample:
try:
self.sample_job()
headerargs = self.get_headerargs()
outfile = self.get_sbatch()
bash_cmd = "sbatch {} {}".format(headerargs, outfile)
if not dry and outfile != "":
samproc = subprocess.Popen(bash_cmd.split(),
stdout=subprocess.PIPE)
output, error = samproc.communicate()
jobno = re.search(r"(\d+)", str(output)).group(0)
jobarray.append(jobno)
else:
self.logger.info("Suppressed command: {}".format(bash_cmd))
except Exception as e:
self.logger.error("Unable to analyze single sample {}".format(
self.name))
else:
for ldir in glob.glob("{}/*/".format(self.indir)):
ldir = os.path.basename(os.path.normpath(ldir))
try:
sample_in = "{}/{}".format(self.indir, ldir)
sample_out = "{}/{}".format(self.finishdir, ldir)
linkedjson = None
local_sampleinfo = [
p for p in self.sampleinfo if p["CG_ID_sample"] == ldir
]
if local_sampleinfo == []:
raise Exception(
"Sample {} has no counterpart in json file".format(
ldir))
else:
local_sampleinfo = local_sampleinfo[0]
sample_settings = dict(self.run_settings)
sample_settings["input"] = sample_in
sample_settings["finishdir"] = sample_out
sample_settings["timestamp"] = self.now
sample_instance = Job_Creator(
config=self.config,
log=self.logger,
sampleinfo=local_sampleinfo,
run_settings=sample_settings,
)
sample_instance.sample_job()
headerargs = sample_instance.get_headerargs()
outfile = ""
if os.path.isfile(sample_instance.get_sbatch()):
outfile = sample_instance.get_sbatch()
bash_cmd = "sbatch {} {}".format(headerargs, outfile)
if not dry and outfile != "":
projproc = subprocess.Popen(bash_cmd.split(),
stdout=subprocess.PIPE)
output, error = projproc.communicate()
jobno = re.search(r"(\d+)", str(output)).group(0)
jobarray.append(jobno)
else:
self.logger.info(
"Suppressed command: {}".format(bash_cmd))
except Exception as e:
pass
if not dry:
self.finish_job(jobarray, single_sample)
def finish_job(self, joblist, single_sample=False):
""" Uploads data and sends an email once all analysis jobs are complete. """
report = "default"
if self.qc_only:
report = "qc"
custom_conf = ""
if "config_path" in self.config:
custom_conf = "--config {}".format(self.config["config_path"])
process = subprocess.Popen("id -un".split(), stdout=subprocess.PIPE)
user, error = process.communicate()
user = str(user).replace(".", " ").title()
# if not os.path.exists(self.finishdir):
# os.makedirs(self.finishdir)
startfile = "{}/run_started.out".format(self.finishdir)
configfile = "{}/config.log".format(self.finishdir)
mailfile = "{}/mailjob.sh".format(self.finishdir)
samplefile = "{}/sampleinfo.json".format(self.finishdir)
with open(samplefile, "w+") as outfile:
json.dump(self.sampleinfo, outfile)
sb = open(startfile, "w+")
cb = open(configfile, "w+")
mb = open(mailfile, "w+")
sb.write("#!/usr/bin/env bash\n")
sb.close()
configout = self.config.copy()
if "genologics" in configout:
del configout["genologics"]
cb.write("ANALYSIS STARTED BY: {}\n".format(user))
cb.write(json.dumps(configout, indent=2, separators=(",", ":")))
cb.close()
mb.write("#!/usr/bin/env bash\n\n")
mb.write(
"#Uploading of results to database and production of report\n")
if "MICROSALT_CONFIG" in os.environ:
mb.write("export MICROSALT_CONFIG={}\n".format(
os.environ["MICROSALT_CONFIG"]))
mb.write("source activate $CONDA_DEFAULT_ENV\n")
mb.write(
"microSALT utils finish {0}/sampleinfo.json --input {0} --email {1} --report {2} {3}\n"
.format(
self.finishdir,
self.config["regex"]["mail_recipient"],
report,
custom_conf,
))
mb.write("touch {}/run_complete.out".format(self.finishdir))
mb.close()
massagedJobs = list()
final = ":".join(joblist)
# Create subtracker if more than 50 samples
maxlen = 50
if len(joblist) > maxlen:
i = 1
while i <= len(joblist):
if i + maxlen < len(joblist):
massagedJobs.append(":".join(joblist[i - 1:i + maxlen -
1]))
else:
massagedJobs.append(":".join(joblist[i - 1:-1]))
i += maxlen
for entry in massagedJobs:
if massagedJobs.index(entry) < len(massagedJobs) - 1:
head = "-A {} -p core -n 1 -t 00:00:10 -J {}_{}_SUBTRACKER --qos {} --dependency=afterany:{}".format(
self.config["slurm_header"]["project"],
self.config["slurm_header"]["job_prefix"],
self.name,
self.config["slurm_header"]["qos"],
entry,
)
bash_cmd = "sbatch {} {}".format(head, startfile)
mailproc = subprocess.Popen(bash_cmd.split(),
stdout=subprocess.PIPE)
output, error = mailproc.communicate()
jobno = re.search(r"(\d+)", str(output)).group(0)
massagedJobs[massagedJobs.index(entry) +
1] += ":{}".format(jobno)
else:
final = entry
break
head = "-A {} -p core -n 1 -t 6:00:00 -J {}_{}_MAILJOB --qos {} --open-mode append --dependency=afterany:{} --output {}".format(
self.config["slurm_header"]["project"],
self.config["slurm_header"]["job_prefix"],
self.name,
self.config["slurm_header"]["qos"],
final,
self.config["folders"]["log_file"],
self.config["regex"]["mail_recipient"],
)
bash_cmd = "sbatch {} {}".format(head, mailfile)
mailproc = subprocess.Popen(bash_cmd.split(), stdout=subprocess.PIPE)
output, error = mailproc.communicate()
try:
jobno = str(re.search(r"(\d+)", str(output)).group(0))
joblist.append(jobno)
except Exception as e:
self.logger.info("Unable to grab SLURMID for {0}".format(
self.name))
try:
#Generates file with all slurm ids
slurmname = "{}_slurm_ids.yaml".format(self.name)
slurmreport_storedir = Path(self.config["folders"]["reports"],
"trailblazer", slurmname)
slurmreport_workdir = Path(self.finishdir, slurmname)
yaml.safe_dump(data={"jobs": [str(job) for job in joblist]},
stream=open(slurmreport_workdir, "w"))
shutil.copyfile(slurmreport_workdir, slurmreport_storedir)
self.logger.info(
"Saved Trailblazer slurm report file to %s and %s",
slurmreport_storedir,
slurmreport_workdir,
)
except Exception as e:
self.logger.info(
"Unable to generate Trailblazer slurm report file")
def sample_job(self):
""" Writes necessary sbatch job for each individual sample """
try:
if not os.path.exists(self.finishdir):
os.makedirs(self.finishdir)
try:
# This is one job
self.batchfile = "{}/runfile.sbatch".format(self.finishdir)
batchfile = open(self.batchfile, "w+")
batchfile.write("#!/bin/sh\n\n")
batchfile.write("mkdir -p {}\n".format(self.finishdir))
batchfile.close()
self.create_preprocsection()
self.create_variantsection()
if not self.qc_only:
self.create_assemblysection()
self.create_assemblystats_section()
self.create_blast_search()
batchfile = open(self.batchfile, "a+")
batchfile.close()
self.logger.info(
"Created runfile for sample {} in folder {}".format(
self.name, self.finishdir))
except Exception as e:
raise
try:
self.create_sample(self.name)
except Exception as e:
self.logger.error(
"Unable to access LIMS info for sample {}".format(
self.name))
except Exception as e:
self.logger.error(
"Unable to create job for sample {}\nSource: {}".format(
self.name, str(e)))
shutil.rmtree(self.finishdir, ignore_errors=True)
raise
def create_blast_search(self):
reforganism = self.ref_resolver.organism2reference(
self.sample.get("organism"))
self.batchfile = "{}/runfile.sbatch".format(self.finishdir)
batchfile = open(self.batchfile, "a+")
batchfile.write("mkdir -p {}/blast_search\n".format(self.finishdir))
batchfile.close()
self.blast_subset(
"mlst",
"{}/{}/*.tfa".format(self.config["folders"]["references"],
reforganism),
)
self.blast_subset(
"resistance",
"{}/*.fsa".format(self.config["folders"]["resistances"]))
if reforganism == "escherichia_coli":
ss = "{}/*{}".format(
os.path.dirname(self.config["folders"]["expec"]),
os.path.splitext(self.config["folders"]["expec"])[1],
)
self.blast_subset("expec", ss)
def snp_job(self):
""" Writes a SNP calling job for a set of samples """
if not os.path.exists(self.finishdir):
os.makedirs(self.finishdir)
self.batchfile = "{}/runfile.sbatch".format(self.finishdir)
batchfile = open(self.batchfile, "w+")
batchfile.write("#!/usr/bin/env bash\n")
batchfile.write("mkdir -p {}\n\n".format(self.finishdir))
batchfile.close()
self.create_snpsection()
batchfile = open(self.batchfile, "a+")
batchfile.close()
headerline = (
"-A {} -p {} -n 1 -t 24:00:00 -J {}_{} --qos {} --output {}/slurm_{}.log"
.format(
self.config["slurm_header"]["project"],
self.config["slurm_header"]["type"],
self.config["slurm_header"]["job_prefix"],
self.name,
self.config["slurm_header"]["qos"],
self.finishdir,
self.name,
))
outfile = self.get_sbatch()
bash_cmd = "sbatch {} {}".format(headerline, outfile)
samproc = subprocess.Popen(bash_cmd.split(), stdout=subprocess.PIPE)
output, error = samproc.communicate()
class Scraper:
def __init__(self, config, log, sampleinfo={}, input=""):
self.config = config
self.logger = log
self.db_pusher = DB_Manipulator(config, log)
self.referencer = Referencer(config, log)
self.job_fallback = Job_Creator(config=config,
log=log,
sampleinfo=sampleinfo)
self.infolder = os.path.abspath(input)
self.sampledir = ""
# Since all scraped folders are generated by Job_Creator, datestring is automatically provided in last folder
last_folder = self.infolder.split("/")[-1]
self.name = last_folder.split("_")[0]
self.sampleinfo = sampleinfo
self.sample = None
if isinstance(self.sampleinfo, list) and len(self.sampleinfo) > 1:
self.name = self.sampleinfo[0].get("CG_ID_project")
self.sample = self.sampleinfo[0]
for entry in self.sampleinfo:
if entry.get("CG_ID_sample") == self.name:
raise Exception(
"Mixed projects in samples_info file. Do not know how to proceed"
)
else:
if isinstance(self.sampleinfo, list):
self.sampleinfo = self.sampleinfo[0]
self.name = self.sampleinfo.get("CG_ID_sample")
self.sample = self.sampleinfo
self.gene2resistance = self.load_resistances()
def scrape_project(self, project=None):
"""Scrapes a project folder for information"""
if project is None:
project = self.name
self.db_pusher.purge_rec(project, "Projects")
if not self.db_pusher.exists("Projects", {"CG_ID_project": project}):
self.logger.warning("Replacing project {}".format(project))
self.job_fallback.create_project(project)
# Scrape order matters a lot!
for dir in os.listdir(self.infolder):
subdir = "{}/{}".format(self.infolder, dir)
local_param = [
p for p in self.sampleinfo if p["CG_ID_sample"] == dir
]
if local_param != []:
local_param = local_param[0]
sample_scraper = Scraper(
config=self.config,
log=self.logger,
sampleinfo=local_param,
input=subdir,
)
sample_scraper.scrape_sample()
else:
self.logger.warning(
"Skipping {} due to lacking info in sample_json file".
format(dir))
def scrape_sample(self, sample=None):
"""Scrapes a sample folder for information"""
if sample is None:
sample = self.name
self.db_pusher.purge_rec(sample, "Samples")
if not self.db_pusher.exists(
"Projects",
{"CG_ID_project": self.sample.get("CG_ID_project")}):
self.logger.warning("Replacing project {}".format(
self.sample.get("CG_ID_project")))
self.job_fallback.create_project(self.sample.get("CG_ID_project"))
if not self.db_pusher.exists("Samples", {"CG_ID_sample": sample}):
self.logger.warning("Replacing sample {}".format(sample))
self.job_fallback.create_sample(sample)
# Scrape order matters a lot!
self.sampledir = self.infolder
self.scrape_blast(type="seq_type")
self.scrape_blast(type="resistance")
if (self.referencer.organism2reference(
self.sample.get("organism")) == "escherichia_coli"):
self.scrape_blast(type="expec")
self.scrape_alignment()
self.scrape_quast()
def scrape_quast(self, filename=""):
"""Scrapes a quast report for assembly information"""
if filename == "":
filename = "{}/assembly/quast/report.tsv".format(self.sampledir)
quast = dict()
try:
with open(filename, "r") as infile:
for line in infile:
lsplit = line.rstrip().split("\t")
if lsplit[0] == "# contigs":
quast["contigs"] = int(lsplit[1])
elif lsplit[0] == "Total length":
quast["genome_length"] = int(lsplit[1])
elif lsplit[0] == "GC (%)":
quast["gc_percentage"] = float(lsplit[1])
elif lsplit[0] == "N50":
quast["n50"] = int(lsplit[1])
self.db_pusher.upd_rec({"CG_ID_sample": self.name}, "Samples",
quast)
self.logger.debug("Project {} recieved quast stats: {}".format(
self.name, quast))
except Exception as e:
self.logger.warning(
"Cannot generate quast statistics for {}".format(self.name))
def get_locilengths(self, foldername, suffix):
""" Generate a dict of length for any given loci """
# Create dict with full name as key, associated nucleotides as value.
alleles = dict()
finalalleles = dict()
for file in os.listdir(foldername):
if file.endswith(suffix):
lastallele = ""
f = open("{}/{}".format(foldername, file), "r")
for row in f:
if ">" in row:
lastallele = row.strip()
alleles[lastallele] = ""
else:
alleles[lastallele] = alleles[lastallele] + row.strip()
f.close()
for k, v in alleles.items():
finalalleles[k] = len(v)
return finalalleles
def scrape_blast(self, type="", file_list=[]):
hypo = list()
type2db = type.capitalize() + "s"
if type == "expec":
type2db = "Expacs"
if file_list == []:
if type == "seq_type":
file_list = glob.glob("{}/blast_search/mlst/*".format(
self.sampledir))
else:
file_list = glob.glob("{}/blast_search/{}/*".format(
self.sampledir, type))
organism = self.referencer.organism2reference(
self.sample.get("organism"))
if organism:
self.db_pusher.upd_rec({"CG_ID_sample": self.name}, "Samples",
{"organism": organism})
res_cols = self.db_pusher.get_columns("{}".format(type2db))
try:
old_ref = ""
for file in file_list:
filename = os.path.basename(file).rsplit(
".", 1)[0] # Removes suffix
if filename == "lactam":
filename = "beta-lactam"
if type == "resistance":
ref_folder = self.config["folders"]["resistances"]
suffix = "fsa"
elif type == "expec":
ref_folder = os.path.dirname(
self.config["folders"]["expec"])
suffix = os.path.basename(
self.config["folders"]["expec"]).rsplit(".", 1)[1]
elif type == "seq_type":
ref_folder = "{}/{}".format(
self.config["folders"]["references"], organism)
suffix = "tfa"
locilengths = self.get_locilengths(ref_folder, suffix)
with open("{}".format(file), "r") as sample:
for line in sample:
# Ignore commented fields
if not line[0] == "#":
elem_list = line.rstrip().split("\t")
if not elem_list[1] == "N/A":
hypo.append(dict())
hypo[-1]["CG_ID_sample"] = self.name
hypo[-1]["identity"] = elem_list[4]
hypo[-1]["evalue"] = elem_list[5]
hypo[-1]["bitscore"] = elem_list[6]
if int(elem_list[7]) < int(elem_list[8]):
hypo[-1]["contig_start"] = int(
elem_list[7])
hypo[-1]["contig_end"] = int(elem_list[8])
else:
hypo[-1]["contig_start"] = int(
elem_list[8])
hypo[-1]["contig_end"] = int(elem_list[7])
hypo[-1]["subject_length"] = int(elem_list[11])
if type == "resistance":
hypo[-1]["instance"] = filename
partials = re.search(
r"(?:\>)*(.+)_(\d+){1,3}(?:_(.+))*",
elem_list[3],
)
hypo[-1]["reference"] = partials.group(3)
hypo[-1]["gene"] = partials.group(1)
if hypo[-1][
"gene"] in self.gene2resistance.keys(
):
hypo[-1][
"resistance"] = self.gene2resistance[
hypo[-1]["gene"]]
else:
hypo[-1]["{}".format(type)] = hypo[-1][
"instance"].capitalize()
hypo[-1]["span"] = (
float(hypo[-1]["subject_length"]) /
locilengths[">{}".format(
elem_list[3])])
elif type == "expec":
hypo[-1]["instance"] = filename
# Thanks, precompiled list standards
if ">" in elem_list[3]:
partials = re.search(
r">*(\w+_\w+\.*\w+).+\((\w+)\).+\((\w+)\)_(\w+)_\[.+\]",
elem_list[3],
)
else:
partials = re.search(
r"(\w+)\(gb\|\w+\)_\((\S+)\)_(.+)_\[(\S+)_.+\]_\[\S+\]",
elem_list[3],
)
if not partials:
partials = re.search(
r"(\w+\.*\w+)\:*\w*_*(?:\(\w+\-\w+\))*_\((\w+)\)_([^[]+)\[\S+\]",
elem_list[3],
)
# NC/Protein reference
hypo[-1]["reference"] = partials.group(1)
# Full gene name
hypo[-1]["gene"] = partials.group(2)
# More generic group
hypo[-1]["instance"] = partials.group(
3).strip("_")
# Description
if len(partials.groups()) >= 4:
hypo[-1]["virulence"] = (
partials.group(4).replace(
"_", " ").capitalize())
else:
hypo[-1]["virulence"] = ""
hypo[-1]["span"] = (
float(hypo[-1]["subject_length"]) /
locilengths[">{}".format(
elem_list[3])])
elif type == "seq_type":
partials = re.search(
r"(.+)_(\d+){1,3}(?:_(\w+))*",
elem_list[3])
hypo[-1]["loci"] = partials.group(1)
hypo[-1]["allele"] = int(partials.group(2))
hypo[-1]["span"] = (
float(hypo[-1]["subject_length"]) /
locilengths[">{}".format(
elem_list[3])])
# split elem 2 into contig node_NO, length, cov
nodeinfo = elem_list[2].split("_")
hypo[-1]["contig_name"] = "{}_{}".format(
nodeinfo[0], nodeinfo[1])
hypo[-1]["contig_length"] = int(nodeinfo[3])
hypo[-1]["contig_coverage"] = nodeinfo[5]
self.logger.debug(
"scrape_blast scrape loop hit")
self.logger.info("{} candidate {} hits found".format(
len(hypo), type2db))
except Exception as e:
self.logger.error("Unable to process the pattern of {}".format(
str(e)))
# Cleanup of overlapping hits
if type == "seq_type":
identifier = "loci"
elif type == "resistance" or type == "expec":
identifier = "gene"
ind = 0
while ind < len(hypo) - 1:
targ = ind + 1
while targ < len(hypo):
ignore = False
if (hypo[ind]["contig_name"] == hypo[targ]["contig_name"]
or hypo[ind][identifier] == hypo[targ][identifier]):
# Overlapping or shared gene
if ((hypo[ind].get("contig_start") >=
hypo[targ].get("contig_start")
and hypo[ind].get("contig_start") <=
hypo[targ].get("contig_end"))
or (hypo[ind].get("contig_end") >=
hypo[targ].get("contig_start")
and hypo[ind].get("contig_end") <=
hypo[targ].get("contig_end"))
or (hypo[ind].get(identifier)
== hypo[targ].get(identifier))):
# Rightmost is worse
if float(hypo[ind].get("identity")) * (
1 - abs(1 - hypo[ind].get("span"))) > float(
hypo[targ].get("identity")) * (
1 - abs(1 - hypo[targ].get("span"))):
del hypo[targ]
ignore = True
# Leftmost is worse
elif float(hypo[ind].get("identity")) * (
1 - abs(1 - hypo[ind].get("span"))) < float(
hypo[targ].get("identity")) * (
1 - abs(1 - hypo[targ].get("span"))):
del hypo[ind]
targ = ind + 1
ignore = True
# Identical identity and span, seperating based on contig coverage
else:
# Rightmost is worse
if float(
hypo[ind].get("contig_coverage")) >= float(
hypo[targ].get("contig_coverage")):
del hypo[targ]
ignore = True
# Leftmost is worse
elif float(
hypo[ind].get("contig_coverage")) < float(
hypo[targ].get("contig_coverage")):
del hypo[ind]
targ = ind + 1
ignore = True
if not ignore:
targ += 1
else:
pass
ind += 1
self.logger.info(
"{} {} hits were added after removing overlaps and duplicate hits".
format(len(hypo), type))
for hit in hypo:
self.logger.debug("Kept {}:{} with span {} and id {}".format(
hit.get("loci"),
hit.get("allele"),
hit.get("span"),
hit.get("identity"),
))
self.db_pusher.add_rec(hit, "{}".format(type2db))
if type == "seq_type":
try:
ST = self.db_pusher.alleles2st(self.name)
self.db_pusher.upd_rec({"CG_ID_sample": self.name}, "Samples",
{"ST": ST})
self.logger.info("Sample {} received ST {}".format(
self.name, ST))
except Exception as e:
self.logger.warning(
"Unable to type sample {} due to data value '{}'".format(
self.name, str(e)))
def load_resistances(self):
"""Legacy function, loads common resistance names for genes from notes file"""
conversions = dict()
try:
with open("{}/notes.txt".format(
self.config["folders"]["resistances"])) as fh:
for line in fh:
if "#" not in line:
line = line.split(":")
cropped = re.sub(" resistance", "", line[1])
conversions[line[0]] = cropped
# Workaround for case issues
conversions[line[0].lower()] = cropped
except Exception as e:
self.logger.error(
"Unable to initialize trivial names for resistances ({})".
format(e))
return conversions
def scrape_alignment(self, file_list=[]):
"""Scrapes a single alignment result"""
if file_list == []:
file_list = glob.glob("{}/alignment/*.stats.*".format(
self.sampledir))
ins_list = list()
cov_dict = dict()
align_dict = dict()
align_dict["reference_genome"] = self.sample.get("reference")
# Reading
file_list = glob.glob("{}/alignment/*.stats.*".format(self.sampledir))
map_rate = 0.0
median_ins = 0
ref_len = 0.0
tot_reads = 0
tot_map = 0
duprate = 0.0
for file in file_list:
with open(file, "r") as fh:
type = file.split(".")[-1]
for line in fh.readlines():
lsplit = line.rstrip().split("\t")
if type == "raw":
try:
tot_reads = int(lsplit[0])
except Exception as e:
pass
elif type == "ins":
if len(lsplit) >= 18 and lsplit[-12] in ["FF", "FR"]:
try:
median_ins = int(lsplit[0])
except Exception as e:
pass
elif type == "cov":
cov_dict[lsplit[1]] = int(lsplit[2])
elif type == "ref":
if lsplit[0] != "*" and len(lsplit) >= 2:
ref_len = ref_len + int(lsplit[1])
elif type == "dup":
if lsplit[0] == "Unknown Library":
try:
duprate = float(lsplit[8])
except Exception as e:
duprate = -1.0
elif type == "map":
dsplit = line.rstrip().split(" ")
if len(dsplit) >= 5 and dsplit[4] == "total":
tot_map = int(dsplit[0])
elif len(dsplit) >= 4 and dsplit[3] == "mapped":
if tot_map > 0:
map_rate = int(dsplit[0]) / float(tot_map)
# Mangling
sumz, plus10, plus30, plus50, plus100, total = 0, 0, 0, 0, 0, 0
for k, v in cov_dict.items():
sumz += int(k) * v
total += v
if int(k) > 10:
plus10 += v
if int(k) > 30:
plus30 += v
if int(k) > 50:
plus50 += v
if int(k) > 100:
plus100 += v
if total > 0:
align_dict["coverage_10x"] = plus10 / float(ref_len)
align_dict["coverage_30x"] = plus30 / float(ref_len)
align_dict["coverage_50x"] = plus50 / float(ref_len)
align_dict["coverage_100x"] = plus100 / float(ref_len)
else:
align_dict["coverage_10x"] = 0.0
align_dict["coverage_30x"] = 0.0
align_dict["coverage_50x"] = 0.0
align_dict["coverage_100x"] = 0.0
align_dict["mapped_rate"] = map_rate
align_dict["insert_size"] = median_ins
if ref_len > 0:
align_dict["duplication_rate"] = duprate
align_dict["average_coverage"] = sumz / float(ref_len)
else:
align_dict["duplication_rate"] = 0.0
align_dict["average_coverage"] = 0.0
align_dict["total_reads"] = tot_reads
self.db_pusher.upd_rec({"CG_ID_sample": self.name}, "Samples",
align_dict)