def run_presto(input_file, output_dir, log=None, remove_tmp=True):
if log is None:
log = FakeLog()
mkdir_p(output_dir)
# gunzip
input_file_new = "%s/input_reads.fasta" % output_dir
fastx2fastx(input_file, input_file_new)
args = {"input_file": input_file_new, "output_dir": output_dir}
timer = Timer()
support.sys_call(
"CollapseSeq.py -s %(input_file)s --outdir %(output_dir)s --outname presto"
% args,
log=log)
timer.stamp(output_dir + "/time.txt")
presto_output = output_dir + "/presto_collapse-unique.fasta"
repertoire_fa = output_dir + "/final_repertoire.fa"
with smart_open(presto_output) as fin, smart_open(repertoire_fa,
"w") as fout:
for i, record in enumerate(
SeqIO.parse(fin, idFormatByFileName(presto_output))):
id = record.description
size = parse_presto_id(id)
record.id = record.description = "cluster___%d___size___%d" % (
i, size)
SeqIO.write(record, fout, "fasta")
if remove_tmp:
os.remove(input_file_new)
os.remove(presto_output)
def simulate_data(input_file, output_dir, log=None, **kwargs):
import tempfile
import shutil
if log is None:
log = FakeLog()
mkdir_p(output_dir)
temp_dir = tempfile.mkdtemp()
run_igrec(input_file, temp_dir, remove_tmp=False,
tau=1) # Run IgReC for VJF output
input_file = temp_dir + "/vj_finder/cleaned_reads.fa"
simulated_repertoire_to_rcm(input_file,
"%s/final_repertoire.rcm" % output_dir)
simulated_repertoire_to_final_repertoire(
input_file, "%s/final_repertoire.fa.gz" % output_dir)
args = {
"path": igrec_dir,
"repertoire": output_dir + "/final_repertoire.fa.gz",
"rcm": output_dir + "/final_repertoire.rcm"
}
support.sys_call(
"%(path)s/py/ig_compress_equal_clusters.py %(repertoire)s %(repertoire)s -r %(rcm)s"
% args,
log=log)
# TODO factor this stage
jit_fx_file(input_file, "%s/input_reads.fa.gz" % output_dir, **kwargs)
shutil.rmtree(temp_dir)
def simulate_data_from_dir(input_dir, output_dir, log=None, **kwargs):
if log is None:
log = FakeLog()
mkdir_p(output_dir)
jit_fx_file(input_dir + "/error_free_reads.fa.gz",
"%s/input_reads.fa.gz" % output_dir, **kwargs)
def run_mixcr2_alignment_only(input_file,
output_dir,
log=None,
loci="all",
enforce_fastq=False,
threads=16,
remove_tmp=True,
species="hsa"):
if log is None:
log = FakeLog()
mkdir_p(output_dir)
if enforce_fastq and idFormatByFileName(input_file) == "fasta":
input_file_fq = "%s/input_reads.fq" % output_dir
fastx2fastx(input_file, input_file_fq)
input_file = input_file_tmp = input_file_fq
elif idFormatByFileName(input_file) == "fasta":
input_file_fasta = "%s/input_reads.fasta" % output_dir
fastx2fastx(input_file, input_file_fasta)
input_file = input_file_tmp = input_file_fasta
else:
input_file_tmp = None
path = path_to_mixcr2
args = {
"path": path,
"compress_eq_clusters_cmd":
path_to_igrec + "/py/ig_compress_equal_clusters.py",
"mixcr_cmd": "java -jar %s/mixcr.jar" % path,
"threads": threads,
"input_file": input_file,
"output_dir": output_dir,
"species": species,
"loci": loci,
"loci_arg": "chains"
}
# support.sys_call("%(mixcr_cmd)s align -t %(threads)d -f -g -r %(output_dir)s/align_report.txt --%(loci_arg)s %(loci)s --noMerge --species %(species)s %(input_file)s %(output_dir)s/mixcr.vdjca" % args,
# log=log)
timer = Timer()
support.sys_call(
"%(mixcr_cmd)s align -p kaligner2 --species %(species)s -t %(threads)d -f -g -r %(output_dir)s/align_report.txt --noMerge --%(loci_arg)s %(loci)s -OreadsLayout=Collinear -OvParameters.geneFeatureToAlign=VTranscript -OallowPartialAlignments=true %(input_file)s %(output_dir)s/mixcr.vdjca"
% args,
log=log)
timer.stamp(output_dir + "/time.txt")
if remove_tmp:
if input_file_tmp is not None:
os.remove(input_file_tmp)
os.remove(output_dir + "/align_report.txt")
os.remove(output_dir + "/mixcr.vdjca")
def ref_free_plots(rep, name, dir):
if args.figure_format:
mkdir_p(dir)
rep.plot_distribution_of_errors_in_reads(
out=dir + "/%s_distribution_of_errors_in_reads" % name,
format=args.figure_format)
rep.plot_estimation_of_max_error_distribution(
out=dir + "/%s_max_error_scatter" % name,
format=args.figure_format)
if args.page_mode:
ymax = 0.041
else:
ymax = 0
for i in range(5):
cluster = rep.largest(i)
cluster.plot_profile(
out=dir + "/%s_cluster_discordance_profile_largest_%d" %
(name, i + 1),
format=args.figure_format,
ymax=ymax)
cluster.plot_profile(out=dir +
"/%s_cluster_error_profile_largest_%d" %
(name, i + 1),
discordance=False,
format=args.figure_format,
ymax=ymax)
rep.plot_profile(out=dir +
"/%s_cluster_discordance_profile" % name,
format=args.figure_format,
ymax=ymax)
rep.plot_profile(out=dir + "/%s_cluster_error_profile" % name,
discordance=False,
format=args.figure_format,
ymax=ymax)
if args.export_bad_clusters:
mkdir_p(dir)
rep.export_bad_clusters(out=dir + "/bad_%s_clusters/" % name)
rep.report(report, "%s_stats" % name)
def run_mixcr2(input_file,
output_dir,
log=None,
loci="all",
enforce_fastq=False,
threads=16,
remove_tmp=True,
species="hsa",
region_from="FR1Begin",
region_to="FR4Begin"):
if log is None:
log = FakeLog()
mkdir_p(output_dir)
if enforce_fastq and idFormatByFileName(input_file) == "fasta":
input_file_fq = "%s/input_reads.fq" % output_dir
fastx2fastx(input_file, input_file_fq)
input_file = input_file_tmp = input_file_fq
elif idFormatByFileName(input_file) == "fasta":
input_file_fasta = "%s/input_reads.fasta" % output_dir
fastx2fastx(input_file, input_file_fasta)
input_file = input_file_tmp = input_file_fasta
else:
input_file_tmp = None
path = path_to_mixcr2
args = {
"path": path,
"compress_eq_clusters_cmd":
path_to_igrec + "/py/ig_compress_equal_clusters.py",
"mixcr_cmd": "java -jar %s/mixcr.jar" % path,
"threads": threads,
"input_file": input_file,
"output_dir": output_dir,
"species": species,
"loci": loci,
"from": region_from,
"to": region_to,
"loci_arg": "chains"
}
# support.sys_call("%(mixcr_cmd)s align -t %(threads)d -f -g -r %(output_dir)s/align_report.txt --%(loci_arg)s %(loci)s --noMerge --species %(species)s %(input_file)s %(output_dir)s/mixcr.vdjca" % args,
timer = Timer()
# log=log)
support.sys_call(
"%(mixcr_cmd)s align -p kaligner2 --species %(species)s -t %(threads)d -f -g -r %(output_dir)s/align_report.txt --noMerge --%(loci_arg)s %(loci)s -OreadsLayout=Collinear -OvParameters.geneFeatureToAlign=VTranscript -OallowPartialAlignments=true %(input_file)s %(output_dir)s/mixcr.vdjca"
% args,
log=log)
# support.sys_call("%(mixcr_cmd)s assemble -p default_affine -OassemblingFeatures=VDJRegion -OseparateByC=true -OqualityAggregationType=Average -OclusteringFilter.specificMutationProbability=1E-5 -OmaxBadPointsPercent=0 -t %(threads)d -r %(output_dir)s/assemble_report.txt --index %(output_dir)s/index_file %(output_dir)s/mixcr.vdjca %(output_dir)s/mixcr.clns" % args,
# support.sys_call("%(mixcr_cmd)s assemble -f -p default_affine -OassemblingFeatures=VDJRegion -OseparateByC=true -OqualityAggregationType=Average -OclusteringFilter.specificMutationProbability=1E-5 -OmaxBadPointsPercent=0 -r %(output_dir)s/assemble_report.txt --index %(output_dir)s/index_file %(output_dir)s/mixcr.vdjca %(output_dir)s/mixcr.clns" % args,
# log=log)
# support.sys_call("%(mixcr_cmd)s assemble -t %(threads)d -f -r %(output_dir)s/assemble_report.txt --index %(output_dir)s/index_file %(output_dir)s/mixcr.vdjca %(output_dir)s/mixcr.clns" % args,
# log=log)
support.sys_call(
"%(mixcr_cmd)s assemble -t %(threads)d -f -r %(output_dir)s/assemble_report.txt --index %(output_dir)s/index_file -OassemblingFeatures=\"{%(from)s:%(to)s}\" %(output_dir)s/mixcr.vdjca %(output_dir)s/mixcr.clns"
% args,
log=log)
args[
"small_features"] = "-sequence -count -readIds %(output_dir)s/index_file" % args
support.sys_call(
"%(mixcr_cmd)s exportClones %(small_features)s -f --no-spaces %(output_dir)s/mixcr.clns %(output_dir)s/mixcr.txt"
% args,
log=log)
timer.stamp(output_dir + "/time.txt")
args[
"features"] = "-count -sequence -nFeature CDR3 -vHit -jHit -vAlignment -jAlignment -aaFeature CDR3 -readIds %(output_dir)s/index_file" % args
support.sys_call(
"%(mixcr_cmd)s exportClones %(features)s -f --no-spaces %(output_dir)s/mixcr.clns %(output_dir)s/features.txt"
% args,
log=log)
# convert_mixcr_output_to_igrec("%(output_dir)s/mixcr.txt" % args, "%(output_dir)s/mixcr_uncompressed.fa" % args)
convert_mixcr2_output_to_igrec(
"%(output_dir)s/mixcr.txt" % args,
"%(output_dir)s/mixcr_uncompressed.fa" % args, input_file,
"%(output_dir)s/mixcr_uncompressed.rcm" % args)
support.sys_call(
"%(compress_eq_clusters_cmd)s %(output_dir)s/mixcr_uncompressed.fa %(output_dir)s/final_repertoire.fa -r %(output_dir)s/mixcr_uncompressed.rcm -R %(output_dir)s/final_repertoire.rcm"
% args)
if remove_tmp:
if input_file_tmp is not None:
os.remove(input_file_tmp)
os.remove(output_dir + "/align_report.txt")
os.remove(output_dir + "/assemble_report.txt")
os.remove(output_dir + "/mixcr.clns")
os.remove(output_dir + "/mixcr.txt")
os.remove(output_dir + "/features.txt")
os.remove(output_dir + "/mixcr.vdjca")
os.remove(output_dir + "/mixcr_uncompressed.fa")
os.remove(output_dir + "/mixcr_uncompressed.rcm")
os.remove(output_dir + "/index_file")
def run_mixcr(input_file,
output_dir,
log=None,
loci="all",
enforce_fastq=False,
threads=16,
remove_tmp=True,
species="hsa",
version=1):
if log is None:
log = FakeLog()
mkdir_p(output_dir)
if enforce_fastq and idFormatByFileName(input_file) == "fasta":
input_file_fq = "%s/input_reads.fq" % output_dir
fastx2fastx(input_file, input_file_fq)
input_file = input_file_tmp = input_file_fq
elif idFormatByFileName(input_file) == "fasta":
input_file_fasta = "%s/input_reads.fasta" % output_dir
fastx2fastx(input_file, input_file_fasta)
input_file = input_file_tmp = input_file_fasta
else:
input_file_tmp = None
path = path_to_mixcr if version == 1 else path_to_mixcr2
args = {
"path": path,
"compress_eq_clusters_cmd":
path_to_igrec + "/py/ig_compress_equal_clusters.py",
"mixcr_cmd": "java -jar %s/mixcr.jar" % path,
"threads": threads,
"input_file": input_file,
"output_dir": output_dir,
"species": species,
"loci": loci,
"loci_arg": "loci" if version == 1 else "chains"
}
timer = Timer()
support.sys_call(
"%(mixcr_cmd)s align -t %(threads)d -f -g -r %(output_dir)s/align_report.txt --%(loci_arg)s %(loci)s --noMerge -OvParameters.geneFeatureToAlign=VTranscript --species %(species)s %(input_file)s %(output_dir)s/mixcr.vdjca"
% args,
log=log)
support.sys_call(
"%(mixcr_cmd)s assemble -t %(threads)d -f -r %(output_dir)s/assemble_report.txt -OassemblingFeatures=\"{FR1Begin:FR4Begin}\" %(output_dir)s/mixcr.vdjca %(output_dir)s/mixcr.clns"
% args,
log=log)
support.sys_call(
"%(mixcr_cmd)s exportClones -sequence -count -f --no-spaces %(output_dir)s/mixcr.clns %(output_dir)s/mixcr.txt"
% args,
log=log)
timer.stamp(output_dir + "/time.txt")
args[
"features"] = "-count -sequence -nFeature CDR3 -vHit -jHit -vAlignment -jAlignment -aaFeature CDR3"
support.sys_call(
"%(mixcr_cmd)s exportClones %(features)s -f --no-spaces %(output_dir)s/mixcr.clns %(output_dir)s/features.txt"
% args,
log=log)
convert_mixcr_output_to_igrec(
"%(output_dir)s/mixcr.txt" % args,
"%(output_dir)s/mixcr_uncompressed.fa" % args)
support.sys_call(
"%(compress_eq_clusters_cmd)s %(output_dir)s/mixcr_uncompressed.fa %(output_dir)s/final_repertoire.fa"
% args)
if remove_tmp:
if input_file_tmp is not None:
os.remove(input_file_tmp)
os.remove(output_dir + "/mixcr.clns")
os.remove(output_dir + "/mixcr.txt")
os.remove(output_dir + "/mixcr.vdjca")
os.remove(output_dir + "/mixcr_uncompressed.fa")
def main(args):
if args.reconstruct:
if args.initial_reads and args.constructed_repertoire and not args.constructed_rcm:
log.info("Try to reconstruct repertoire RCM file...")
rcm = reconstruct_rcm(args.initial_reads,
args.constructed_repertoire,
threads=args.threads)
args.constructed_rcm = args.output_dir + "/constructed.rcm"
write_rcm(rcm, args.constructed_rcm)
if args.initial_reads and not args.constructed_repertoire and args.constructed_rcm:
log.info("Try to reconstruct repertoire sequence file...")
args.constructed_repertoire = args.output_dir + "/constructed.fa.gz"
run_consensus_constructor(rcm_file=args.constructed_rcm,
initial_reads=args.initial_reads,
output_file=args.constructed_repertoire,
threads=args.threads)
if args.initial_reads and args.reference_repertoire and not args.reference_rcm and args.rcm_based:
log.info("Try to reconstruct reference RCM file...")
rcm = reconstruct_rcm(args.initial_reads,
args.reference_repertoire,
threads=args.threads)
args.reference_rcm = args.output_dir + "/reference.rcm"
write_rcm(rcm, args.reference_rcm)
if args.initial_reads and not args.reference_repertoire and args.reference_rcm and args.rcm_based:
log.info(
"Try to reconstruct reference repertoire sequence file...")
args.reference_repertoire = args.output_dir + "/reference.fa.gz"
run_consensus_constructor(rcm_file=args.reference_rcm,
initial_reads=args.initial_reads,
output_file=args.reference_repertoire,
threads=args.threads)
if args.initial_reads and args.constructed_repertoire and args.constructed_rcm and args.rcm_based:
rep = Repertoire(args.constructed_rcm, args.initial_reads,
args.constructed_repertoire)
report = Report()
report.min_size = args.reference_size_cutoff
def ref_free_plots(rep, name, dir):
if args.figure_format:
mkdir_p(dir)
rep.plot_distribution_of_errors_in_reads(
out=dir + "/%s_distribution_of_errors_in_reads" % name,
format=args.figure_format)
rep.plot_estimation_of_max_error_distribution(
out=dir + "/%s_max_error_scatter" % name,
format=args.figure_format)
if args.page_mode:
ymax = 0.041
else:
ymax = 0
for i in range(5):
cluster = rep.largest(i)
cluster.plot_profile(
out=dir + "/%s_cluster_discordance_profile_largest_%d" %
(name, i + 1),
format=args.figure_format,
ymax=ymax)
cluster.plot_profile(out=dir +
"/%s_cluster_error_profile_largest_%d" %
(name, i + 1),
discordance=False,
format=args.figure_format,
ymax=ymax)
rep.plot_profile(out=dir +
"/%s_cluster_discordance_profile" % name,
format=args.figure_format,
ymax=ymax)
rep.plot_profile(out=dir + "/%s_cluster_error_profile" % name,
discordance=False,
format=args.figure_format,
ymax=ymax)
if args.export_bad_clusters:
mkdir_p(dir)
rep.export_bad_clusters(out=dir + "/bad_%s_clusters/" % name)
rep.report(report, "%s_stats" % name)
if args.initial_reads and args.constructed_repertoire and args.constructed_rcm and args.reference_free:
ref_free_plots(rep, "constructed", args.reference_free_dir)
if args.initial_reads and args.reference_repertoire and args.reference_rcm and args.reference_free:
rep_ideal = Repertoire(args.reference_rcm, args.initial_reads,
args.reference_repertoire)
ref_free_plots(rep_ideal, "reference", args.reference_free_dir)
if args.constructed_repertoire and args.reference_repertoire:
res = RepertoireMatch(
args.constructed_repertoire,
args.reference_repertoire,
tmp_file=None,
max_tau=args.tau,
reference_trash_cutoff=args.reference_trash_cutoff,
reference_trust_cutoff=args.reference_trust_cutoff,
log=log,
threads=args.threads)
res.report(report)
if args.figure_format:
mkdir_p(args.reference_based_dir)
for size in [1, 3, 5, 10]:
res.plot_sensitivity_precision(
what="ref2cons",
out=args.reference_based_dir +
"/reference_to_constructed_distance_distribution_size_%d" %
size,
size=size,
differential=True,
format=args.figure_format)
res.plot_sensitivity_precision(
what="cons2ref",
out=args.reference_based_dir +
"/constructed_to_reference_distance_distribution_size_%d" %
size,
size=size,
differential=True,
format=args.figure_format)
res.plot_octoplot(out=args.reference_based_dir +
"/distance_distribution",
format=args.figure_format)
res.plot_min_cluster_size_choose(out=args.reference_based_dir +
"/sensitivity_precision",
format=args.figure_format)
res.plot_error_pos_dist(out=args.reference_based_dir +
"/error_position_distribution",
format=args.figure_format)
res.plot_reference_vs_constructed_size(
out=args.reference_based_dir +
"/cluster_abundances_scatterplot",
format=args.figure_format,
marginals=False)
if args.experimental:
res.plot_reference_vs_constructed_size(
out=args.reference_based_dir +
"/cluster_abundances_scatterplot_hexes",
points=False,
format=args.figure_format,
marginals=False)
res.plot_multiplicity_distributions(out=args.reference_based_dir +
"/abundance_distributions_log",
ylog=True,
format=args.figure_format)
res.plot_multiplicity_distributions(out=args.reference_based_dir +
"/abundance_distributions",
ylog=False,
format=args.figure_format)
if args.constructed_rcm and args.reference_rcm and args.partition_based:
rcm2rcm = RcmVsRcm(args.constructed_rcm, args.reference_rcm)
rcm2rcm.report(report, "rcm_stats_all_clusters")
size = args.reference_size_cutoff
rcm2rcm_large = rcm2rcm.prune_copy(size, 1)
rcm2rcm_large.report(report)
if args.figure_format:
mkdir_p(args.reference_based_dir)
if args.page_mode:
ymax = 17000
else:
ymax = 0
rcm2rcm.plot_purity_distribution(
out=args.reference_based_dir +
"/constructed_purity_distribution",
format=args.figure_format,
ymax=ymax)
rcm2rcm.plot_discordance_distribution(
out=args.reference_based_dir +
"/constructed_discordance_distribution",
format=args.figure_format,
ymax=ymax)
if args.experimental:
rcm2rcm.plot_purity_distribution(
out=args.reference_based_dir +
"/constructed_purity_distribution_ylog",
format=args.figure_format,
ylog=True,
ymax=ymax)
rcm2rcm.plot_discordance_distribution(
out=args.reference_based_dir +
"/constructed_discordance_distribution_ylog",
format=args.figure_format,
ylog=True,
ymax=ymax)
rcm2rcm.plot_purity_distribution(out=args.reference_based_dir +
"/reference_purity_distribution",
format=args.figure_format,
constructed=False,
ymax=ymax)
rcm2rcm.plot_discordance_distribution(
out=args.reference_based_dir +
"/reference_discordance_distribution",
format=args.figure_format,
constructed=False,
ymax=ymax)
if args.experimental:
rcm2rcm.plot_purity_distribution(
out=args.reference_based_dir +
"/reference_purity_distribution_ylog",
format=args.figure_format,
constructed=False,
ylog=True,
ymax=ymax)
rcm2rcm.plot_discordance_distribution(
out=args.reference_based_dir +
"/reference_discordance_distribution_ylog",
format=args.figure_format,
constructed=False,
ylog=True,
ymax=ymax)
rcm2rcm_large.plot_purity_distribution(
out=args.reference_based_dir +
"/constructed_purity_distribution_large",
format=args.figure_format,
ymax=ymax)
rcm2rcm_large.plot_discordance_distribution(
out=args.reference_based_dir +
"/constructed_discordance_distribution_large",
format=args.figure_format,
ymax=ymax)
if args.experimental:
rcm2rcm_large.plot_purity_distribution(
out=args.reference_based_dir +
"/constructed_purity_distribution_large_ylog",
format=args.figure_format,
ylog=True,
ymax=ymax)
rcm2rcm_large.plot_discordance_distribution(
out=args.reference_based_dir +
"/constructed_discordance_distribution_large_ylog",
format=args.figure_format,
ylog=True,
ymax=ymax)
rcm2rcm_large.plot_purity_distribution(
out=args.reference_based_dir +
"/reference_purity_distribution_large",
format=args.figure_format,
constructed=False,
ymax=ymax)
rcm2rcm_large.plot_discordance_distribution(
out=args.reference_based_dir +
"/reference_discordance_distribution_large",
format=args.figure_format,
constructed=False,
ymax=ymax)
if args.experimental:
rcm2rcm_large.plot_discordance_distribution(
out=args.reference_based_dir +
"/reference_discordance_distribution_large_ylog",
format=args.figure_format,
constructed=False,
ylog=True,
ymax=ymax)
rcm2rcm_large.plot_purity_distribution(
out=args.reference_based_dir +
"/reference_purity_distribution_large_ylog",
format=args.figure_format,
constructed=False,
ylog=True,
ymax=ymax)
if args.experimental:
rcm2rcm.plot_majority_secondary(
out=args.reference_based_dir +
"/constructed_majority_secondary",
format=args.figure_format)
rcm2rcm.plot_size_nomajority(out=args.reference_based_dir +
"/constructed_size_nomajority",
format=args.figure_format)
rcm2rcm.plot_majority_secondary(
out=args.reference_based_dir +
"/reference_majority_secondary",
format=args.figure_format,
constructed=False)
rcm2rcm.plot_size_nomajority(out=args.reference_based_dir +
"/reference_size_nomajority",
format=args.figure_format,
constructed=False)
rcm2rcm_large.plot_majority_secondary(
out=args.reference_based_dir +
"/constructed_majority_secondary_large",
format=args.figure_format)
rcm2rcm_large.plot_size_nomajority(
out=args.reference_based_dir +
"/constructed_size_nomajority_large",
format=args.figure_format)
rcm2rcm_large.plot_majority_secondary(
out=args.reference_based_dir +
"/reference_majority_secondary_large",
format=args.figure_format,
constructed=False)
rcm2rcm_large.plot_size_nomajority(
out=args.reference_based_dir +
"/reference_size_nomajority_large",
format=args.figure_format,
constructed=False)
if args.constructed_rcm and args.reference_rcm and args.constructed_repertoire and args.reference_repertoire and args.experimental:
splittering(rcm2rcm, rep, args, report)
log.info(report)
if args.text:
report.toText(args.text)
if args.json:
report.toJson(args.json)
if args.text:
report.toText(args.text)
if args.json:
report.toJson(args.json)
def SupportInfo(log):
log.info("\nIn case you have troubles running IgQUAST, "
"you can write to [email protected].")
log.info("Please provide us igquast.log file from the output directory.")
if __name__ == "__main__":
args = parse_command_line()
mkdir_p(args.output_dir)
log = CreateLogger("IgQUAST")
if args.log:
AttachFileLogger(log, args.log)
try:
log.info("Command line: %s" % " ".join(sys.argv))
main(args)
log.info("\nThank you for using IgQUAST!")
except (KeyboardInterrupt):
log.info("\nIgQUAST has been interrupted!")
except Exception:
exc_type, exc_value, _ = sys.exc_info()
if exc_type == SystemExit:
sys.exit(exc_value)
else:
param['organism'] = item['Content']
elif name == 'Input.app-session-name':
param['AppSessionName'] = item['Content']
elif name == 'Input.min-cluster-size':
param["min-cluster-size"] = safe_cast(item['Content'], int, 5)
elif name == 'Input.min-fillin':
param["min-fillin"] = safe_cast(item['Content'], float, 0.6)
elif name == 'Input.additionalfiles':
param["additionalfiles"] = "save" in item['Items']
elif name == 'Input.pseudogenes':
param["pseudogenes"] = "pseudogenes" in item['Items']
elif name == 'Input.Projects':
projectID = item['Items'][0]['Id']
param['outdir'] = '/data/output/appresults/%s/%s' % (projectID, "IgReC")
mkdir_p(param['outdir'])
igrec_path = os.path.join(igrec_dir, "igrec.py")
if param['readtype'] == "merged":
command = '%s -s "%s" ' % (igrec_path, param["reads"])
elif param['readtype'] == "paired":
command = '%s -1 "%s" -2 "%s" ' % (igrec_path, param["reads"][0], param["reads"][1])
else:
sys.exit(1)
command += ' --tau=%(tau)d --loci=%(loci)s -o "%(outdir)s" --threads=%(threads)d --min-cluster-size=%(min-cluster-size)d --min-fillin=%(min-fillin)f' % param
if not param["pseudogenes"]:
command += " --no-pseudogenes"
if param["additionalfiles"]:
command += " --debug"