def _run_fastqc(global_config, sample_config, sorted_libraries_by_insert):
mainDir = os.getcwd()
FastqcFolder = os.path.join(os.getcwd(), "fastqc")
if not os.path.exists(FastqcFolder):
os.makedirs(FastqcFolder)
program = global_config["Tools"]["fastqc"]["bin"]
program_options = global_config["Tools"]["fastqc"]["options"]
for library, libraryInfo in sorted_libraries_by_insert:
command = [program]
for option in program_options:
command.append(option)
read1 = libraryInfo["pair1"]
read2 = libraryInfo["pair2"]
command.append(read1)
if read2 is not None:
command.append(read2)
common.print_command(command)
folder_output_name = os.path.join(
FastqcFolder,
os.path.basename(read1).split(".fastq.gz")[0])
if not common.check_dryrun(sample_config) and not os.path.exists(
"{}_fastqc.zip".format(folder_output_name)):
fastq_stdOut = open(
os.path.join(FastqcFolder, "{}_fastqc.stdout".format(library)),
"a")
fastq_stdErr = open(
os.path.join(FastqcFolder, "{}_fastqc.stderr".format(library)),
"a")
subprocess.call(command, stdout=fastq_stdOut, stderr=fastq_stdErr)
sample_config["fastqc"] = FastqcFolder
return sample_config
def _run_qaTools(global_config, sample_config, sorted_libraries_by_insert):
mainDir = os.getcwd()
qaToolsFolder = os.path.join(os.getcwd(), "QAstats")
if not os.path.exists(qaToolsFolder):
os.makedirs(qaToolsFolder)
os.chdir("QAstats")
program=global_config["Tools"]["qaTools"]["bin"]
genomeSize = sample_config["genomeSize"]
reference = sample_config["reference"]
output = sample_config["output"]
alignments = sample_config["alignments"][0]
BAMfile = alignments[1]
command = ["{}".format(program), "-m", "-q", "0", "-i", BAMfile, "{}.cov".format(os.path.basename(BAMfile))]
common.print_command(command)
if not common.check_dryrun(sample_config) and not os.path.exists("{}.cov".format(os.path.basename(BAMfile))):
stdOut = open("QAtools.stdOut", "a")
stdErr = open("QAtools.stdErr", "a")
returnValue = subprocess.call(command , stdout=stdOut , stderr=stdErr)
if not returnValue == 0:
sys.exit("error, while running QAtools: {}".format(command))
#now add GC content
QAtools_dict = {}
header = ""
with open( "{}.cov".format(os.path.basename(BAMfile)), "r") as QA_csv:
header = QA_csv.readline().rstrip()
for line in QA_csv:
line = line.strip().split("\t")
QAtools_dict[line[0]] = [line[1],line[2],line[3]]
QA_GC_file = "{}.cov.gc".format(os.path.basename(BAMfile))
with open(QA_GC_file, "w") as QA_GC_fd:
QA_GC_fd.write("{}\tGCperc\n".format(header))
with open(reference, "r") as ref_fd:
fasta_raw_header = ref_fd.readline().strip()
fasta_raw_header = fasta_raw_header.split(" ")[0]
fasta_raw_header = fasta_raw_header.split("\t")[0]
fasta_header = fasta_raw_header.split(">")[1]
sequence = ""
for line in ref_fd:
line = line.strip()
if line.startswith(">"):
GC = computeGC(sequence)
if fasta_header not in QAtools_dict:
sys.exit("error while parsing QAcompute output: probably some wired contig name is present in your assmebly file")
QA_GC_fd.write("{}\t{}\t{}\t{}\t{}\n".format(fasta_header, QAtools_dict[fasta_header][0], QAtools_dict[fasta_header][1], QAtools_dict[fasta_header][2], GC ))
sequence = ""
fasta_raw_header = line.split(" ")[0]
fasta_raw_header = fasta_raw_header.split("\t")[0]
fasta_header = fasta_raw_header.split(">")[1]
else:
sequence+=line
GC = computeGC(sequence)
if fasta_header not in QAtools_dict:
sys.exit("error while parsing QAcompute output: probably some wired contig name is present in your assmebly file")
QA_GC_fd.write("{}\t{}\t{}\t{}\t{}\n".format(fasta_header, QAtools_dict[fasta_header][0], QAtools_dict[fasta_header][1], QAtools_dict[fasta_header][2], GC ))
plotQA(QA_GC_file)
os.chdir("..")
return sample_config
def _run_fastqc(global_config, sample_config, sorted_libraries_by_insert):
mainDir = os.getcwd()
FastqcFolder = os.path.join(os.getcwd(), "fastqc")
if not os.path.exists(FastqcFolder):
os.makedirs(FastqcFolder)
program=global_config["Tools"]["fastqc"]["bin"]
program_options=global_config["Tools"]["fastqc"]["options"]
for library, libraryInfo in sorted_libraries_by_insert:
command = [program]
for option in program_options:
command.append(option)
read1=libraryInfo["pair1"]
read2=libraryInfo["pair2"]
command.append(read1)
if read2 is not None:
command.append(read2)
common.print_command(command)
folder_output_name = os.path.join(FastqcFolder, os.path.basename(read1).split(".fastq.gz")[0])
if not common.check_dryrun(sample_config) and not os.path.exists("{}_fastqc.zip".format(folder_output_name)):
fastq_stdOut = open(os.path.join(FastqcFolder , "{}_fastqc.stdout".format(library)), "a")
fastq_stdErr = open(os.path.join(FastqcFolder , "{}_fastqc.stderr".format(library)), "a")
subprocess.call(command, stdout=fastq_stdOut, stderr=fastq_stdErr)
sample_config["fastqc"] = FastqcFolder
return sample_config
def _run_FRC(global_config, sample_config, sorted_libraries_by_insert):
mainDir = os.getcwd()
FRCurveFolder = os.path.join(os.getcwd(), "FRCurve")
if not os.path.exists(FRCurveFolder):
os.makedirs(FRCurveFolder)
os.chdir("FRCurve")
program=global_config["Tools"]["FRC"]["bin"]
genomeSize = sample_config["genomeSize"]
reference = sample_config["reference"]
output = sample_config["output"]
alignments = sample_config["alignments"]
peBam = alignments[0][1]
peInsert = alignments[0][0]
peMinInsert = int(peInsert - peInsert*0.60)
peMaxInsert = int(peInsert + peInsert*0.60)
command = [program, "--pe-sam", peBam, "--pe-min-insert", "{}".format(peMinInsert) , "--pe-max-insert", "{}".format(peMaxInsert), "--CEstats-PE-min", "-4", "--CEstats-PE-max", "4"]
if len(alignments) > 1:
mpBam = alignments[1][1]
mpInsert = alignments[1][0]
mpMinInsert = int(mpInsert - mpInsert*0.50)
mpMaxInsert = int(mpInsert + mpInsert*0.50)
command += ["--mp-sam", mpBam, "--mp-min-insert", "{}".format(mpMinInsert), "--mp-max-insert", "{}".format(mpMaxInsert)]
command += [ "--genome-size", "{}".format(genomeSize), "--output", output]
common.print_command(command)
if not common.check_dryrun(sample_config) and not os.path.exists("{}_FRC.png".format(output)):
stdOut = open("FRC.stdOut", "a")
stdErr = open("FRC.stdErr", "a")
returnValue = subprocess.call(command , stdout=stdOut , stderr=stdErr)
if not returnValue == 0:
sys.exit("error, while running FRCurve: {}".format(command))
plotFRCurve(output)
os.chdir("..")
return sample_config
def _run_abyss(global_config, sample_config, sorted_libraries_by_insert):
mainDir = os.getcwd()
ABySS_Kmer_Folder = os.path.join(os.getcwd(), "abyss_kmer")
if "kmer" not in sample_config:
sys.exit(
"error in _run_abyss QCcontrol: kmer must be present in sample_config.yaml"
)
kmer = sample_config["kmer"]
if not os.path.exists(ABySS_Kmer_Folder):
os.makedirs(ABySS_Kmer_Folder)
os.chdir(ABySS_Kmer_Folder)
program = global_config["Tools"]["abyss"]["bin"]
program = os.path.join(os.path.dirname(program), "ABYSS-P")
program_options = global_config["Tools"]["abyss"]["options"]
if "abyss" in sample_config:
program_options = sample_config["abyss"]
threads = 16 # default for UPPMAX
if "threads" in sample_config:
threads = sample_config["threads"]
command = "mpirun -np {} {} ".format(threads, program)
command += "-k {} ".format(kmer)
command += "--coverage-hist=histogram.hist -o preUnitgs.fa"
for library, libraryInfo in sorted_libraries_by_insert:
read1 = libraryInfo["pair1"]
read2 = libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
if orientation == "innie" or orientation == "outtie":
command += " {} ".format(read1)
if read2 is not None:
command += " {} ".format(read2)
if orientation == "none":
command += " {} ".format(read1)
common.print_command(command)
if not common.check_dryrun(sample_config) and not os.path.exists(
"histogram.hist"):
ABySS_Kmer_stdOut = open("ABySS_Kmer_Folder.stdOut", "a")
ABySS_Kmer_stdErr = open("ABySS_Kmer_Folder.stdErr", "a")
returnValue = subprocess.call(command,
shell=True,
stdout=ABySS_Kmer_stdOut,
stderr=ABySS_Kmer_stdErr)
if returnValue > 0:
print "ABySS kmer plotting failed: unkwnown reason"
else:
subprocess.call(("rm", "preUnitgs.fa"))
_plotKmerPlot(1, 200, kmer, "kmer_coverage_1_200.png")
_plotKmerPlot(1, 500, kmer, "kmer_coverage_1_500.png")
_plotKmerPlot(15, 200, kmer, "kmer_coverage_15_200.png")
_plotKmerPlot(15, 500, kmer, "kmer_coverage_15_500.png")
os.chdir("..")
sample_config["abyss"] = ABySS_Kmer_Folder
return sample_config
def _run_abyss(global_config, sample_config, sorted_libraries_by_insert):
mainDir = os.getcwd()
ABySS_Kmer_Folder = os.path.join(os.getcwd(), "abyss_kmer")
if "kmer" not in sample_config:
sys.exit("error in _run_abyss QCcontrol: kmer must be present in sample_config.yaml")
kmer = sample_config["kmer"]
if not os.path.exists(ABySS_Kmer_Folder):
os.makedirs(ABySS_Kmer_Folder)
os.chdir(ABySS_Kmer_Folder)
program = global_config["Tools"]["abyss"]["bin"]
program = os.path.join(os.path.dirname(program), "ABYSS-P")
program_options=global_config["Tools"]["abyss"]["options"]
if "abyss" in sample_config:
program_options=sample_config["abyss"]
threads = 16 # default for UPPMAX
if "threads" in sample_config :
threads = sample_config["threads"]
command = "mpirun -np {} {} ".format(threads, program)
command += "-k {} ".format(kmer)
command += "--coverage-hist=histogram.hist -o preUnitgs.fa"
for library, libraryInfo in sorted_libraries_by_insert:
read1=libraryInfo["pair1"]
read2=libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
if orientation=="innie" or orientation=="outtie":
command += " {} ".format(read1)
if read2 is not None:
command += " {} ".format(read2)
if orientation == "none":
command += " {} ".format(read1)
common.print_command(command)
if not common.check_dryrun(sample_config) and not os.path.exists("histogram.hist"):
ABySS_Kmer_stdOut = open("ABySS_Kmer_Folder.stdOut", "a")
ABySS_Kmer_stdErr = open("ABySS_Kmer_Folder.stdErr", "a")
returnValue = subprocess.call(command, shell=True, stdout=ABySS_Kmer_stdOut, stderr=ABySS_Kmer_stdErr)
if returnValue > 0:
print "ABySS kmer plotting failed: unkwnown reason"
else :
subprocess.call(("rm", "preUnitgs.fa"))
_plotKmerPlot(1,200, kmer, "kmer_coverage_1_200.png")
_plotKmerPlot(1,500, kmer, "kmer_coverage_1_500.png")
_plotKmerPlot(15,200, kmer, "kmer_coverage_15_200.png")
_plotKmerPlot(15,500, kmer, "kmer_coverage_15_500.png")
os.chdir("..")
sample_config["abyss"] = ABySS_Kmer_Folder
return sample_config
def main(args):
with open(args.global_config) as in_handle:
global_config = yaml.load(in_handle)
with open(args.sample_config) as sample_config_handle:
sample_config = yaml.load(sample_config_handle)
check_consistency(global_config,sample_config)
if common.check_dryrun(sample_config):
print "Option dryrun idenitfied: commands will only be printed, not executed"
if sample_config["pipeline"] in global_config["Pipelines"]:
run_analys(global_config, sample_config)
else:
sys.exit("Error: pipeline {} is not one of the supported ones:{}".format(sample_config["pipeline"], global_config["Pipelines"]))
return 0
def _run_trimmomatic(global_config, sample_config, sorted_libraries_by_insert):
program = global_config["Tools"]["trimmomatic"]["bin"]
program_folder = os.path.dirname(program)
if "adapters" not in sample_config:
sys.exit("running MP pipeline, adapters file to be used in trimming are needed for Trimmomatic. Please specify them\
in the sample configuration file and rerun")
adapterFile = sample_config["adapters"]
if not os.path.exists(adapterFile):
sys.exit("Trimmomatic cannot be run as adapter file is not specified or points to unknown position: {}".format(adapterFile))
mainDirectory = os.getcwd()
trimmomaticDir = os.path.join(mainDirectory, "Trimmomatic")
if not os.path.exists(trimmomaticDir):
os.makedirs(trimmomaticDir)
os.chdir(trimmomaticDir)
#now I am in running dir, I need to process one by one the libraries
threads = 8
if "threads" in sample_config:
threads = sample_config["threads"]
for library, libraryInfo in sorted_libraries_by_insert:
read1=libraryInfo["pair1"]
read2=libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
if read2 is not None:
read1_baseName = os.path.split(read1)[1].split(".")[0]
read2_baseName = os.path.split(read2)[1].split(".")[0]
output_read1_pair = os.path.join(trimmomaticDir, "{}.fastq.gz".format(read1_baseName))
output_read1_sing = os.path.join(trimmomaticDir, "{}_u.fastq.gz".format(read1_baseName))
output_read2_pair = os.path.join(trimmomaticDir, "{}.fastq.gz".format(read2_baseName))
output_read2_sing = os.path.join(trimmomaticDir, "{}_u.fastq.gz".format(read2_baseName))
command = ["java", "-jar", program, "PE", "-threads", "{}".format(threads), "-phred33", read1, read2, output_read1_pair ,output_read1_sing , output_read2_pair, output_read2_sing ,"ILLUMINACLIP:{}:2:30:10".format(adapterFile), "LEADING:3", "TRAILING:3", "SLIDINGWINDOW:4:15", "MINLEN:30" ]
common.print_command(command)
if not common.check_dryrun(sample_config) and not os.path.exists(output_read1_pair): # do not execute is files have been already gennerated
stdOut = open("{}_trimmomatic.stdOut".format(read1_baseName), "w")
stdErr = open("{}_trimmomatic.stdErr".format(read1_baseName), "w")
returnValue = subprocess.call(command, stdout=stdOut, stderr=stdErr) # run the program
if returnValue != 0:
print "error while running command: {}".format(command)
libraryInfo["pair1"] = output_read1_pair
libraryInfo["pair2"] = output_read2_pair
libraryInfo["trimmomatic"] = os.path.join(trimmomaticDir, "{}_trimmomatic.stdErr".format(read1_baseName))
os.chdir(mainDirectory)
return sample_config
def _run_FRC(global_config, sample_config, sorted_libraries_by_insert):
mainDir = os.getcwd()
FRCurveFolder = os.path.join(os.getcwd(), "FRCurve")
if not os.path.exists(FRCurveFolder):
os.makedirs(FRCurveFolder)
os.chdir("FRCurve")
program = global_config["Tools"]["FRC"]["bin"]
genomeSize = sample_config["genomeSize"]
reference = sample_config["reference"]
output = sample_config["output"]
alignments = sample_config["alignments"]
peBam = alignments[0][1]
peInsert = alignments[0][0]
peMinInsert = int(peInsert - peInsert * 0.60)
peMaxInsert = int(peInsert + peInsert * 0.60)
#command = [program, "--pe-sam", peBam, "--pe-min-insert", "{}".format(peMinInsert) , "--pe-max-insert", "{}".format(peMaxInsert), "--CEstats-PE-min", "-4", "--CEstats-PE-max", "4"]
command = [program, "--pe-sam", peBam, "--pe-max-insert", "5000"]
if len(alignments) > 1:
mpBam = alignments[1][1]
mpInsert = alignments[1][0]
mpMinInsert = int(mpInsert - mpInsert * 0.50)
mpMaxInsert = int(mpInsert + mpInsert * 0.50)
#command += ["--mp-sam", mpBam, "--mp-min-insert", "{}".format(mpMinInsert), "--mp-max-insert", "{}".format(mpMaxInsert)]
command += ["--mp-sam", mpBam, "--mp-max-insert", "25000"]
command += ["--genome-size", "{}".format(genomeSize), "--output", output]
common.print_command(command)
if not common.check_dryrun(sample_config) and not os.path.exists(
"{}_FRC.png".format(output)):
stdOut = open("FRC.stdOut", "a")
stdErr = open("FRC.stdErr", "a")
returnValue = subprocess.call(command, stdout=stdOut, stderr=stdErr)
if not returnValue == 0:
sys.exit("error, while running FRCurve: {}".format(command))
plotFRCurve(output)
os.chdir("..")
return sample_config
def _run_qaTools(global_config, sample_config, sorted_libraries_by_insert):
mainDir = os.getcwd()
qaToolsFolder = os.path.join(os.getcwd(), "QAstats")
if not os.path.exists(qaToolsFolder):
os.makedirs(qaToolsFolder)
os.chdir("QAstats")
program = global_config["Tools"]["qaTools"]["bin"]
genomeSize = sample_config["genomeSize"]
reference = sample_config["reference"]
output = sample_config["output"]
alignments = sample_config["alignments"][0]
BAMfile = alignments[1]
command = [
"{}".format(program), "-m", "-q", "0", "-i", BAMfile,
"{}.cov".format(os.path.basename(BAMfile))
]
common.print_command(command)
if not common.check_dryrun(sample_config) and not os.path.exists(
"{}.cov".format(os.path.basename(BAMfile))):
stdOut = open("QAtools.stdOut", "a")
stdErr = open("QAtools.stdErr", "a")
returnValue = subprocess.call(command, stdout=stdOut, stderr=stdErr)
if not returnValue == 0:
sys.exit("error, while running QAtools: {}".format(command))
#now add GC content
QAtools_dict = {}
header = ""
with open("{}.cov".format(os.path.basename(BAMfile)), "r") as QA_csv:
header = QA_csv.readline().rstrip()
for line in QA_csv:
line = line.strip().split("\t")
QAtools_dict[line[0]] = [line[1], line[2], line[3]]
QA_GC_file = "{}.cov.gc".format(os.path.basename(BAMfile))
with open(QA_GC_file, "w") as QA_GC_fd:
QA_GC_fd.write("{}\tGCperc\n".format(header))
with open(reference, "r") as ref_fd:
fasta_raw_header = ref_fd.readline().strip()
fasta_raw_header = fasta_raw_header.split(" ")[0]
fasta_raw_header = fasta_raw_header.split("\t")[0]
fasta_header = fasta_raw_header.split(">")[1]
sequence = ""
for line in ref_fd:
line = line.strip()
if line.startswith(">"):
GC = computeGC(sequence)
if fasta_header not in QAtools_dict:
sys.exit(
"error while parsing QAcompute output: probably some wired contig name is present in your assmebly file"
)
QA_GC_fd.write("{}\t{}\t{}\t{}\t{}\n".format(
fasta_header, QAtools_dict[fasta_header][0],
QAtools_dict[fasta_header][1],
QAtools_dict[fasta_header][2], GC))
sequence = ""
fasta_raw_header = line.split(" ")[0]
fasta_raw_header = fasta_raw_header.split("\t")[0]
fasta_header = fasta_raw_header.split(">")[1]
else:
sequence += line
GC = computeGC(sequence)
if fasta_header not in QAtools_dict:
sys.exit(
"error while parsing QAcompute output: probably some wired contig name is present in your assmebly file"
)
QA_GC_fd.write("{}\t{}\t{}\t{}\t{}\n".format(
fasta_header, QAtools_dict[fasta_header][0],
QAtools_dict[fasta_header][1],
QAtools_dict[fasta_header][2], GC))
plotQA(QA_GC_file)
os.chdir("..")
return sample_config
def _run_trimmomatic(global_config, sample_config, sorted_libraries_by_insert):
program = global_config["Tools"]["trimmomatic"]["bin"]
program_folder = os.path.dirname(program)
if "adapters" not in sample_config:
sys.exit(
"running MP pipeline, adapters file to be used in trimming are needed for Trimmomatic. Please specify them\
in the sample configuration file and rerun")
adapterFile = sample_config["adapters"]
if not os.path.exists(adapterFile):
sys.exit(
"Trimmomatic cannot be run as adapter file is not specified or points to unknown position: {}"
.format(adapterFile))
mainDirectory = os.getcwd()
trimmomaticDir = os.path.join(mainDirectory, "Trimmomatic")
if not os.path.exists(trimmomaticDir):
os.makedirs(trimmomaticDir)
os.chdir(trimmomaticDir)
#now I am in running dir, I need to process one by one the libraries
threads = 8
if "threads" in sample_config:
threads = sample_config["threads"]
for library, libraryInfo in sorted_libraries_by_insert:
read1 = libraryInfo["pair1"]
read2 = libraryInfo["pair2"]
orientation = libraryInfo["orientation"]
if read2 is not None:
read1_baseName = os.path.split(read1)[1].split(".")[0]
read2_baseName = os.path.split(read2)[1].split(".")[0]
output_read1_pair = os.path.join(
trimmomaticDir, "{}.fastq.gz".format(read1_baseName))
output_read1_sing = os.path.join(
trimmomaticDir, "{}_u.fastq.gz".format(read1_baseName))
output_read2_pair = os.path.join(
trimmomaticDir, "{}.fastq.gz".format(read2_baseName))
output_read2_sing = os.path.join(
trimmomaticDir, "{}_u.fastq.gz".format(read2_baseName))
command = [
"java", "-jar", program, "PE", "-threads",
"{}".format(threads), "-phred33", read1, read2,
output_read1_pair, output_read1_sing, output_read2_pair,
output_read2_sing,
"ILLUMINACLIP:{}:2:30:10".format(adapterFile), "LEADING:3",
"TRAILING:3", "SLIDINGWINDOW:4:15", "MINLEN:30"
]
common.print_command(command)
if not common.check_dryrun(sample_config) and not os.path.exists(
"{}.fastq.gz".format(read1_baseName)
): # do not execute is files have been already gennerated
stdOut = open("{}_trimmomatic.stdOut".format(read1_baseName),
"w")
stdErr = open("{}_trimmomatic.stdErr".format(read1_baseName),
"w")
returnValue = subprocess.call(command,
stdout=stdOut,
stderr=stdErr) # run the program
if returnValue != 0:
print "error while running command: {}".format(command)
libraryInfo["pair1"] = output_read1_pair
libraryInfo["pair2"] = output_read2_pair
libraryInfo["trimmomatic"] = os.path.join(
trimmomaticDir, "{}_trimmomatic.stdErr".format(read1_baseName))
os.chdir(mainDirectory)
return sample_config