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#############
# Functions #
#############
def get_trimmomatic_result(files, params):
n_reads = 0
total_reads = 0
for file in files:
with open(file,"r") as logfile:
for line in logfile.readlines():
if re.match("Input Read", line):
if geninfo_config["Sample information"]["type"]=="PE":
pattern = re.match("Input Read Pairs:\s+(?P<total>\d+)\s+"
"Both Surviving:\s+(?P<nSurvived>\d+) \((?P<pSurvived>\d+.\d+)%\)\s+"
"Forward Only Surviving:\s+(?P<forward>\d+) \(\d+.\d+%\)\s+"
"Reverse Only Surviving:\s+(?P<reverse>\d+) \(\d+.\d+%\).*", line)
total_reads += int(pattern.group("total")) * 2
n_reads += int(pattern.group("nSurvived")) * 2 + int(pattern.group("forward")) + int(pattern.group("reverse"))
else:
pattern = re.match(".*Surviving: (?P<nSurvived>\d+) \((?P<survived>\d+.\d+)%\)", line)
pattern2 = re.match("Input Reads: (?P<total>\d+)", line)
total_reads += int(pattern2.group("total"))
n_reads+= int(pattern.group("nSurvived"))
all_params ={}
for param in params:
with open(param,"r") as paramfile:
all_params[os.path.basename(param).replace(".trimmomatic.params", "")] = paramfile.read()
if total_reads != 0:
perc_remaining = round( 100*(n_reads/total_reads),2)
else:
perc_remaining = 0
return OrderedDict([
("#Remaining Reads", n_reads),
("%Remaining Reads", perc_remaining),
("Trim parameter", all_params)])
def get_defaults():
params = ""
if config["technology"] == "Illumina":
params +="ILLUMINACLIP:%s:%s " % (geninfo_config["adapter"], config["illuminaclip"])
if not config["only_trim_adapters"]:
params+="%s MINLEN:%s " % (config["trimOption"],
str(config["minlen"]))
return params
def perc_slope(a,b,perc):
if abs(numpy.diff([a,b]))>(b*float(perc)):
return True
return False
def optimize_trimming(filename, outname, perc=0.1):
if not exists(filename):
with open(outname, "w") as paramfile:
pass
else:
mytable=None
with open(filename, "rb") as fastqcdata:
table = []
ifwrite = False
#previous_line = ''
while True:
line = fastqcdata.readline()
if not line:
break
line = line.decode()
line = line.replace("\n", "")
if line.startswith(">>END_MODULE") and ifwrite:
try:
dtype = {'names': table[0], 'formats': ['|S15', float, float, float, float]}
mytable = numpy.asarray([tuple(x) for x in table[1:]], dtype=dtype)
break
except:
pass
elif re.search("Sequence length\s+\d+", line):
seq_length = re.search("Sequence length\s+(?P<length>\d+)", line).group("length")
#elif re.search("Sequence length\s+\d+(?P<length>\d+)", line):
# The culprit ^^^ this killed trimBetter
# seq_length = re.search("Sequence length\s+\d+(?P<length>\d+)", line).group("length")
elif line.startswith(">>Per base sequence content"):
#print(line, seq_length)
ifwrite = True
temp = line.split("\t")
if temp[1].lower() == "pass":
with open(outname, "w") as paramfile:
paramfile.write("%s;%s" % (0, seq_length))
return True
elif ifwrite:
table.append(line.split("\t"))
# previous_line = line
headcrop = 0
tailcrop = len(mytable["A"])
column = numpy.ma.array(mytable)
print(rep(column))
for i in range(-4, int(round(len(mytable["A"]) / 3, 0)), 1):
for nucl in ["A", "C", "G", "T"]:
column[nucl].mask[max(i, 0):i + 5] = True
if headcrop >0:
column[nucl].mask[:headcrop] = True
if tailcrop < len(mytable["A"]):
column[nucl].mask[tailcrop:] = True
# check heacrop
if (perc_slope(numpy.mean(mytable[nucl][max(i, 0):i + 5]), numpy.mean(column[nucl]), perc=perc)) & (headcrop < (i + 5)):
headcrop = i + 5
trim_bool = True
elif headcrop < i:
column[nucl].mask[max(i, 0):i + 5] = False
# now crop from the end
column[nucl].mask[-(i + 5):(min(len(mytable[nucl]), len(mytable[nucl]) - i))] = True
if (perc_slope(numpy.mean(mytable[nucl][-(i + 6): (min(len(mytable[nucl]) - 1, len(mytable[nucl]) - 1 - i))]), numpy.mean(column[nucl]), perc=perc)) & (tailcrop > len(mytable[nucl]) - (i + 5)):
tailcrop = len(mytable[nucl]) - (i + 5)
trim_bool = True
else:
column[nucl].mask[-(i + 5): (min(len(mytable["A"]) - 1, len(mytable[nucl]) - 1 - i))] = False
with open(outname, "w") as paramfile:
paramfile.write("%s;%s" % (headcrop, tailcrop-headcrop))
return True
def get_best_params(output, r1, r2=None):
with open (r1,"r") as r1_file:
r1_params =r1_file.read().replace("\n","").split(";")
# print('head-/tail-crop params:\nread1:', r1_params)
if r2 is not None:
with open(r2, "r") as r2_file:
r2_params = r2_file.read().replace("\n","").split(";")
# print('read2:', r2_params)
else:
r2_params = [-float("inf"), float("inf")]
if not r1_params[0]=="":
new_params = " ".join([
get_defaults(),
"HEADCROP:" + str(max(int(r1_params[0]),int(r2_params[0]))),
"CROP:" + str(min(int(r1_params[1]),int(r2_params[1]))),
"MINLEN:" + str(config["minlen"])])
else:
new_params = get_defaults()
with open(output, "w") as outfile:
outfile.write(new_params)
return new_params
def get_trimmomatic_input(wildcards):
input = {}
#if geninfo_config["Sample information"]["samples"][wildcards.sample][0].endswith(".bam"):
# input["fastq_files"] = bam_to_fastq(geninfo_config["Sample information"]["samples"][wildcards.sample][0])
#else:
# input["fastq_files"] = geninfo_config["Sample information"]["samples"][wildcards.sample]
input["fastq_files"] = get_all_reads(wildcards, True)
if config["trimBetter"]:
if geninfo_config["Sample information"]["type"] == "PE":
input["params"] = list(expand("{path}/{sample}_{read}.params", read=["R1", "R2"], sample=wildcards.sample,
path=trimbetter_path))
else:
input["params"] = list(expand("{path}/{sample}.params", sample = wildcards.sample, path = trimbetter_path))
return input
def get_trimmomatic_output(path, is_temp = False):
output = {}
if is_temp:
#output["pseudo_trimfile"] = (path +
# "/{sample}.trimBetter.trimmomatic.pseudo")
#output["params_file"] = temp( path + "/{sample}.trimmomatic.params")
output["logfile"] = log_path + "/{sample}.trimBetter.trimmomatic.log"
else:
output["params_file"] = temp(path + "/{sample}.trimmomatic.params")
#output["pseudo_trimfile"] = path + "/{sample}.trimmomatic.pseudo"
output["logfile"] = log_path + "/{sample}.trimmomatic.log"
if geninfo_config["Sample information"]["type"]=="SE":
if is_temp:
output["trimmed_files"] = [temp(path + "/{sample}.fastq.gz")]
else:
output["trimmed_files"] = [path + "/{sample}.fastq.gz"]
else:
if is_temp:
output["trimmed_files"] = [temp(path + "/{sample}.1P.fastq.gz"),
temp(path + "/{sample}.1U.fastq.gz"),
temp(path + "/{sample}.2P.fastq.gz"),
temp(path + "/{sample}.2U.fastq.gz")]
else:
output["trimmed_files"] =[ path + "/{sample}.1P.fastq.gz",
path + "/{sample}.1U.fastq.gz",
path + "/{sample}.2P.fastq.gz",
path + "/{sample}.2U.fastq.gz"]
return output
#--------------------------------------------< RULES >-----------------------------------------------------------------#
if not config["notrimming"]:
if config["trimBetter"]:
rule join_reads_trimBetter:
input:
r1 = [trimbetter_path + "/{sample}.1P.fastq.gz", trimbetter_path + "/{sample}.1U.fastq.gz"],
r2 = [trimbetter_path + "/{sample}.2P.fastq.gz", trimbetter_path + "/{sample}.2U.fastq.gz"]
output:
r1_out = temp(trimbetter_path + "/{sample}_R1.fastq.gz"),
r2_out = temp(trimbetter_path + "/{sample}_R2.fastq.gz")
shell:
"cat {input.r1} > {output.r1_out} | "
"cat {input.r2} > {output.r2_out} "
rule fastqc_trimBetter:
input:
fastq_files = trimbetter_path + "/{sample}_{read}.fastq.gz"
output:
temp(trimbetter_path + "/FastQC/{sample}_{read}_fastqc.zip"),
temp(trimbetter_path + "/FastQC/{sample}_{read}_fastqc.html"),
fastqc = temp(trimbetter_path + "/FastQC/{sample}_{read}_fastqc"),
log = temp(trimbetter_path + "/FastQC/{sample}_{read}.fastqc.log")
threads:
max_threads
message:
"Run FastQC to obtain better trimming paramters."
run:
#print('sizes:', ' '.join(['%s:%i|' % (x,os.path.getsize(x))
# for x in input]), file=sys.stderr)
shell(
"if [ `zcat '{input}' | head -n 1 | wc -c ` -eq 0 ]; "
"then touch {output}; "
"else fastqc {input} -o $(dirname {output.fastqc})"
" --extract --nogroup -t {threads} > {output.log} 2>&1; "
"fi; ")
rule optimize_trimming_parameter:
input:
trimbetter_path + "/FastQC/{sample}_{read}_fastqc"
output:
temp(trimbetter_path + "/{sample}_{read}.params")
params:
perc_slope = config["trimBetter_threshold"]
run: # Apperently os.path.join is loaded somehow
res = optimize_trimming(join(str(input),"fastqc_data.txt"),
str(output), float(params.perc_slope))
if not res:
shell('exit 1')
rule trimmomatic_trimBetter:
input:
fastq_files = lambda x: geninfo_config["Sample information"]["samples"][x.sample]
output:
**get_trimmomatic_output(trimbetter_path, is_temp = True)
threads:
max_threads
log:
get_trimmomatic_output(trimbetter_path, is_temp = True)['logfile']
#log_path + "/{sample}.trimmomatic.trimBetter.log"
params:
get_defaults()
shell:
("trimmomatic %s -threads {threads} {input.fastq_files}"
" {output.trimmed_files} {params}"
" 2> {log}") % geninfo_config["Sample information"]["type"]
#-- end trimbetter
rule trimmomatic:
input:
unpack(get_trimmomatic_input)
output:
**get_trimmomatic_output(trimming_path)
log:
log_path + "/{sample}.trimmomatic.log"
params:
minlen = config["minlen"],
trimOption = config["trimOption"]
threads:
max_threads
run:
#print('sizes:', ' '.join(['%s:%i|' % (x,os.path.getsize(x))
# for x in input]), file=sys.stderr)
try:
new_params = get_best_params(str(output.params_file), *list(input.params))
except:
new_params = get_defaults()
if params.minlen:
pass
if params.trimOption:
pass
paramfile = open(str(output.params_file),"w")
paramfile.write(new_params)
paramfile.close()
shell("trimmomatic %s -threads {threads} " # -Xmx512m "
"{input.fastq_files} {output.trimmed_files} %s 2> {output.logfile}" % (
geninfo_config["Sample information"]["type"], new_params))
#shell("touch {output.pseudo_trimfile}")
rule join_reads:
input:
r1 = [trimming_path + "/{sample}.1P.fastq.gz",trimming_path + "/{sample}.1U.fastq.gz"],
r2 = [trimming_path + "/{sample}.2P.fastq.gz",trimming_path + "/{sample}.2U.fastq.gz"]
output:
r1_out = temp(trimming_path + "/{sample}_R1.fastq.gz"),
r2_out = temp(trimming_path + "/{sample}_R2.fastq.gz")
run:
# print('sizes:', ' '.join(['%s:%i|' % (x,os.path.getsize(x))
# for x in input]), file=sys.stderr)
shell(
"cat {input.r1} > {output.r1_out} | "
"cat {input.r2} > {output.r2_out}")
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