def fastqc(self, datalocation, analysislocation, options):
"""Run FastQC for trimmed data files."""
cd = check_dependencies_linux.CheckDependencies()
os.chdir(os.path.join(cd.getSPARTAdir(options), "QC_analysis"))
if not os.path.lexists(
cd.getSPARTAdir(options) + "/QC_analysis/FastQC"):
subprocess.call(["unzip", "fastqc_v0.11.3.zip"],
stdout=open(os.devnull, 'wb'))
os.chdir(os.path.join(cd.getpwd(), "FastQC"))
subprocess.call("chmod 755 fastqc", shell=True)
print "FastQC is assessing your data set for overall quality"
for file in os.listdir(datalocation):
extension = file.split(".")[1]
if extension == "fastq" or extension == "fq":
if options.verbose:
subprocess.Popen(
"./fastqc " +
os.path.join(analysislocation, "QC", "trimmed" + file),
shell=True).wait()
else:
subprocess.Popen(
"./fastqc --quiet " +
os.path.join(analysislocation, "QC", "trimmed" + file),
shell=True).wait()
return
def trimmomatic(self, datalocation, analysislocation, options):
"""Run trimmomatic for SE reads and add the file prefix
'trim' to the file name."""
cd = check_dependencies_linux.CheckDependencies()
os.chdir(os.path.join(cd.getSPARTAdir(options), "QC_analysis"))
if not os.path.lexists(
os.path.join(cd.getSPARTAdir(options), "QC_analysis",
"Trimmomatic-0.33")):
#This will be a problem for Windows. Just distribute with unzipped binaries?
subprocess.call(["unzip", "Trimmomatic-0.33.zip"],
stdout=open(os.devnull, 'wb'))
os.chdir(os.path.join(cd.getpwd(), "Trimmomatic-0.33"))
for file in os.listdir(datalocation):
extension = file.split(".")[1]
if extension == "fastq" or extension == "fq":
subprocess.Popen(
"java -jar trimmomatic-0.33.jar SE -threads {threads} ".
format(threads=options.threads) +
os.path.join(datalocation, file) + " " +
os.path.join(analysislocation, "QC", "trimmed" + file) +
" ILLUMINACLIP:" + cd.getpwd() +
"/adapters/{illuminaclip} LEADING:{leading} TRAILING:{trailing} SLIDINGWINDOW:{slidingwindow} MINLEN:{minlen}"
.format(illuminaclip=options.illuminaclip,
leading=options.leading,
trailing=options.trailing,
slidingwindow=options.slidingwindow,
minlen=options.minlentrim),
shell=True).wait()
return
__author__ = 'benkjohnson'
import check_dependencies_linux
import optparse
import sys
cd = check_dependencies_linux.CheckDependencies()
optParser = optparse.OptionParser(
usage="python SPARTA.py [options]",
description=
"Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis (SPARTA)",
epilog=
"Written by Benjamin K. Johnson ([email protected]), Michigan State University Department of "
+ "Microbiology and Molecular Genetics. (c) 2015")
#Future functionality
# optParser.add_option("--SE", help="Single-end read input. Default input choice is single-end if nothing is specified",
# action="store_true", default="True", dest="seqtype")
# optParser.add_option("--PE", help="Paired-end read input. Must have the exact same file name and end with _F for the forward read and _R for the reverse read",
# action="store_false", default="False", dest="seqtype")
optParser.add_option(
"--cleanup",
help=
"Clean up the intermediate files to save space. Default action is to retain the intermediate files.",
action="store_true",
dest="cleanup")
optParser.add_option("--verbose",
help="Display more output for each step of the analysis.",
action="store_true",
dest="verbose")
def bowtie(self, datalocation, analysislocation, options):
"""Run Bowtie for SE reads less than 50 bp in length.
Will add the ability to run Bowtie2 for PE and SE with
reads greater than 50 bp."""
cd = check_dependencies_linux.CheckDependencies()
qc = qc_analysis.QC_analysis()
gff, genref = qc.findreferencefiles(datalocation)
copy(genref, os.path.join(analysislocation, 'Bowtie'))
genrefname = genref.split("/")[-1]
copy(gff, os.path.join(analysislocation, 'HTSeq'))
# subprocess.Popen("cp " + genref + " " + analysislocation + "/Bowtie", shell=True).wait()
# subprocess.Popen("cp " + gff + " " + analysislocation + "/HTSeq", shell=True).wait()
os.chdir(os.path.join(cd.getSPARTAdir(options),
"Mapping_and_counting"))
# os.chdir(cd.getSPARTAdir() + "/Mapping_and_counting")
if not os.path.lexists(
os.path.join(cd.getSPARTAdir(options), "Mapping_and_counting",
"bowtie-1.1.1")):
#This will be a problem for Windows users. Distribute with unzipped binaries?
subprocess.call(["unzip", "bowtie-1.1.1-linux-x86_64.zip"],
stdout=open(os.devnull, 'wb'))
os.chdir(os.path.join(cd.getpwd(), "bowtie-1.1.1"))
for file in os.listdir(os.path.join(analysislocation, "QC")):
extension = file.split(".")[-1]
if extension == "gz":
subprocess.Popen(
"gunzip -c " + os.path.join(analysislocation, "QC", file) +
" > " + os.path.join(analysislocation, "Bowtie",
os.path.splitext(file)[0]),
shell=True).wait()
else:
copy(os.path.join(analysislocation, "QC", file),
os.path.join(analysislocation, "Bowtie"))
if options.cleanup:
for file in os.listdir(os.path.join(analysislocation, "QC")):
extension = file.split(".")[-1]
if extension == "gz" or extension in ["fq, fastq"]:
subprocess.Popen("rm " + os.path.join(
analysislocation, "QC", "{file}".format(file=file)),
shell=True).wait()
print "Building the Bowtie index from the reference genome"
if options.verbose:
subprocess.Popen(
"./bowtie-build -f " +
os.path.join(analysislocation, "Bowtie", genrefname) + " " +
glob.glob(os.path.join(analysislocation, "Bowtie") +
"/*.fa*")[0].split(".")[0],
shell=True).wait()
else:
subprocess.Popen(
"./bowtie-build -q -f " +
os.path.join(analysislocation, "Bowtie", genrefname) + " " +
glob.glob(os.path.join(analysislocation, "Bowtie") +
"/*.fa*")[0].split(".")[0],
shell=True).wait()
allebwtfiles = glob.glob("*.ebwt")[:]
for ebwtfile in allebwtfiles:
copy(ebwtfile, os.path.join(analysislocation, "Bowtie"))
# subprocess.Popen("cp " + ebwtfile + " " + analysislocation + "/Bowtie/", shell=True).wait()
print "Mapping reads to the reference genome with Bowtie"
for file in os.listdir(os.path.join(analysislocation, "Bowtie")):
extension = os.path.splitext(file)[1]
if extension == ".fq" or extension == ".fastq":
fname = os.path.splitext(file)[0]
strippedfile = fname[len('trimmed'):]
if options.verbose:
subprocess.Popen(
"./bowtie -S --threads {threads} -p {procs} ".format(
threads=options.threads, procs=options.procs) +
glob.glob(
os.path.join(analysislocation, "Bowtie") +
"/*.fa*")[0].split(".")[0] + " " +
os.path.join(analysislocation, "Bowtie", file) +
" > " + os.path.join(analysislocation, "Bowtie",
"align" + strippedfile + ".sam"),
shell=True).wait()
elif options.mismatch:
subprocess.Popen(
"./bowtie -S --threads {threads} -p {procs} -v {mismatch} "
.format(threads=options.threads,
procs=options.procs,
mismatch=options.mismatch) + glob.glob(
os.path.join(analysislocation, "Bowtie") +
"/*.fa*")[0].split(".")[0] + " " +
os.path.join(analysislocation, "Bowtie", file) +
" > " + os.path.join(analysislocation, "Bowtie",
"align" + strippedfile + ".sam"),
shell=True).wait()
elif options.otherbowtieoptions:
subprocess.Popen(
"./bowtie -S --threads {threads} -p {procs} {otherbowtieoptions} "
.format(threads=options.threads,
procs=options.procs,
otherbowtieoptions=options.otherbowtieoptions)
+ glob.glob(
os.path.join(analysislocation, "Bowtie") +
"/*.fa*")[0].split(".")[0] + " " +
os.path.join(analysislocation, "Bowtie", file) +
" > " + os.path.join(analysislocation, "Bowtie",
"align" + strippedfile + ".sam"),
shell=True).wait()
elif options.mismatch and options.otherbowtieoptions:
subprocess.Popen(
"./bowtie -S --threads {threads} -p {procs} -v {mismatch} {otherbowtieoptions} "
.format(threads=options.threads,
procs=options.procs,
mismatch=options.mismatch,
otherbowtieoptions=options.otherbowtieoptions)
+ glob.glob(
os.path.join(analysislocation, "Bowtie") +
"/*.fa*")[0].split(".")[0] + " " +
os.path.join(analysislocation, "Bowtie", file) +
" > " + os.path.join(analysislocation, "Bowtie",
"align" + strippedfile + ".sam"),
shell=True).wait()
else:
subprocess.Popen(
"./bowtie -S --quiet --threads {threads} ".format(
threads=options.threads) + glob.glob(
os.path.join(analysislocation, "Bowtie") +
"/*.fa*")[0].split(".")[0] + " " +
os.path.join(analysislocation, "Bowtie", file) +
" > " + os.path.join(analysislocation, "Bowtie",
"align" + strippedfile + ".sam"),
shell=True).wait()
return
def htseq(self, analysislocation, options):
"""Run htseq-count to count gene features post-Bowtie mapping"""
cd = check_dependencies_linux.CheckDependencies()
os.chdir(os.path.join(cd.getSPARTAdir(options),
"Mapping_and_counting"))
if not os.path.lexists(
os.path.join(cd.getSPARTAdir(options), "Mapping_and_counting",
"HTSeq-0.6.1")):
subprocess.Popen("tar -zxf HTSeq-0.6.1.tar.gz",
stdout=open(os.devnull, 'w'),
shell=True).wait()
# htseqcheck = cd.checkhtseq()
# if htseqcheck == False:
os.chdir(os.path.join(cd.getpwd(), "HTSeq-0.6.1"))
subprocess.Popen("python setup.py build install --user",
shell=True,
stdout=open(os.devnull, 'wb'),
stderr=open(os.devnull, 'wb')).wait()
os.chdir(os.path.join(cd.getpwd(), "build", "scripts-2.7"))
gff = glob.glob(os.path.join(analysislocation, "HTSeq") + "/*.g*")[0]
print "Counting gene features with HTSeq"
for mapfile in os.listdir(os.path.join(analysislocation, "Bowtie")):
extension = os.path.splitext(mapfile)[1]
if extension == ".sam":
fname = os.path.splitext(mapfile)[0]
strippedmapfile = fname[len('align'):]
if options.verbose:
subprocess.Popen(
"./htseq-count --mode={mode} --stranded={stranded} --order={order} --type={type} -a {minqual} --idattr={idattr} "
.format(mode=options.mode,
stranded=options.stranded,
order=options.order,
type=options.type,
minqual=options.minqual,
idattr=options.idattr) +
os.path.join(analysislocation, "Bowtie", mapfile) +
" " + gff + " > " +
os.path.join(analysislocation, "HTSeq",
"map" + strippedmapfile + ".sam"),
shell=True).wait()
else:
subprocess.Popen(
"./htseq-count --quiet --mode={mode} --stranded={stranded} --order={order} --type={type} -a {minqual} --idattr={idattr} "
.format(mode=options.mode,
stranded=options.stranded,
order=options.order,
type=options.type,
minqual=options.minqual,
idattr=options.idattr) +
os.path.join(analysislocation, "Bowtie", mapfile) +
" " + gff + " > " +
os.path.join(analysislocation, "HTSeq",
"map" + strippedmapfile + ".sam"),
shell=True).wait()
if options.cleanup:
for file in os.listdir(os.path.join(analysislocation, "Bowtie")):
subprocess.Popen("rm " + os.path.join(
analysislocation, "Bowtie", "{file}".format(file=file)),
shell=True).wait()
return
def __init__(self):
cd = check_dependencies_linux.CheckDependencies()
self._mydesktoppath = cd.getdesktoppath()