cd.getNumPy(options)
cd.installNumPy(options)
# elif numpycheck == False and matplotlibcheck == True:
# cd.getNumPy()
# cd.installNumPy()
# elif numpycheck == True and matplotlibcheck == False:
# cd.getmatplotlib()
# cd.installmatplotlib()
print "Everything appears to be fine. Moving on.\n"
import qc_analysis
import mapping_and_counting
import differential_expression
qc = qc_analysis.QC_analysis()
mac = mapping_and_counting.Mapping_and_Counting()
de = differential_expression.DifferentialExpression()
if options.noninteractive:
#Create a folder called RNAseq_Data with which to store all of the data analysis
subfolderpath = qc.create_folder()
#Read in the data and sort out the genome feature file and genome sequence files
qc.findreferencefiles(data_path)
#Trimmomatic
qc.trimmomatic(data_path, subfolderpath, options)
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