def upload_file():
if request.method == 'POST':
if 'files[]' not in request.files:
flash('No file part')
return redirect(request.url)
files = request.files.getlist('files[]')
whichtorun_list = request.form.getlist('whichToRun')
print(whichtorun_list)
global genome_ref
genome_ref = request.form["genome"]
print(genome_ref)
if genome_ref == "GRCm37":
genInstall.install('GRCm37', rsync=False, bash=True)
if genome_ref == "GRCm38.p6":
genInstall.install('GRCm38.p6', rsync=False, bash=True)
if genome_ref == "Rnor_6.0":
genInstall.install('Rnor_6.0', rsync=False, bash=True)
if "runMutationalPatterns" in whichtorun_list:
global mutationalPattern
mutationalPattern = "TRUE"
if "runSigflow" in whichtorun_list :
global sigflow
sigflow = "TRUE"
if "runSigfit" in whichtorun_list :
global sigfit
sigfit = "TRUE"
if "runDeconstructSigs" in whichtorun_list :
global deconstructSigs
deconstructSigs = "TRUE"
for file in files:
if file and allowed_file(file.filename):
filename = secure_filename(file.filename)
file.save(os.path.join(app.config['UPLOAD_FOLDER'], filename))
print(filename)
# time.sleep(10)
print("files succcessfully uploaded ")
return redirect('/upload')
from SigProfilerMatrixGenerator import install as genInstall
genInstall.install('GRCh37', rsync=False, bash=True)
import argparse
from SigProfilerMatrixGenerator import install as genInstall
def parse_args():
parser = argparse.ArgumentParser()
parser.add_argument("-r",
"--reference",
dest="ref",
default="GRCh37",
help="The name of the reference to install",
type=str)
return parser.parse_args()
if __name__ == "__main__":
args = parse_args()
genInstall.install(args.ref, rsync=False, bash=True)
matrices = matGen.SigProfilerMatrixGeneratorFunc(project, genome, vcfFiles, exome=True, bed_file=None, chrom_based=False, plot=True, tsb_stat=True, seqInfo=True)
"""
#sample = snakemake.wildcards["sample"]
#genome_version = snakemake.params["genome_version"]
#out_dir = snakemake.params["out_dir"]
#bed = snakemake.input["bed"]
sample = "SJCBF"
genome_version = "GRCh37"
out_dir = ".tests/"
bed = None
from SigProfilerMatrixGenerator import install as genInstall
genInstall.install(genome_version, rsync=False, bash=True)
from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen
matrices = matGen.SigProfilerMatrixGeneratorFunc(sample,
genome_version,
out_dir,
plot=True,
exome=True,
bed_file=bed,
chrom_based=False,
tsb_stat=False,
seqInfo=False,
cushion=100)
matrix_path = out_dir + "output/SBS/{sample}.SBS96.exome".format(sample=sample)
if output_dir == None:
output_dir = "/app/input_vcf_dir"
if genome_ref == None:
genome_ref = "GRCh37"
if genome_ref == "GRCh37":
# genInstall.install('GRCh37', rsync=False, bash=True)
genome_ref = "GRCh37"
if genome_ref == "GRCh38":
# genInstall.install('GRCh38', rsync=False, bash=True)
genome_ref = "GRCh38"
if genome_ref == "GRCm37":
genInstall.install('GRCm37', rsync=False, bash=True)
genome_ref = "GRCm37"
if genome_ref == "GRCm38.p6":
genInstall.install('GRCm38.p6', rsync=False, bash=True)
genome_ref = "GRCm38.p6"
if genome_ref == "Rnor_6.0":
genInstall.install('Rnor_6.0', rsync=False, bash=True)
genome_ref = "Rnor_6.0"
if runMutationalPatterns == False:
runMutationalPatterns = "TRUE"
if runMutationalPatterns == True:
runMutationalPatterns = "FALSE"
def init(genome_build: GenomeBuild) -> None:
install(str(genome_build))