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))