import subprocess
import os
import argparse
def run_msi(bamfile,outdir,prefix):
    MSIsensor = "export LD_LIBRARY_PATH=/software/gcc/gcc-v6.5.0/lib64/:LD_LIBRARY_PATH && /software/MSIsensor/msisensor-ML/msisensor"
    models = "/software/MSIsensor/msisensor-ML/models_hg19_275genes"
    if not os.path.exists(outdir):
        os.mkdir(outdir)
    out=outdir+"/"+prefix
    cmd="%s msi -t %s -o %s.msi.tsv -M %s -d %s/1030c0aa35ca5c263daeae866ad18632" %(MSIsensor,bamfile,out,models,models)
    subprocess.check_call(cmd,shell=True)

if __name__=="__main__":
    parser=argparse.ArgumentParser("Run MSI analysis.")
    parser.add_argument("-t", "--tumor", type=str, help="tumor bam file", required=True)
    parser.add_argument("-o", "--outdir", type=str, help="output directory", default=os.getcwd())
    parser.add_argument("-p", "--prefix", type=str, help="prefix of output", default="MSI")
    args = parser.parse_args()
    run_msi(args.tumor,args.outdir,args.prefix)
6a6925f52db2323d3be809a4388e3a7b55cd831e
<mask token>

<mask token>


def run_msi(bamfile, outdir, prefix):
    MSIsensor = (
        'export LD_LIBRARY_PATH=/software/gcc/gcc-v6.5.0/lib64/:LD_LIBRARY_PATH && /software/MSIsensor/msisensor-ML/msisensor'
        )
    models = '/software/MSIsensor/msisensor-ML/models_hg19_275genes'
    if not os.path.exists(outdir):
        os.mkdir(outdir)
    out = outdir + '/' + prefix
    cmd = (
        '%s msi -t %s -o %s.msi.tsv -M %s -d %s/1030c0aa35ca5c263daeae866ad18632'
         % (MSIsensor, bamfile, out, models, models))
    subprocess.check_call(cmd, shell=True)


<mask token>

<mask token>


def run_msi(bamfile, outdir, prefix):
    MSIsensor = (
        'export LD_LIBRARY_PATH=/software/gcc/gcc-v6.5.0/lib64/:LD_LIBRARY_PATH && /software/MSIsensor/msisensor-ML/msisensor'
        )
    models = '/software/MSIsensor/msisensor-ML/models_hg19_275genes'
    if not os.path.exists(outdir):
        os.mkdir(outdir)
    out = outdir + '/' + prefix
    cmd = (
        '%s msi -t %s -o %s.msi.tsv -M %s -d %s/1030c0aa35ca5c263daeae866ad18632'
         % (MSIsensor, bamfile, out, models, models))
    subprocess.check_call(cmd, shell=True)


if __name__ == '__main__':
    parser = argparse.ArgumentParser('Run MSI analysis.')
    parser.add_argument('-t', '--tumor', type=str, help='tumor bam file',
        required=True)
    parser.add_argument('-o', '--outdir', type=str, help='output directory',
        default=os.getcwd())
    parser.add_argument('-p', '--prefix', type=str, help='prefix of output',
        default='MSI')
    args = parser.parse_args()
    run_msi(args.tumor, args.outdir, args.prefix)

import subprocess
import os
import argparse


def run_msi(bamfile, outdir, prefix):
    MSIsensor = (
        'export LD_LIBRARY_PATH=/software/gcc/gcc-v6.5.0/lib64/:LD_LIBRARY_PATH && /software/MSIsensor/msisensor-ML/msisensor'
        )
    models = '/software/MSIsensor/msisensor-ML/models_hg19_275genes'
    if not os.path.exists(outdir):
        os.mkdir(outdir)
    out = outdir + '/' + prefix
    cmd = (
        '%s msi -t %s -o %s.msi.tsv -M %s -d %s/1030c0aa35ca5c263daeae866ad18632'
         % (MSIsensor, bamfile, out, models, models))
    subprocess.check_call(cmd, shell=True)


if __name__ == '__main__':
    parser = argparse.ArgumentParser('Run MSI analysis.')
    parser.add_argument('-t', '--tumor', type=str, help='tumor bam file',
        required=True)
    parser.add_argument('-o', '--outdir', type=str, help='output directory',
        default=os.getcwd())
    parser.add_argument('-p', '--prefix', type=str, help='prefix of output',
        default='MSI')
    args = parser.parse_args()
    run_msi(args.tumor, args.outdir, args.prefix)

import subprocess
import os
import argparse
def run_msi(bamfile,outdir,prefix):
    MSIsensor = "export LD_LIBRARY_PATH=/software/gcc/gcc-v6.5.0/lib64/:LD_LIBRARY_PATH && /software/MSIsensor/msisensor-ML/msisensor"
    models = "/software/MSIsensor/msisensor-ML/models_hg19_275genes"
    if not os.path.exists(outdir):
        os.mkdir(outdir)
    out=outdir+"/"+prefix
    cmd="%s msi -t %s -o %s.msi.tsv -M %s -d %s/1030c0aa35ca5c263daeae866ad18632" %(MSIsensor,bamfile,out,models,models)
    subprocess.check_call(cmd,shell=True)

if __name__=="__main__":
    parser=argparse.ArgumentParser("Run MSI analysis.")
    parser.add_argument("-t", "--tumor", type=str, help="tumor bam file", required=True)
    parser.add_argument("-o", "--outdir", type=str, help="output directory", default=os.getcwd())
    parser.add_argument("-p", "--prefix", type=str, help="prefix of output", default="MSI")
    args = parser.parse_args()
    run_msi(args.tumor,args.outdir,args.prefix)