def bamDiff(bamfn1, bamfn2, path):
bamutil_path = params.GetConfigReader().get('SOFTWARE', 'bamutil_path')
command = " ".join([
bamutil_path, "diff", "--in1", bamfn1, "--in2", bamfn2, "--out",
"/".join([path, "diff.bam"])
])
runCommand(command)
def GetProjectNamePathRunID():
results_path = params.GetConfigReader().get('RESULTS', 'results_path')
cancer_type = params.GetCancerType()
cancer_dir_path = "/".join([results_path, cancer_type])
haplotype_path = "/".join([cancer_dir_path, "haplotypedir"])
tmpbams_path = "/".join([cancer_dir_path, "tmpbams"])
finalbams_path = "/".join([cancer_dir_path, "finalbams"])
sentinel_path = CheckPath(cancer_dir_path + '/' + params.GetProjectName() +
"_" + rid.GetRunID() + '/sentinels/')
return sentinel_path, results_path, haplotype_path, cancer_dir_path, tmpbams_path, finalbams_path
def main(args):
outbamfn = args.outBamFile
configReader = params.GetConfigReader()
params.InitConfigReader(args.configfile)
params.SetCancerType(args.cancerType)
params.SetOutputFileName(args.outBamFile)
params.SetSplitBamsPath(args.splitbams)
params.SetPhase(args.phase)
params.SetctDNA(args.ctDNA)
params.SetXY(args.singleXY)
params.SetCNV(args.cnvBed)
results_path = configReader.get('RESULTS', 'results_path')
cnvdir = "/".join([results_path, "cnv_dir"])
if (not os.path.exists(cnvdir)):
os.makedirs(cnvdir)
createEventBedFiles(cnvdir, params.GetCNV())
params.SetCNVDir(cnvdir)
# set software paths
java_path = bamhelp.GetJavaPath()
beagle_path = bamhelp.GetBeaglePath()
samtools_path = bamhelp.GetSamtoolsPath()
bedtools_path = bamhelp.GetBedtoolsPath()
vcftools_path = bamhelp.GetVCFtoolsPath()
sambamba_path = bamhelp.GetSambambaPath()
params.SetSoftwarePath(java_path, beagle_path, samtools_path,
bedtools_path, vcftools_path, sambamba_path)
if (args.phase):
run_pipeline(results_path)
else:
print('Please provide costume phasing algorithm')
def main(args):
outbamfn = args.outBamFile
configReader = params.GetConfigReader()
params.InitConfigReader(args.configfile)
params.SetGainCNV(args.cnvAmpFile)
params.SetLossCNV(args.cnvDelFile)
params.SetCancerType(args.cancerType)
params.SetOutputFileName(args.outBamFile)
params.SetSplitBamsPath(args.splitbams)
results_path = configReader.get('RESULTS', 'results_path')
#set software paths
java_path = bamhelp.GetJavaPath()
beagle_path = bamhelp.GetBeaglePath()
samtools_path = bamhelp.GetSamtoolsPath()
bedtools_path = bamhelp.GetBedtoolsPath()
vcftools_path = bamhelp.GetVCFtoolsPath()
sambamba_path = bamhelp.GetSambambaPath()
params.SetSoftwarePath(java_path, beagle_path, samtools_path,
bedtools_path, vcftools_path, sambamba_path)
if (args.phase):
run_pipeline(results_path)
parser.add_argument(
'--project-name', action='store', required=True, dest='project_name',
help='name of the project')
parser.add_argument(
'-r', '--run_id', action='store', type=int, dest='custom_run_id',
help='manually enter run_id (used to re-launch a run)', default=False)
args = parser.parse_args()
t0 = time.time()
args = parser.parse_args()
current_path = os.path.dirname(os.path.realpath(__file__))
outbamfn = args.outBamFile
configReader = params.GetConfigReader()
params.InitConfigReader(args.configfile)
params.SetProjectName(args.project_name)
params.SetProgramPath(current_path)
params.SetInfile(args.infile)
params.SetGainCNV(args.cnvAmpFile)
params.SetLossCNV(args.cnvDelFile)
params.SetCancerType(args.cancerType)
params.SetOutputFileName(args.outBamFile)
# set the run id used for this run
if args.custom_run_id == False:
# increment and set runID