def test_polysolver(self):
command = ['source /Users/schubert/Dropbox/phd/software/polysolver/scripts/config.bash && env']
proc = subprocess.Popen(command, stdout = subprocess.PIPE,shell=True)
for line in proc.stdout:
(key, _, value) = line.partition("=")
os.environ[key] = value.strip()
proc.communicate()
origin = "/Users/schubert/Dropbox/phd/software/polysolver/scripts/"
os.environ["PATH"] += os.pathsep + origin
pprint.pprint(dict(os.environ))
command = ["/Users/schubert/Dropbox/phd/software/polysolver/debugg.sh"]
proc = subprocess.Popen(command, stdout = subprocess.PIPE,shell=True)
print "SAMTool call"
print "\n".join( l for l in proc.stdout)
print
print str(proc.stderr)
proc.communicate()
#sys.exit()
polysolver = HLATypingFactory("polysolver")
print polysolver.predict("/Users/schubert/Dropbox/phd/software/polysolver/test/test.bam",
"/Users/schubert/Dropbox/phd/software/polysolver/debugging2/", options="Unknown 1 hg19 STDFQ 0",
delete=False,
command=origin+"shell_call_hla_type")
def test_athlates(self):
origin = "/Users/schubert/Dropbox/PhD/software/Athlates_2014_04_26/bin"
os.environ["PATH"] += os.pathsep + origin
atlates = HLATypingFactory("athlates")
print atlates.predict("/Users/schubert/Dropbox/PhD/software/Athlates_2014_04_26/demo/HG01756/HG01756_a.sort.bam",
"/Users/schubert/Dropbox/PhD/software/Athlates_2014_04_26/demo/output/Fred2_",
options="-msa /Users/schubert/Dropbox/PhD/software/Athlates_2014_04_26/db/msa/A_nuc.txt",
delete=False)
def main():
#Specify CTD interface
# Every CTD Model has to have at least a name and a version, plus any of the optional attributes below them.
model = argparse.ArgumentParser(
description='Commandline tool for HLA typing', )
model.add_argument('-m',
'--method',
type=str,
choices=HLATypingFactory.available_methods().keys(),
default="optitype",
help='The name of the prediction method')
model.add_argument('-v',
'--version',
type=str,
default="",
help='The version of the prediction method')
model.add_argument('-i',
'--input',
type=str,
required=True,
help='Path to the input file')
model.add_argument('-p',
'--paired',
type=str,
default="",
help="Additional input for paired-end typing")
model.add_argument('-r',
'--reference',
type=str,
choices=["rna", "dna"],
default="dna",
help='The reference type to use')
model.add_argument('-o',
'--output',
type=str,
required=True,
help='Path to the output file')
args = model.parse_args()
version = "" if args.version == "" else args.version
if args.method == "optitype":
options = "--" + args.reference if args.paired == "" else args.paired + " " + "--" + args.reference
else:
options = "" if args.paired == "" else "-2 " + args.paired
genotype = HLATypingFactory(args.method).predict(args.input,
"/tmp/",
options=options)
with open(args.output, "w") as f:
f.write("\n".join("HLA-" + a.name for a in genotype))
return 0
def test_seq2HLA(self):
origin = "/home/schubert/Dropbox/PhD/software/seq2hla"
os.environ["PATH"] += os.pathsep + origin
seq2HLA = HLATypingFactory("Seq2HLA")
print(
seq2HLA.predict(
"/home/schubert/Desktop/ERR009105_1.fastq.gz",
origin + "/delete",
options="-2 /home/schubert/Desktop/ERR009105_2.fastq.gz"))
def test_optitype(self):
os.environ[
"PATH"] += os.pathsep + "/Users/schubert/Dropbox/PhD/Porgramming/OptiType/"
#print os.environ["PATH"]
opti = HLATypingFactory("OptiType")
print(
opti.predict(
"/Users/schubert/Dropbox/PhD/Porgramming/OptiType/test/exome/NA11995_SRR766010_1_fished.fastq",
"/tmp/",
options="-d"))
def test_seq2HLA(self):
origin = "/home/schubert/Dropbox/PhD/software/seq2hla"
os.environ["PATH"] += os.pathsep + origin
seq2HLA = HLATypingFactory("Seq2HLA")
print seq2HLA.predict("/home/schubert/Desktop/ERR009105_1.fastq.gz", origin+"/delete", options="-2 /home/schubert/Desktop/ERR009105_2.fastq.gz")
def test_optitype(self):
os.environ["PATH"] += os.pathsep + "/Users/schubert/Dropbox/PhD/Porgramming/OptiType/"
#print os.environ["PATH"]
opti = HLATypingFactory("OptiType")
print opti.predict("/Users/schubert/Dropbox/PhD/Porgramming/OptiType/test/exome/NA11995_SRR766010_1_fished.fastq", "/tmp/", options="-d")
def main():
#Specify CTD interface
# Every CTD Model has to have at least a name and a version, plus any of the optional attributes below them.
model = argparse.ArgumentParser(
description='Commandline tool for HLA typing',
)
model.add_argument('-m',
'--method',
type=str,
choices=HLATypingFactory.available_methods().keys(),
default="optitype",
help='The name of the prediction method'
)
model.add_argument('-v',
'--version',
type=str,
default="",
help='The version of the prediction method'
)
model.add_argument('-i',
'--input',
type=str,
required=True,
help='Path to the input file'
)
model.add_argument('-p',
'--paired',
type=str,
default="",
help="Additional input for paired-end typing"
)
model.add_argument('-r',
'--reference',
type=str,
choices=["rna", "dna"],
default="dna",
help='The reference type to use'
)
model.add_argument('-o',
'--output',
type=str,
required=True,
help='Path to the output file'
)
args = model.parse_args()
version = "" if args.version == "" else args.version
if args.method == "optitype":
options = "--"+args.reference if args.paired == "" else args.paired+" "+"--"+args.reference
else:
options = "" if args.paired == "" else "-2 "+args.paired
genotype = HLATypingFactory(args.method).predict(args.input, "/tmp/", options=options)
with open(args.output, "w") as f:
f.write("\n".join("HLA-"+a.name for a in genotype))
return 0