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 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")