Exemplo n.º 1
0
    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")
Exemplo n.º 2
0
 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)
Exemplo n.º 3
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"))
Exemplo n.º 4
0
 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"))
Exemplo n.º 5
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")
Exemplo n.º 6
0
 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")