def test_RunExtProg_check(self): prog1 = runExtProg("./program1", pdir=self.data_dir, check_OS=True) self.assertEqual(prog1.program_name, "./program1_" + TestRunExtProg.platform) prog1 = runExtProg("./muscle3.8.31_i86linux64", pdir=self.data_dir, check_OS=True) self.assertEqual(prog1.program_name, "./muscle3.8.31_i86linux64") with self.assertRaises(TypeError): runExtProg("./muscle3.8.31_i86linux64", check_OS=True)
def __init__(self, pdir, wdir, infile, outfile=None, check_exist=True): """ Constructor """ super(RunGlimmer, self).__init__(pdir, wdir, infile, check_exist) self.all_exts = ALL_EXTS # self.parameter_check(pdir, wdir, infile, outfile, check_exist, ".glimmer") self.outfile = self.check_outfile_filename(outfile, ".glimmer") self.glimmer = runExtProg(GLIMMER, pdir=self.pdir, length=2, check_OS=True) self.extract = runExtProg(EXTRACT, pdir=self.pdir, length=2, check_OS=True) self.init_prog()
def __init__(self, pdir, wdir, infile, no_iter=DEFAULT_XGENOVO_NO_ITER, thresh=DEFAULT_XGENOVO_THRESH, outfile=None, check_exist=True): """ Constructor """ super(RunXGenovo, self).__init__(pdir, wdir, infile, check_exist) self.all_exts = ALL_EXTS self.outfile = self.check_outfile_filename(outfile, ".xgenovo") # self.parameter_check(self.pdir, self.wdir, infile, outfile, check_exist, ".genovo") self.assemble = runExtProg(ASSEMBLE, pdir=self.pdir, length=2, check_OS=True) self.finalize = runExtProg(FINALIZE, pdir=self.pdir, length=3, check_OS=True) self.init_prog(no_iter, thresh)
def test_RunExtProg_run_command(self): prog1 = runExtProg("ls") prog1.add_switch("-l") prog1.run() self.out = prog1.output self.assertTrue(self.out.find("main.py")) self.assertTrue(self.out.find("test_run_ext_prog.py"))
def __init__(self, model_file, no_reads, taxon_infile, pdir, wdir, filename=None, check_exist=True): """ Constructor """ # FIXME: allow 454 or Sanger model; put on -c switch. self.all_exts = ALL_EXTS self.parameter_check(pdir, wdir, model_file, taxon_infile, filename, check_exist) self.metasim = runExtProg(METASIM, pdir=self.pdir, length=5, check_OS=True) self.metasim.set_param_at("cmd", 1) self.init_prog(no_reads)
def test_RunExtProg_set_switch(self): prog1 = runExtProg("ls") self.assertEqual(prog1.get_all_switches(), []) prog1.set_switch("-l") self.assertEqual(prog1.get_all_switches(), ["-l"]) prog1.set_switch("-s") self.assertEqual(prog1.get_all_switches(), ["-s"]) prog1.set_switch(["-111", "-222"]) self.assertEqual(prog1.get_all_switches(), ["-111", "-222"])
def test_RunExtProg_update_switch(self): prog1 = runExtProg("ls") prog1.add_switch(["-a", "1", "--b", "2"]) self.assertEqual(prog1.get_all_switches(), ["-a", "1", "--b", "2"]) prog1.update_switch("-a", "3") self.assertEqual(prog1.get_all_switches(), ["-a", "3", "--b", "2"]) prog1.update_switch("-c", "4") self.assertEqual(prog1.get_all_switches(), ["-a", "3", "--b", "2", "-c", "4"]) prog1.update_switch("-b", "5") self.assertEqual(prog1.get_all_switches(), ["-a", "3", "--b", "2", "-c", "4", "-b", "5"]) prog1.update_switch("-C", "6") self.assertEqual(prog1.get_all_switches(), ["-a", "3", "--b", "2", "-c", "4", "-b", "5", "-C", "6"]) prog1.update_switch("--b", "7") self.assertEqual(prog1.get_all_switches(), ["-a", "3", "--b", "7", "-c", "4", "-b", "5", "-C", "6"])
def test_RunExtProg_toggle_switch(self): prog1 = runExtProg("ls") prog1.add_switch(["-a", "1"]) prog1.toggle_switch("-t") self.assertEqual(prog1.get_all_switches(), ["-a", "1", "-t"]) prog1.toggle_switch("-t") self.assertEqual(prog1.get_all_switches(), ["-a", "1"]) prog1.toggle_switch("-t", 0) self.assertEqual(prog1.get_all_switches(), ["-a", "1"]) prog1.toggle_switch("-t", 1) self.assertEqual(prog1.get_all_switches(), ["-a", "1", "-t"]) prog1.toggle_switch("-t", 1) self.assertEqual(prog1.get_all_switches(), ["-a", "1", "-t"]) prog1.toggle_switch("-t", 0) self.assertEqual(prog1.get_all_switches(), ["-a", "1"])
def test_RunExtProg_run_program(self): self.filename = "tempAlignmentOutput.fasta" if os.path.isfile(self.data_dir + self.filename): os.remove(self.data_dir + self.filename) self.assertFalse(os.listdir(self.data_dir).count(self.filename)) prog2 = runExtProg("./muscle3.8.31_i86linux64", pdir=self.data_dir) self._switch = "-in testAlignmentInput.fasta -out".split() self._switch.append(self.filename) prog2.add_switch(self._switch) prog2.run() self.out = prog2.errors # not sure why output capture by stderr, but it works self.assertTrue(os.listdir(self.data_dir).count(self.filename)) self.assertTrue(self.out.find("MUSCLE v3.8.31")) self.assertTrue(self.out.find("testAlignmentInput 2 seqs")) # clean up os.remove(self.data_dir + self.filename)
def test_RunExtProg_append_reset_switch(self): prog1 = runExtProg("ls") self.assertEqual(prog1.get_all_switches(), []) prog1.add_switch("-l") self.assertEqual(prog1.get_all_switches(), ["-l"]) prog1.add_switch("-s") self.assertEqual(prog1.get_all_switches(), ["-l", "-s"]) prog1.add_switch(["-1", "-2"]) self.assertEqual(prog1.get_all_switches(), ["-l", "-s", "-1", "-2"]) prog1.add_switch(["-x"]) self.assertEqual(prog1.get_all_switches(), ["-l", "-s", "-1", "-2", "-x"]) prog1.reset_switch() self.assertEqual(prog1.get_all_switches(), []) prog1.add_switch(["-a", "-b"]) self.assertEqual(prog1.get_all_switches(), ["-a", "-b"])
def __init__(self, pdir, wdir, infile, comparison='-allPairs', cv=DEFAULT_CV, exp=DEFAULT_EXP, clumps=DEFAULT_CLUMPS, jobID=None, csv_files=None, check_exist=True, overwrite=False): """ Constructor """ super(RunMINE, self).__init__(pdir, wdir, infile, check_exist) self.all_exts = ALL_EXTS if jobID is None: self.jobID = "MineOutput" else: self.jobID = jobID self.overwrite = overwrite # self.parameter_check(pdir, wdir, infile, infile, False, "") # if not self.infile.endswith(".csv"): # self.infile = self.infile + ".csv" # self.outfile = self.infile + "," + self.jobID self.outfile = self.check_outfile_filename(self.infile, ".mine.csv") # print self.infile, self.outfile, self.pdir # print self.check_outfiles_with_filetag_exist(self.outfile) //FIXME: anothre hack self.mine = runExtProg(MINE, pdir=self.pdir, length=6 + offset, check_OS=True) self.mine.set_param_at("-jar", 1) self.mine.set_param_at("MINE.jar", 2) self.init_prog(comparison, cv, exp, clumps) self.csv_files = csv_files if self.csv_files is None: print "TODO?"
def __init__(self, infile, pdir, blast_db, wdir=None, outfile=None, check_exist=True, e_value='1e-15', blast_thread=1): """ :param infile: The input sequence to blast :param pdir: program dir :param wdir: working dir? :param outfile: output file to write csv summary :param check_exist: check if files exist :param e_value: threshhold to provide to blast :param blast_db: the local NCBI formatted blast databae :return: an initialized RunBlast """ super(RunBlast, self).__init__(pdir, wdir, infile) self.all_exts = ALL_EXTS self.e_value = e_value self.blast_db = blast_db self.blast_thread = blast_thread self.outfile = self.check_outfile_filename(outfile, ".blast.csv") self.intermediate_file = infile + INT_FILE_EXT # print "BLAST Setting", self.blast_db, self.infile, self.outfile, self.pdir self.blastx = runExtProg(BLASTX, pdir=self.pdir, length=14, check_OS=True) # step 2 is a python script. self.init_prog()