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()