def test_RunGlimmer_init(self): infile_var = "all_reads.fa" test_glimmer = RunGlimmer(infile_var, pdir=self.data_dir, check_exist=False) expected = [self.data_dir + infile_var, self.data_dir + "all_reads.glimmer"] self.assertEqual(test_glimmer.get_all_switches()[0], expected) expected = [self.data_dir + infile_var, self.data_dir + "all_reads.glimmer.predict"] self.assertEqual(test_glimmer.get_all_switches()[1], expected)
def test_RunGlimmer_set_infile_outfile(self): infile_var = "test_infile.fasta" outfile_var = "test_outfile.fasta" glimmer = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) expected = ([self.data_dir + infile_var, self.data_dir + "test_outfile.fasta"], [self.data_dir + infile_var, self.data_dir + "test_outfile.fasta.predict"]) self.assertEqual(glimmer.get_all_switches(), expected) # orf_var = "testORF" # glimmer = RunGlimmer(infile=infile_var, filename=outfile_var, orfs=orf_var, pdir=self.data_dir, check_exist=False) # self.assertEqual(3, len(glimmer.get_switch())) # self.assertEqual(glimmer.get_switch(), [self.data_dir + infile_var, self.data_dir + outfile_var, # self.data_dir + orf_var]) infile_var = "test_infile2.fasta" glimmer.set_infile_name(infile_var) expected = ([ infile_var, self.data_dir + "test_outfile.fasta"], [ infile_var, self.data_dir + "test_outfile.fasta.predict"]) self.assertEqual(glimmer.get_all_switches(), expected) outfile_var = "test_outfile2.fasta" glimmer.set_outfile(outfile_var) expected = ([ infile_var, "test_outfile2.fasta"], [ infile_var, "test_outfile2.fasta.predict"]) self.assertEqual(glimmer.get_all_switches(), expected)
def init_program(self): # self.metasim = RunMetaSim.create_metasim_from_setting(self.setting) if self.setting.run_mine: self.mine = RunMINE.create_class_from_setting(self.setting) else: if self.setting.get("assembler_prog") is "genovo": self.assembler = RunGenovo.create_genovo_from_setting(self.setting) elif self.setting.get("assembler_prog") is "xgenovo": self.assembler = RunXGenovo.create_xgenovo_from_setting(self.setting) self.glimmer = RunGlimmer.create_glimmer_from_setting(self.setting) # self.blast = run_BLAST.RunBlast.create_blast_from_setting(self.setting) self.blast = RunBlast.create_blast_from_setting(self.setting)
def test_RunGlimmer_run(self): """ with debug=True should be able to see all 8 steps debug - output message: Step 1 of 8: Finding long orfs for training Step 2 of 8: Extracting training sequences Step 3 of 8: Building ICM Step 4 of 8: Running first Glimmer3 Step 5 of 8: Getting training coordinates Step 6 of 8: Making PWM from upstream regions Step 7 of 8: Getting start-codon usage Step 8 of 8: Running second Glimmer3 """ infile_var = "tIn.fasta" outfile_var = "tOut" glimmer = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var) self.assertFalse(is_exist) glimmer.run(debug=1) is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var) self.assertTrue(is_exist)
def test_RunGlimmer_check_outfiles_exist(self): """ check if ./g3iterated.csh finished running, should produce 10 output files only pass if all 10 exist """ infile_var = "tIn.fasta" outfile_var = "tOut" glimmer = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var) self.assertFalse(is_exist) glimmer.run(True) is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var) self.assertTrue(is_exist) # negative test, outfiles are not suppose to exist outfile_var = "fileNotExist" glimmer = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) is_exist, _ = glimmer.check_outfiles_with_filetag_exist(self.data_dir + outfile_var) self.assertFalse(is_exist)
def test_RunGlimmer_set_outfile(self): infile_var = "test_infile.fasta" outfile_var = "testOutfile" extract = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) expected = ([self.data_dir + infile_var, self.data_dir + "testOutfile"], [self.data_dir + infile_var, self.data_dir + "testOutfile.predict"]) self.assertEqual(extract.get_all_switches(), expected) infile_var = "test_infile.xyz.fasta.abc" extract = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) expected = ([self.data_dir + infile_var, self.data_dir + "testOutfile"], [self.data_dir + infile_var, self.data_dir + "testOutfile.predict"]) self.assertEqual(extract.get_all_switches(), expected) infile_var = "test_infile" extract = RunGlimmer(infile=infile_var, outfile=outfile_var, pdir=self.data_dir, check_exist=False) expected = ([self.data_dir + infile_var, self.data_dir + "testOutfile"], [self.data_dir + infile_var, self.data_dir + "testOutfile.predict"]) self.assertEqual(extract.get_all_switches(), expected)