コード例 #1
0
ファイル: test_run_glimmer.py プロジェクト: YoderLab/MMAP
    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)
コード例 #2
0
ファイル: test_run_glimmer.py プロジェクト: YoderLab/MMAP
    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)
コード例 #3
0
ファイル: software_assembler.py プロジェクト: YoderLab/MMAP
    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)
コード例 #4
0
ファイル: test_run_glimmer.py プロジェクト: YoderLab/MMAP
    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)
コード例 #5
0
ファイル: test_run_glimmer.py プロジェクト: YoderLab/MMAP
    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)
コード例 #6
0
ファイル: test_run_glimmer.py プロジェクト: YoderLab/MMAP
    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)