コード例 #1
0
def mouse_prepare():
    parent_path = "/home/zerodel/GitProject"
    work_path = "/home/zerodel/Workspace/mouse"
    source_path = "/home/zerodel/Workspace/mouse/mouse_rnasnp"
    output_path = "/home/zerodel/Workspace/mouse/cpd"
    single_codon_file_path = os.path.join(work_path, "codon_codon_lst")
    cc_significant_file_path = os.path.join(work_path, "codon_all.lst")
    rnasnp_files, snppathname = RNAsnp.snp_dir_list(source_path)

    # # step 1 , set up  .cpd files
    # RNAsnp.snp_dir_traversal(rnasnp_files, snppathname, output_path, True)
    # # # step 2 , print each codon lst file
    # for codon in gc.codon_list_hypothesis:
    #     codon_with_direction = codon + "_"
    #     print "--->", codon_with_direction
    #     RNAsnp.cpd_dir_traversal(codon_with_direction, output_path, single_codon_file_path)

    RNAsnp.group_divide(single_codon_file_path, cc_significant_file_path)

    gu_model_file = "/home/zerodel/GitProjects/python-rna-structure/gu_model.mdl"
    rebuild_model_file = "/home/zerodel/GitProjects/python-rna-structure/rebuild_model.mdl"
    nested_model_file = os.path.join(work_path, "rna_structure_full_mouse.mdl")

    # matrixh.degenerate(gu_model_file,
    #                    rebuild_model_file)

    matrixh.nest_export(rebuild_model_file, nested_model_file,
                        cc_significant_file_path)
コード例 #2
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ファイル: 1015.py プロジェクト: zerodel/python-rna-structure
def make_model():
    work_path = "d:/Workspace/Ecoli"
    source_path = "d:/Workspace/Ecoli/ecoli_snp"
    output_path = "d:/Workspace/Ecoli/cpd_full"
    single_codon_file_path = os.path.join(work_path, "codon_lst")
    cc_significant_file_path = os.path.join(work_path, "codon_all.lst")
    #step 1 , set up  .cpd files

    gu_model_file = "d:/Home/GitProject/python-rna-structure/gu_model.mdl"
    rebuild_model_file = "d:/Workspace/Ecoli/rebuild_model_full_length.mdl"
    nested_model_file = "d:/Workspace/Ecoli/rna_full_length_structure.mdl"
    rnasnp_files, snppathname = RNAsnp.snp_dir_list(source_path)
    RNAsnp.snp_dir_traversal(rnasnp_files, snppathname, output_path, True,
                             True)
    ###step 2 , print each codon lst file
    for codon in gc.codon_list_hypothesis:
        codon_with_direction = codon + "_"
        print "--->", codon_with_direction
        RNAsnp.cpd_dir_traversal(codon_with_direction, output_path,
                                 single_codon_file_path)

    RNAsnp.group_divide(single_codon_file_path, cc_significant_file_path)

    matrixh.degenerate(gu_model_file, rebuild_model_file)

    matrixh.nest_export(rebuild_model_file, nested_model_file,
                        cc_significant_file_path)
コード例 #3
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    def test_nest_export(self):
        pyMatrix.degenerate(gtr_nested_file="gu_model.mdl",
                            gtr_mdl_file="rebuilt_gtr.mdl")
        model_your = pyMatrix.nest_export(gtr_mdl="rebuilt_gtr.mdl",
                                          gtr_nested="rna_structure.mdl",
                                          ccl_file="../50CCl.lst")
        print len(re.findall("\*psi", model_your)), "psi in model_your"
        self.assertTrue(os.path.exists("rna_structure.mdl"))

        index_codon = gc.codon_list_hypothesis
        mg2 = pyMH.ModelHYPHY()
        tuple_list = mg2.read_lst("../50CCl.lst")

        zero_psi = True
        with open(name="rna_structure.mdl", mode="r") as readerG:
            model_nest = [line for line in readerG]

        print len(model_nest), " lines in model"
        for line_num, line in enumerate(model_nest):
            entry_in_line = line.split(",")
            for entry_index, single_entry in enumerate(entry_in_line):
                if "psi" in single_entry:
                    zero_psi = False
                    self.assertIn(
                        (index_codon[line_num], index_codon[entry_index]),
                        tuple_list)

        self.assertFalse(zero_psi)
コード例 #4
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def mouse_prepare():
    parent_path = "/home/zerodel/GitProject"
    work_path = "/home/zerodel/Workspace/mouse"
    source_path = "/home/zerodel/Workspace/mouse/mouse_rnasnp"
    output_path = "/home/zerodel/Workspace/mouse/cpd"
    single_codon_file_path = os.path.join(work_path, "codon_codon_lst")
    cc_significant_file_path = os.path.join(work_path, "codon_all.lst")
    rnasnp_files, snppathname = RNAsnp.snp_dir_list(source_path)

    # # step 1 , set up  .cpd files
    # RNAsnp.snp_dir_traversal(rnasnp_files, snppathname, output_path, True)
    # # # step 2 , print each codon lst file
    # for codon in gc.codon_list_hypothesis:
    #     codon_with_direction = codon + "_"
    #     print "--->", codon_with_direction
    #     RNAsnp.cpd_dir_traversal(codon_with_direction, output_path, single_codon_file_path)

    RNAsnp.group_divide(single_codon_file_path, cc_significant_file_path)

    gu_model_file = "/home/zerodel/GitProjects/python-rna-structure/gu_model.mdl"
    rebuild_model_file = "/home/zerodel/GitProjects/python-rna-structure/rebuild_model.mdl"
    nested_model_file = os.path.join(work_path, "rna_structure_full_mouse.mdl")

    # matrixh.degenerate(gu_model_file,
    #                    rebuild_model_file)

    matrixh.nest_export(rebuild_model_file, nested_model_file, cc_significant_file_path)
コード例 #5
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ファイル: 1015.py プロジェクト: zerodel/python-rna-structure
def make_model():
    work_path = "d:/Workspace/Ecoli"
    source_path = "d:/Workspace/Ecoli/ecoli_snp"
    output_path = "d:/Workspace/Ecoli/cpd_full"
    single_codon_file_path = os.path.join(work_path, "codon_lst")
    cc_significant_file_path = os.path.join(work_path, "codon_all.lst")
        #step 1 , set up  .cpd files

    gu_model_file = "d:/Home/GitProject/python-rna-structure/gu_model.mdl"
    rebuild_model_file = "d:/Workspace/Ecoli/rebuild_model_full_length.mdl"
    nested_model_file = "d:/Workspace/Ecoli/rna_full_length_structure.mdl"
    rnasnp_files, snppathname = RNAsnp.snp_dir_list(source_path)
    RNAsnp.snp_dir_traversal(rnasnp_files, snppathname, output_path, True, True)
    ###step 2 , print each codon lst file
    for codon in gc.codon_list_hypothesis:
        codon_with_direction = codon + "_"
        print "--->", codon_with_direction
        RNAsnp.cpd_dir_traversal(codon_with_direction, output_path, single_codon_file_path)

    RNAsnp.group_divide(single_codon_file_path, cc_significant_file_path)

    matrixh.degenerate(gu_model_file,
                       rebuild_model_file)

    matrixh.nest_export(rebuild_model_file, nested_model_file, cc_significant_file_path)
コード例 #6
0
ファイル: 0912.py プロジェクト: zerodel/python-rna-structure
def built_model():
    parent_path = "/home/zerodel/GitProject"
    work_path = "/home/zerodel/Workspace"
    source_path = "/home/zerodel/Workspace/ecoli_snp"
    output_path = "/home/zerodel/Workspace/cpd_store_site"
    single_codon_file_path = os.path.join(work_path, "codon_lst")
    cc_significant_file_path = os.path.join(work_path, "codon_all.lst")
    rnasnp_files, snppathname = RNAsnp.snp_dir_list(source_path)



    #step 1 , set up  .cpd files
    # RNAsnp.snp_dir_traversal(rnasnp_files, snppathname, output_path, True)
    # # step 2 , print each codon lst file
    # for codon in gc.codon_list_hypothesis:
    #     codon_with_direction = codon + "_"
    #     print "--->", codon_with_direction
    #     RNAsnp.cpd_dir_traversal(codon_with_direction, output_path, single_codon_file_path, 60)



    # kmeans meet some problem here 20140912
    # # R kmeans part ******
    # print "kmeans of cluster"
    # kmeans_script_path = os.path.join(parent_path,"kmeans.R")
    # cc_significant_file_path = os.path.join(work_path, "codon20.lst")
    # cmd_line = "Rscript " + kmeans_script_path + " " +  single_codon_file_path + " > " + cc_significant_file_path
    # os.system(cmd_line)

    # here we choose a  new way to infer the group 20140912



    # read the result of R process
    cc_significant_raw = RNAsnp.get_large_codon_group(cc_significant_file_path)
    cc_significant = [x for x in cc_significant_raw]
    print len(cc_significant)

    gu_model_file = "/home/zerodel/GitProjects/python-rna-structure/gu_model.mdl"
    rebuild_model_file = "/home/zerodel/GitProjects/python-rna-structure/rebuild_model.mdl"
    nested_model_file = "/home/zerodel/GitProjects/python-rna-structure/rna_structure.mdl"
    matrixh.degenerate(gu_model_file,
                       rebuild_model_file)

    matrixh.nest_export(rebuild_model_file, nested_model_file, cc_significant_file_path)
コード例 #7
0
ファイル: 0926.py プロジェクト: zerodel/python-rna-structure
def make_model():
    single_codon_file_path = os.path.join(work_path, "codon_lst")
    cc_significant_file_path = os.path.join(work_path, "codon_all.lst")

    #step 1 , set up  .cpd files

    rnasnp_files, snppathname = RNAsnp.snp_dir_list(source_path)
    RNAsnp.snp_dir_traversal(rnasnp_files, snppathname, output_path, True, True)
    # step 2 , print each codon lst file
    for codon in gc.codon_list_hypothesis:
        codon_with_direction = codon + "_"
        print "--->", codon_with_direction
        RNAsnp.cpd_dir_traversal(codon_with_direction, output_path, single_codon_file_path)

    # RNAsnp.group_divide(single_codon_file_path, cc_significant_file_path)

    matrixh.degenerate(gu_model_file,
                       rebuild_model_file)

    matrixh.nest_export(rebuild_model_file, nested_model_file, cc_significant_file_path)
コード例 #8
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def built_model():
    parent_path = "/home/zerodel/GitProject"
    work_path = "/home/zerodel/Workspace"
    source_path = "/home/zerodel/Workspace/ecoli_snp"
    output_path = "/home/zerodel/Workspace/cpd_store_site"
    single_codon_file_path = os.path.join(work_path, "codon_lst")
    cc_significant_file_path = os.path.join(work_path, "codon_all.lst")
    rnasnp_files, snppathname = RNAsnp.snp_dir_list(source_path)

    #step 1 , set up  .cpd files
    # RNAsnp.snp_dir_traversal(rnasnp_files, snppathname, output_path, True)
    # # step 2 , print each codon lst file
    # for codon in gc.codon_list_hypothesis:
    #     codon_with_direction = codon + "_"
    #     print "--->", codon_with_direction
    #     RNAsnp.cpd_dir_traversal(codon_with_direction, output_path, single_codon_file_path, 60)

    # kmeans meet some problem here 20140912
    # # R kmeans part ******
    # print "kmeans of cluster"
    # kmeans_script_path = os.path.join(parent_path,"kmeans.R")
    # cc_significant_file_path = os.path.join(work_path, "codon20.lst")
    # cmd_line = "Rscript " + kmeans_script_path + " " +  single_codon_file_path + " > " + cc_significant_file_path
    # os.system(cmd_line)

    # here we choose a  new way to infer the group 20140912

    # read the result of R process
    cc_significant_raw = RNAsnp.get_large_codon_group(cc_significant_file_path)
    cc_significant = [x for x in cc_significant_raw]
    print len(cc_significant)

    gu_model_file = "/home/zerodel/GitProjects/python-rna-structure/gu_model.mdl"
    rebuild_model_file = "/home/zerodel/GitProjects/python-rna-structure/rebuild_model.mdl"
    nested_model_file = "/home/zerodel/GitProjects/python-rna-structure/rna_structure.mdl"
    matrixh.degenerate(gu_model_file, rebuild_model_file)

    matrixh.nest_export(rebuild_model_file, nested_model_file,
                        cc_significant_file_path)
コード例 #9
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ファイル: 0926.py プロジェクト: zerodel/python-rna-structure
def make_model():
    single_codon_file_path = os.path.join(work_path, "codon_lst")
    cc_significant_file_path = os.path.join(work_path, "codon_all.lst")

    #step 1 , set up  .cpd files

    rnasnp_files, snppathname = RNAsnp.snp_dir_list(source_path)
    RNAsnp.snp_dir_traversal(rnasnp_files, snppathname, output_path, True,
                             True)
    # step 2 , print each codon lst file
    for codon in gc.codon_list_hypothesis:
        codon_with_direction = codon + "_"
        print "--->", codon_with_direction
        RNAsnp.cpd_dir_traversal(codon_with_direction, output_path,
                                 single_codon_file_path)

    # RNAsnp.group_divide(single_codon_file_path, cc_significant_file_path)

    matrixh.degenerate(gu_model_file, rebuild_model_file)

    matrixh.nest_export(rebuild_model_file, nested_model_file,
                        cc_significant_file_path)
コード例 #10
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    def test_nest_export(self):
        pyMatrix.degenerate(gtr_nested_file="gu_model.mdl", gtr_mdl_file="rebuilt_gtr.mdl")
        model_your = pyMatrix.nest_export(gtr_mdl="rebuilt_gtr.mdl", gtr_nested="rna_structure.mdl", ccl_file="../50CCl.lst")
        print len(re.findall("\*psi", model_your)), "psi in model_your"
        self.assertTrue(os.path.exists("rna_structure.mdl"))

        index_codon = gc.codon_list_hypothesis
        mg2 = pyMH.ModelHYPHY()
        tuple_list = mg2.read_lst("../50CCl.lst")

        zero_psi = True
        with open(name="rna_structure.mdl", mode="r") as readerG:
            model_nest = [line for line in readerG ]

        print len(model_nest), " lines in model"
        for line_num, line in enumerate(model_nest):
            entry_in_line = line.split(",")
            for entry_index, single_entry in enumerate(entry_in_line):
                if "psi" in single_entry:
                    zero_psi = False
                    self.assertIn((index_codon[line_num], index_codon[entry_index]), tuple_list)

        self.assertFalse(zero_psi)