Ejemplo n.º 1
0
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)
Ejemplo n.º 2
0
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)
Ejemplo n.º 3
0
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)
Ejemplo n.º 4
0
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)