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)
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)
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)
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)
def test_group_divide():
path = "/home/zerodel/Workspace/codon_lst"
divide_file = "/home/zerodel/Workspace/codon_all.lst"
RNAsnp.group_divide(path, divide_file)
def test_group_divide():
path = "/home/zerodel/Workspace/codon_lst"
divide_file = "/home/zerodel/Workspace/codon_all.lst"
RNAsnp.group_divide(path, divide_file)