def cpd_reshape_export(cpd_path, ccl_file, output_file, codon_vector=gc.codon_list_hypothesis[:]):
cpd_main = RNAsnp.get_whole_cpd(cpd_path)
#codon_vector = gc.codon_list_hypothesis[:]
mp = pyMH.ModelHYPHY(lst_2_tuple_file_name=ccl_file)
with open(output_file, "w") as writer:
writer.write("from\tto\tMutationCount\tMutationClass\n")
available_cc = cpd_main.keys()
for codon_origin in codon_vector:
for codon_target in codon_vector:
# build a line for lst file
num_mutation = 0
class_mutation = 0
if (codon_origin, codon_target) in available_cc:
num_mutation = len(cpd_main[codon_origin, codon_target])
codon_check_response = mp.check_codons(codon_origin, codon_target)
if type(codon_check_response) == tuple: # two codon only differ one site
is_transversion, is_sysnonmous, is_larger, nt_diff = codon_check_response
class_mutation += 1
if not is_sysnonmous:
class_mutation += 1
if is_larger:
class_mutation += 2
writer.write("%d\t%d\t%d\t%d\n" % (codon_vector.index(codon_origin) + 1,
codon_vector.index(codon_target) + 1,
num_mutation,
class_mutation))
def main2():
cpd_main = RNAsnp.get_whole_cpd("/home/zerodel/Workspace/cpd_store_site")
codon_vector = gc.codon_list_hypothesis
with open("/home/zerodel/GitProjects/python-rna-structure/data/rnasnp.matrix", "w") as writer:
for codon1 in codon_vector:
# build a line for lst file
line_single = []
for codon2 in codon_vector:
line_single.append(str(len(cpd_main[(codon1, codon2)])))
writer.write("\t".join(line_single) + "\n")
with open("/home/zerodel/GitProjects/python-rna-structure/data/codon_vector.txt", "w") as writer:
writer.write("\n".join(gc.codon_list_hypothesis))
def main2():
cpd_main = RNAsnp.get_whole_cpd("/home/zerodel/Workspace/cpd_store_site")
codon_vector = gc.codon_list_hypothesis
with open(
"/home/zerodel/GitProjects/python-rna-structure/data/rnasnp.matrix",
"w") as writer:
for codon1 in codon_vector:
# build a line for lst file
line_single = []
for codon2 in codon_vector:
line_single.append(str(len(cpd_main[(codon1, codon2)])))
writer.write("\t".join(line_single) + "\n")
with open(
"/home/zerodel/GitProjects/python-rna-structure/data/codon_vector.txt",
"w") as writer:
writer.write("\n".join(gc.codon_list_hypothesis))
def main3():
cpd_main = RNAsnp.get_whole_cpd("/home/zerodel/Workspace/cpd_store_site")
codon_vector = gc.codon_list_64
with open("/home/zerodel/GitProjects/python-rna-structure/data/fullRnasnp.matrix", "w") as writer:
available_cc = cpd_main.keys()
for codon1 in codon_vector:
# build a line for lst file
line_single = []
for codon2 in codon_vector:
if (codon1, codon2) in available_cc:
line_single.append(str(len(cpd_main[(codon1, codon2)])))
else:
line_single.append(str(0))
writer.write("\t".join(line_single) + "\n")
with open("/home/zerodel/GitProjects/python-rna-structure/data/codon_vector64.txt", "w") as writer:
writer.write("\n".join(gc.codon_list_64))
def main3():
cpd_main = RNAsnp.get_whole_cpd("/home/zerodel/Workspace/cpd_store_site")
codon_vector = gc.codon_list_64
with open(
"/home/zerodel/GitProjects/python-rna-structure/data/fullRnasnp.matrix",
"w") as writer:
available_cc = cpd_main.keys()
for codon1 in codon_vector:
# build a line for lst file
line_single = []
for codon2 in codon_vector:
if (codon1, codon2) in available_cc:
line_single.append(str(len(cpd_main[(codon1, codon2)])))
else:
line_single.append(str(0))
writer.write("\t".join(line_single) + "\n")
with open(
"/home/zerodel/GitProjects/python-rna-structure/data/codon_vector64.txt",
"w") as writer:
writer.write("\n".join(gc.codon_list_64))
if sys.platform == 'win32':
x = x.lower()
if new_path in (x, x + os.sep):
return 0
sys.path.append(new_path)
# if you want the new_path to take precedence over existing
# directories already in sys.path, instead of appending, use:
# sys.path.insert(0, new_path)
return 1
AddSysPath("..")
import pyRNAsnp.pyRNAsnp as pyr
### for test in emacs python mode
test_emacs = True
if __name__ == "__main__":
test_emacs = False
if (test_emacs):
print "hello world"
cpd_path = '/media/zerodel/Program/Workspace/Ecoli/cpd_full'
print cpd_path
whole = pyr.get_whole_cpd(
"/media/zerodel/Program/Workspace/Ecoli/cpd_full")
print len(whole)
if __name__ == "__main__":
pass
if new_path in (x, x + os.sep):
return 0
sys.path.append(new_path)
# if you want the new_path to take precedence over existing
# directories already in sys.path, instead of appending, use:
# sys.path.insert(0, new_path)
return 1
AddSysPath("..")
import pyRNAsnp.pyRNAsnp as pyr
### for test in emacs python mode
test_emacs = True
if __name__ == "__main__":
test_emacs = False
if (test_emacs):
print "hello world"
cpd_path = '/media/zerodel/Program/Workspace/Ecoli/cpd_full'
print cpd_path
whole = pyr.get_whole_cpd("/media/zerodel/Program/Workspace/Ecoli/cpd_full")
print len(whole)
if __name__ == "__main__":
pass
"w") as writer:
writer.write("\n".join(gc.codon_list_hypothesis))
if __name__ == "__main__":
parent_path = "/home/zerodel/GitProject"
work_path = "/home/zerodel/Workspace"
source_path = "/home/zerodel/Workspace/yeast_rnasnp"
output_path = "/home/zerodel/Workspace/yeast_cpd"
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)
cpd_main = RNAsnp.get_whole_cpd(output_path)
codon_vector = gc.codon_list_64
with open(
"/home/zerodel/GitProjects/python-rna-structure/data/YeastfullRnasnp.matrix",
"w") as writer:
available_cc = cpd_main.keys()
for codon1 in codon_vector:
# build a line for lst file
line_single = []
for codon2 in codon_vector:
if (codon1, codon2) in available_cc:
line_single.append(str(len(cpd_main[(codon1, codon2)])))
else:
line_single.append(str(0))
writer.write("\t".join(line_single) + "\n")
# sys.path.insert(0, new_path)
return 1
AddSysPath("..")
import pyRNAsnp.pyRNAsnp as pyr
import pyHYPHY.global_constants as gc
# testing part in emacs
DEBUG_WITH_EMACS = True
if __name__ == "__main__":
DEBUG_WITH_EMACS = False
if DEBUG_WITH_EMACS:
print "hello world"
cpd_path = "/Users/zerodel/WorkSpace/data/cpd_full"
whole_cpd = pyr.get_whole_cpd(cpd_path)
length_cc = [(key, len(whole_cpd[key])) for key in whole_cpd.keys() if len(whole_cpd[key])]
length_cc = sorted(length_cc)
codon_order = gc.codon_list_hypothesis
with open("length_cpd.lst", "w") as writek:
writek.write("\t".join(codon_order) + "\n")
for c1 in codon_order:
for c2 in codon_order:
writek.write(str(len(whole_cpd[(c1, c2)])))
writek.write("\t")
wri
if __name__ == "__main__":
pass
line_single.append(str(len(cpd_main[(codon1, codon2)])))
writer.write("\t".join(line_single) + "\n")
with open("/home/zerodel/GitProjects/python-rna-structure/data/codon_vector.txt", "w") as writer:
writer.write("\n".join(gc.codon_list_hypothesis))
if __name__ == "__main__":
parent_path = "/home/zerodel/GitProject"
work_path = "/home/zerodel/Workspace"
source_path = "/home/zerodel/Workspace/yeast_rnasnp"
output_path = "/home/zerodel/Workspace/yeast_cpd"
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)
cpd_main = RNAsnp.get_whole_cpd(output_path)
codon_vector = gc.codon_list_64
with open("/home/zerodel/GitProjects/python-rna-structure/data/YeastfullRnasnp.matrix", "w") as writer:
available_cc = cpd_main.keys()
for codon1 in codon_vector:
# build a line for lst file
line_single = []
for codon2 in codon_vector:
if (codon1, codon2) in available_cc:
line_single.append(str(len(cpd_main[(codon1, codon2)])))
else:
line_single.append(str(0))
writer.write("\t".join(line_single) + "\n")