def convert_phyche_index_to_dict(phyche_index, alphabet):
"""Convert phyche index from list to dict."""
# for e in phyche_index:
# print e
len_index_value = len(phyche_index[0])
k = 0
for i in range(1, 10):
if len_index_value < 4**i:
error_infor = 'Sorry, the number of each index value is must be 4^k.'
sys.stdout.write(error_infor)
sys.exit(0)
if len_index_value == 4**i:
k = i
break
from repDNA.nacutil import make_kmer_list
kmer_list = make_kmer_list(k, alphabet)
# print kmer_list
len_kmer = len(kmer_list)
phyche_index_dict = {}
for kmer in kmer_list:
phyche_index_dict[kmer] = []
# print phyche_index_dict
phyche_index = list(zip(*phyche_index))
for i in range(len_kmer):
phyche_index_dict[kmer_list[i]] = list(phyche_index[i])
return phyche_index_dict
def convert_phyche_index_to_dict(phyche_index, alphabet):
"""Convert phyche index from list to dict."""
# for e in phyche_index:
# print e
len_index_value = len(phyche_index[0])
k = 0
for i in range(1, 10):
if len_index_value < 4**i:
error_infor = 'Sorry, the number of each index value is must be 4^k.'
sys.stdout.write(error_infor)
sys.exit(0)
if len_index_value == 4**i:
k = i
break
from repDNA.nacutil import make_kmer_list
kmer_list = make_kmer_list(k, alphabet)
# print kmer_list
len_kmer = len(kmer_list)
phyche_index_dict = {}
for kmer in kmer_list:
phyche_index_dict[kmer] = []
# print phyche_index_dict
phyche_index = list(zip(*phyche_index))
for i in range(len_kmer):
phyche_index_dict[kmer_list[i]] = list(phyche_index[i])
return phyche_index_dict
def write_rna(rna_dict, filename):
kmer_list = make_kmer_list(k=2, alphabet='ACGU')
dinucle_prop_vals = {}
for _property, vals in rna_dict.items():
for ind, val in enumerate(vals):
dinucle = kmer_list[ind]
if dinucle not in dinucle_prop_vals:
dinucle_prop_vals[dinucle] = []
dinucle_prop_vals[dinucle].append((_property, val))
print(len(dinucle_prop_vals['AA']), dinucle_prop_vals)
with open(filename, 'wb') as f_write:
pickle.dump(dinucle_prop_vals, f_write, protocol=2)
def write_rna(rna_dict, filename):
kmer_list = make_kmer_list(k=2, alphabet='ACGU')
dinucle_prop_vals = {}
for _property, vals in rna_dict.items():
for ind, val in enumerate(vals):
dinucle = kmer_list[ind]
if dinucle not in dinucle_prop_vals:
dinucle_prop_vals[dinucle] = []
dinucle_prop_vals[dinucle].append((_property, val))
print(len(dinucle_prop_vals['AA']), dinucle_prop_vals)
with open(filename, 'wb') as f_write:
pickle.dump(dinucle_prop_vals, f_write, protocol=2)
def combine_dna_dict(dna_dict, alphabet, write_file):
tri_dna_file = os.path.abspath('..') + '/data/mmc3.data'
with open(tri_dna_file, 'rb') as f:
dinucle_property_val = pickle.load(f)
kmer_list = make_kmer_list(k=2, alphabet=alphabet)
for _property, vals in dna_dict.items():
for ind, val in enumerate(vals):
for e in dinucle_property_val[kmer_list[ind]]:
if e[0] == _property:
print(kmer_list[ind], e, _property)
break
dinucle_property_val[kmer_list[ind]].append((_property, val))
with open(write_file, 'wb') as f_write:
pickle.dump(dinucle_property_val, f_write, protocol=2)
return dinucle_property_val
def combine_dna_dict(dna_dict, alphabet, write_file):
tri_dna_file = os.path.abspath('..') + '/data/mmc3.data'
with open(tri_dna_file, 'rb') as f:
dinucle_property_val = pickle.load(f)
kmer_list = make_kmer_list(k=2, alphabet=alphabet)
for _property, vals in dna_dict.items():
for ind, val in enumerate(vals):
for e in dinucle_property_val[kmer_list[ind]]:
if e[0] == _property:
print(kmer_list[ind], e, _property)
break
dinucle_property_val[kmer_list[ind]].append((_property, val))
with open(write_file, 'wb') as f_write:
pickle.dump(dinucle_property_val, f_write, protocol=2)
return dinucle_property_val