#Open the files you just created with the gapless sequences and read in the sequences.
fp_natural = open(natural_pdb_file_title)
natural_data_arr = fp_natural.readlines()
fp_natural.close()
fp_designed = open(duncan_designed_sequence_path + designed_pdb_file_title)
designed_data_arr = fp_designed.readlines()
fp_designed.close()
#filepointer for the partial result
fpW_natural = open("results_array_natural_" + pdb_id + "_" + chain_id + ".csv","w")
fpW_designed = open("results_array_" + pdb_id + "_" + chain_id + "_" + method + ".csv","w")
#write the RSA values:
fpW_natural.write(af.dump_csv_line(RSA))
fpW_designed.write(af.dump_csv_line(RSA))
if(len(RSA) != len(natural_data_arr[0].strip())):
print "Error !!!!!!!!!"
#print data_arr[0].strip()
bad_list.append(natural_pdb_file_title)
if(len(RSA) != len(natural_data_arr[0].strip())):
print "Error !!!!!!!!!"
print "Length of rsa values {:0}".format(len(RSA))
print "Length of sequence {:0}".format(len(natural_data_arr[0].strip()))
#Re-format sequences
for line in natural_data_arr:
fpW_natural.write(af.dump_csv_line(line.strip()))
#Get all the RSA values using DSSP
seq_data = af.get_noah_RSA_values(pdb_id, chain_id)
RSA = seq_data[1] #Get the RSA values
RSA_dict = seq_data[2] #Get the dict mapping positions to RSA
new_RSA = af.get_cut_RSA_values(pdb_id, RSA, RSA_dict)
index = 0
#Arrays full of the designed and natural sequences
natural_data_arr = cut_natural_sequences
designed_data_arr = af.get_cut_designed_sequences(designed_file)
fpW_natural = open("results_array_natural_" + pdb_id + "_" + chain_id + ".csv","w")
fpW_designed = open("results_array_" + pdb_id + "_" + chain_id + "_" + "soft" + ".csv","w")
#write the RSA values:
fpW_natural.write(af.dump_csv_line(new_RSA))
fpW_designed.write(af.dump_csv_line(new_RSA))
if(len(new_RSA) != len(natural_data_arr[0].strip())):
print "Error !!!!!!!!!"
#print data_arr[0].strip()
bad_list.append(natural_pdb_file_title)
if(len(new_RSA) != len(natural_data_arr[0].strip())):
print "Error !!!!!!!!!"
print "Length of rsa values {:0}".format(len(RSA))
print "Length of sequence {:0}".format(len(natural_data_arr[0].strip()))
print "Length of designed sequence {:0}".format(len(designed_data_arr[0].strip()))
#Re-format sequences
for line in natural_data_arr:
RSAValues = []
RSA = seq_data[1]
print len(RSA)
index = 0
#Open the files you just created with the gapless sequences
fp_natural = open(natural_pdb_file_title)
natural_data_arr = fp_natural.readlines()
fp_natural.close()
#filepointer for the partial result
fpW_natural = open(
"results_array_natural_" + pdb_id + "_" + chain_id + ".csv", "w")
#write the RSA values:
fpW_natural.write(af.dump_csv_line(RSA))
[natural_sample1, natural_sample2] = af.split_natural_sequences(
natural_data_arr) #Splits the sequences into two samples
#filepointer for the partial result
fpW_natural_sample1 = open(
"results_array_natural_sample1_" + pdb_id + "_" + chain_id + ".csv",
"w")
fpW_natural_sample2 = open(
"results_array_natural_sample2_" + pdb_id + "_" + chain_id + ".csv",
"w")
#write the RSA values:
fpW_natural_sample1.write(af.dump_csv_line(RSA))
fpW_natural_sample2.write(af.dump_csv_line(RSA))
seq_data = af.get_values(pdb_id, chain_id)
RSAValues = []
RSA = seq_data[1]
print "RSA Length from dssp script: " + str(len(RSA))
index = 0
#Open the files you just created with the gapless sequences
fp_natural = open(natural_pdb_file_title)
natural_data_arr = fp_natural.readlines()
fp_natural.close()
#filepointer for the partial result
fpW_natural = open("results_array_natural_" + pdb_id + "_" + chain_id + ".csv","w")
#write the RSA values:
fpW_natural.write(af.dump_csv_line(RSA))
[natural_sample1, natural_sample2] = af.split_natural_sequences(natural_data_arr) #Samples
#filepointer for the partial result
fpW_natural_sample1 = open("results_array_natural_sample1_" + pdb_id + "_" + chain_id + ".csv","w")
fpW_natural_sample2 = open("results_array_natural_sample2_" + pdb_id + "_" + chain_id + ".csv","w")
#write the RSA values:
fpW_natural_sample1.write(af.dump_csv_line(RSA))
fpW_natural_sample2.write(af.dump_csv_line(RSA))
if(len(RSA) != len(natural_data_arr[0].strip())):
print "Error !!!!!!!!!"
#print data_arr[0].strip()
bad_list.append(natural_pdb_file_title)
