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preproces.py
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#!/usr/bin/env python
# -*- coding:utf-8-*-
# author: Liukewei time:2020/1/21 QQ:422209303 e-mail:Liukeweiaway@hotmail.com
# ----------------------------------------------------------------------------
import predictType
def cuttingText(seq, num):
seq_split = [] ## 空列表
while (seq != ''):
seq_split.append(seq[0:num])
seq = seq[num:]
return seq_split
def readFile(fileName):
with open(fileName, 'r') as f:
file_data = f.readlines()
return file_data[0], file_data[1]
def preprocesser(inputFile, outputFile, species, modification, threshold):
Fasta_name, sequence = readFile(inputFile)
sequence = sequence.upper()
htmlf = open('iRMRModel.html', 'r', encoding="utf-8")
outputFileR = 'results/' + outputFile
outputFileP = 'results/' + 'Possibility_' + outputFile
result_real = open(outputFileR, 'w', encoding="utf-8")
result_poosi = open(outputFileP, 'w', encoding="utf-8")
if species == 'Human':
if modification == 'm1A':
hg_line_M1A, hg_line_M1A_pro, hg_M1A_list = predictType.human_XG_iRNA_M1A(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
M1A_seq_ = ['-'] * len(sequence)
for i in hg_M1A_list:
M1A_seq_[i - 1] = 'A' # <font color=#1E90FF>A</font>
M1A_seq__split = cuttingText(''.join(M1A_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
M1A_seq = M1A_seq__split[i].replace('A', '<font color=#1E90FF>A</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('m1A:')
result_real.write(''.join(M1A_seq))
result_real.write('<br>')
result_poosi.write('m1A:')
result_poosi.write('<br>')
result_poosi.write(hg_line_M1A_pro)
elif modification == 'm6A':
hg_line_M6A, hg_line_M6A_pro, hg_M6A_list = predictType.human_XG_iRNA_M6A(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
M6A_seq_ = ['-'] * len(sequence)
for i in hg_M6A_list:
M6A_seq_[i - 1] = 'A' # <font color=#00FF00>A</font>
M6A_seq__split = cuttingText(''.join(M6A_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
M6A_seq = M6A_seq__split[i].replace('A', '<font color=#00FF00>A</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('m6A:')
result_real.write(''.join(M6A_seq))
result_real.write('<br>')
result_poosi.write('m6A:')
result_poosi.write('<br>')
result_poosi.write(hg_line_M6A_pro)
elif modification == 'm5C':
hg_line_M5C, hg_line_M5C_pro, hg_M5C_list = predictType.human_XG_iRNA_M5C(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
M5C_seq_ = ['-'] * len(sequence)
for i in hg_M5C_list:
M5C_seq_[i - 1] = 'C' # <font color=#FF7F50>C</font>
M5C_seq__split = cuttingText(''.join(M5C_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
M5C_seq = M5C_seq__split[i].replace('C', '<font color=#FF7F50>C</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('m5C:')
result_real.write(''.join(M5C_seq))
result_real.write('<br>')
result_poosi.write('<br>')
result_poosi.write('m5C:')
result_poosi.write(hg_line_M5C_pro)
elif modification == 'pseudouridine':
hg_line_pse, hg_line_pse_pro, hg_pse_list = predictType.human_XG_iRNA_pse(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
pse_seq_ = ['-'] * len(sequence)
for i in hg_pse_list:
pse_seq_[i - 1] = 'U' # <font color=#FF7F50>C</font>
pse_seq__split = cuttingText(''.join(pse_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
pse_seq = pse_seq__split[i].replace('U', '<font color=#DC143C>U</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('Pse:')
result_real.write(''.join(pse_seq))
result_real.write('<br>')
result_poosi.write('<br>')
result_poosi.write('Pse:')
result_poosi.write(hg_line_pse_pro)
elif modification == 'A-to-I':
hg_line_AI, hg_line_AI_pro, hg_AI_list = predictType.human_XG_iRNA_AI(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
AI_seq_ = ['-'] * len(sequence)
for i in hg_AI_list:
AI_seq_[i - 1] = 'A' # <font color=#FF7F50>C</font>
AI_seq__split = cuttingText(''.join(AI_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
AI_seq = AI_seq__split[i].replace('A', '<font color=#9932CC>A</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('A-I:')
result_real.write(''.join(AI_seq))
result_real.write('<br>')
result_poosi.write('<br>')
result_poosi.write('A-I:')
result_poosi.write(hg_line_AI_pro)
elif modification == 'all':
modification = 'pseudouridine'
hg_line_Pse, hg_line_Pse_pro, hg_Pse_list = predictType.human_XG_iRNA_pse(sequence, species, modification,
threshold)
modification = 'A-to-I'
hg_line_AI, hg_line_AI_pro, hg_AI_list = predictType.human_XG_iRNA_AI(sequence, species, modification,
threshold)
modification = 'm5C'
hg_line_M5C, hg_line_M5C_pro, hg_M5C_list = predictType.human_XG_iRNA_M5C(sequence, species, modification,
threshold)
modification = 'm6A'
hg_line_M6A, hg_line_M6A_pro, hg_M6A_list = predictType.human_XG_iRNA_M6A(sequence, species, modification,
threshold)
modification = 'm1A'
hg_line_M1A, hg_line_M1A_pro, hg_M1A_list = predictType.human_XG_iRNA_M1A(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
pse_seq_ = ['-'] * len(sequence)
AI_seq_ = ['-'] * len(sequence)
M5C_seq_ = ['-'] * len(sequence)
M6A_seq_ = ['-'] * len(sequence)
M1A_seq_ = ['-'] * len(sequence)
for i in hg_Pse_list:
pse_seq_[i - 1] = 'U' # <font color=#DC143C>U</font>
pse_seq__split = cuttingText(''.join(pse_seq_), 60)
for i in hg_AI_list:
AI_seq_[i - 1] = 'A' # <font color=#9932CC>A</font>
AI_seq__split = cuttingText(''.join(AI_seq_), 60)
for i in hg_M5C_list:
M5C_seq_[i - 1] = 'C' # <font color=#FF7F50>C</font>
M5C_seq__split = cuttingText(''.join(M5C_seq_), 60)
for i in hg_M6A_list:
M6A_seq_[i - 1] = 'A' # <font color=#00FF00>A</font>
M6A_seq__split = cuttingText(''.join(M6A_seq_), 60)
for i in hg_M1A_list:
M1A_seq_[i - 1] = 'A' # <font color=#1E90FF>A</font>
M1A_seq__split = cuttingText(''.join(M1A_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
pse_seq = pse_seq__split[i].replace('U', '<font color=#DC143C>U</font>')
AI_seq = AI_seq__split[i].replace('A', '<font color=#9932CC>A</font>')
M5C_seq = M5C_seq__split[i].replace('C', '<font color=#FF7F50>C</font>')
M6A_seq = M6A_seq__split[i].replace('A', '<font color=#00FF00>A</font>')
M1A_seq = M1A_seq__split[i].replace('A', '<font color=#1E90FF>A</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('PSE:')
result_real.write(''.join(pse_seq))
result_real.write('<br>')
result_real.write('A-I:')
result_real.write(''.join(AI_seq))
result_real.write('<br>')
result_real.write('m6A:')
result_real.write(''.join(M6A_seq))
result_real.write('<br>')
result_real.write('m1A:')
result_real.write(''.join(M1A_seq))
result_real.write('<br>')
result_real.write('m5C:')
result_real.write(''.join(M5C_seq))
result_real.write('<br>')
result_poosi.write('PSE:')
result_poosi.write(hg_line_Pse_pro)
result_poosi.write('<br>')
result_poosi.write('AI:')
result_poosi.write(hg_line_AI_pro)
result_poosi.write('<br>')
result_poosi.write('m6A:')
result_poosi.write(hg_line_M6A_pro)
result_poosi.write('<br>')
result_poosi.write('m1A:')
result_poosi.write(hg_line_M1A_pro)
result_poosi.write('<br>')
result_poosi.write('m5C:')
result_poosi.write(hg_line_M5C_pro)
if species == 'Yeast': # --- Yeast -----------------------------------------------------
if modification == 'm1A':
sc_line_M1A, sc_line_M1A_pro, sc_M1A_list = predictType.sc_XG_iRNA_M1A(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
M1A_seq_ = ['-'] * len(sequence)
for i in sc_M1A_list:
M1A_seq_[i - 1] = 'A' # <font color=#1E90FF>A</font>
M1A_seq__split = cuttingText(''.join(M1A_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
M1A_seq = M1A_seq__split[i].replace('A', '<font color=#1E90FF>A</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('m1A:')
result_real.write(''.join(M1A_seq))
result_real.write('<br>')
result_poosi.write('m1A:')
result_poosi.write(sc_line_M1A_pro)
elif modification == 'm6A':
sc_line_M6A, sc_line_M6A_pro, sc_M6A_list = predictType.sc_XG_iRNA_M6A(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
M6A_seq_ = ['-'] * len(sequence)
for i in sc_M6A_list:
M6A_seq_[i - 1] = 'A' # <font color=#00FF00>A</font>
M6A_seq__split = cuttingText(''.join(M6A_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
M6A_seq = M6A_seq__split[i].replace('A', '<font color=#00FF00>A</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('m6A:')
result_real.write(''.join(M6A_seq))
result_real.write('<br>')
result_poosi.write('m6A:')
result_poosi.write(sc_line_M6A_pro)
elif modification == 'm5C':
sc_line_M5C, sc_line_M5C_pro, sc_M5C_list = predictType.sc_XG_iRNA_M5C(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
M5C_seq_ = ['-'] * len(sequence)
for i in sc_M5C_list:
M5C_seq_[i - 1] = 'C' # <font color=#FF7F50>C</font>
M5C_seq__split = cuttingText(''.join(M5C_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
M5C_seq = M5C_seq__split[i].replace('C', '<font color=#FF7F50>C</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('m5C:')
result_real.write(''.join(M5C_seq))
result_real.write('<br>')
result_poosi.write('m5C:')
result_poosi.write(sc_line_M5C_pro)
elif modification == 'pseudouridine':
sc_line_pse, sc_line_pse_pro, sc_pse_list = predictType.sc_XG_iRNA_pse(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
pse_seq_ = ['-'] * len(sequence)
for i in sc_pse_list:
pse_seq_[i - 1] = 'U' # <font color=#FF7F50>C</font>
pse_seq__split = cuttingText(''.join(pse_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
pse_seq = pse_seq__split[i].replace('U', '<font color=#DC143C>U</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('PSE:')
result_real.write(''.join(pse_seq))
result_real.write('<br>')
result_poosi.write('PSE:')
result_poosi.write(sc_line_pse_pro)
elif modification == 'all':
modification = 'pseudouridine'
sc_line_Pse, sc_line_Pse_pro, sc_Pse_list = predictType.sc_XG_iRNA_pse(sequence, species, modification,
threshold)
modification = 'm5C'
sc_line_M5C, sc_line_M5C_pro, sc_M5C_list = predictType.sc_XG_iRNA_M5C(sequence, species, modification,
threshold)
modification = 'm6A'
sc_line_M6A, sc_line_M6A_pro, sc_M6A_list = predictType.sc_XG_iRNA_M6A(sequence, species, modification,
threshold)
modification = 'm1A'
sc_line_M1A, sc_line_M1A_pro, sc_M1A_list = predictType.sc_XG_iRNA_M1A(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
pse_seq_ = ['-'] * len(sequence)
M5C_seq_ = ['-'] * len(sequence)
M6A_seq_ = ['-'] * len(sequence)
M1A_seq_ = ['-'] * len(sequence)
for i in sc_Pse_list:
pse_seq_[i - 1] = 'U' # <font color=#DC143C>U</font>
pse_seq__split = cuttingText(''.join(pse_seq_), 60)
for i in sc_M5C_list:
M5C_seq_[i - 1] = 'C' # <font color=#FF7F50>C</font>
M5C_seq__split = cuttingText(''.join(M5C_seq_), 60)
for i in sc_M6A_list:
M6A_seq_[i - 1] = 'A' # <font color=#00FF00>A</font>
M6A_seq__split = cuttingText(''.join(M6A_seq_), 60)
for i in sc_M1A_list:
M1A_seq_[i - 1] = 'A' # <font color=#1E90FF>A</font>
M1A_seq__split = cuttingText(''.join(M1A_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
pse_seq = pse_seq__split[i].replace('U', '<font color=#DC143C>U</font>')
M5C_seq = M5C_seq__split[i].replace('C', '<font color=#FF7F50>C</font>')
M6A_seq = M6A_seq__split[i].replace('A', '<font color=#00FF00>A</font>')
M1A_seq = M1A_seq__split[i].replace('A', '<font color=#1E90FF>A</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('PSE:')
result_real.write(''.join(pse_seq))
result_real.write('<br>')
result_real.write('m6A:')
result_real.write(''.join(M6A_seq))
result_real.write('<br>')
result_real.write('m1A:')
result_real.write(''.join(M1A_seq))
result_real.write('<br>')
result_real.write('m5C:')
result_real.write(''.join(M5C_seq))
result_real.write('<br>')
result_poosi.write('PSE:')
result_poosi.write(sc_line_Pse_pro)
result_poosi.write('<br>')
result_poosi.write('m6A:')
result_poosi.write(sc_line_M6A_pro)
result_poosi.write('<br>')
result_poosi.write('m1A:')
result_poosi.write(sc_line_M1A_pro)
result_poosi.write('<br>')
result_poosi.write('m5C:')
result_poosi.write(sc_line_M5C_pro)
if species == 'Mouse': # Mouse
if modification == 'm1A':
mm_line_M1A, mm_line_M1A_pro, mm_M1A_list = predictType.mm_XG_iRNA_M1A(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
M1A_seq_ = ['-'] * len(sequence)
for i in mm_M1A_list:
M1A_seq_[i - 1] = 'A' # <font color=#1E90FF>A</font>
M1A_seq__split = cuttingText(''.join(M1A_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
M1A_seq = M1A_seq__split[i].replace('A', '<font color=#1E90FF>A</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('m1A:')
result_real.write(''.join(M1A_seq))
result_real.write('<br>')
result_poosi.write('m1A:')
result_poosi.write(mm_line_M1A_pro)
elif modification == 'm5C':
mm_line_M5C, mm_line_M5C_pro, mm_M5C_list = predictType.mm_XG_iRNA_M5C(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
M5C_seq_ = ['-'] * len(sequence)
for i in mm_M5C_list:
M5C_seq_[i - 1] = 'C' # <font color=#FF7F50>C</font>
M5C_seq__split = cuttingText(''.join(M5C_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
M5C_seq = M5C_seq__split[i].replace('C', '<font color=#FF7F50>C</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('m5C:')
result_real.write(''.join(M5C_seq))
result_real.write('<br>')
result_poosi.write('m5C:')
result_poosi.write(mm_line_M5C_pro)
elif modification == 'pseudouridine':
mm_line_pse, mm_line_pse_pro, mm_pse_list = predictType.mm_XG_iRNA_pse(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
pse_seq_ = ['-'] * len(sequence)
for i in mm_pse_list:
pse_seq_[i - 1] = 'U' # <font color=#FF7F50>C</font>
pse_seq__split = cuttingText(''.join(pse_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
pse_seq = pse_seq__split[i].replace('U', '<font color=#DC143C>U</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('PSE:')
result_real.write(''.join(pse_seq))
result_real.write('<br>')
result_poosi.write('PSE:')
result_poosi.write(mm_line_pse_pro)
elif modification == 'm6A':
mm_line_M6A, mm_line_M6A_pro, mm_M6A_list = predictType.mm_XG_iRNA_M6A(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
M6A_seq_ = ['-'] * len(sequence)
for i in mm_M6A_list:
M6A_seq_[i - 1] = 'A' # <font color=#00FF00>A</font>
M6A_seq__split = cuttingText(''.join(M6A_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
M6A_seq = M6A_seq__split[i].replace('A', '<font color=#00FF00>A</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('m6A:')
result_real.write(''.join(M6A_seq))
result_real.write('<br>')
result_poosi.write('m6A:')
result_poosi.write(mm_line_M6A_pro)
elif modification == 'all':
modification = 'pseudouridine'
mm_line_Pse, mm_line_Pse_pro, mm_Pse_list = predictType.mm_XG_iRNA_pse(sequence, species, modification,
threshold)
modification = 'm5C'
mm_line_M5C, mm_line_M5C_pro, mm_M5C_list = predictType.mm_XG_iRNA_M5C(sequence, species, modification,
threshold)
modification = 'm1A'
mm_line_M1A, mm_line_M1A_pro, mm_M1A_list = predictType.mm_XG_iRNA_M1A(sequence, species, modification,
threshold)
modification = 'm6A'
mm_line_M6A, mm_line_M6A_pro, mm_M6A_list = predictType.mm_XG_iRNA_M6A(sequence, species, modification,
threshold)
seq_split = cuttingText(sequence, 60)
pse_seq_ = ['-'] * len(sequence)
M5C_seq_ = ['-'] * len(sequence)
M1A_seq_ = ['-'] * len(sequence)
M6A_seq_ = ['-'] * len(sequence)
for i in mm_Pse_list:
pse_seq_[i - 1] = 'U' # <font color=#DC143C>U</font>
pse_seq__split = cuttingText(''.join(pse_seq_), 60)
for i in mm_M5C_list:
M5C_seq_[i - 1] = 'C' # <font color=#FF7F50>C</font>
M5C_seq__split = cuttingText(''.join(M5C_seq_), 60)
for i in mm_M1A_list:
M1A_seq_[i - 1] = 'A' # <font color=#1E90FF>A</font>
M1A_seq__split = cuttingText(''.join(M1A_seq_), 60)
for i in mm_M6A_list:
M6A_seq_[i - 1] = 'A' # <font color=#1E90FF>A</font>
M6A_seq__split = cuttingText(''.join(M6A_seq_), 60)
for line in htmlf.readlines():
if '<li>>' not in line:
result_real.write(line.strip())
result_real.write('\n')
elif '<li>>N1 :GUGAUAUAACUCAGUGGCAGA</li>' in line:
result_real.write(Fasta_name)
result_real.write('<br>')
for i in range(len(seq_split)):
pse_seq = pse_seq__split[i].replace('U', '<font color=#DC143C>U</font>')
M5C_seq = M5C_seq__split[i].replace('C', '<font color=#FF7F50>C</font>')
M1A_seq = M1A_seq__split[i].replace('A', '<font color=#1E90FF>A</font>')
M6A_seq = M6A_seq__split[i].replace('A', '<font color=#00FF00>A</font>')
result_real.write('    ')
result_real.write(''.join(seq_split[i]))
result_real.write('    ')
if i < len(seq_split) - 1:
result_real.write(str((i + 1) * 60))
result_real.write('<br>')
result_real.write('PSE:')
result_real.write(''.join(pse_seq))
result_real.write('<br>')
result_real.write('m6A:')
result_real.write(''.join(M6A_seq))
result_real.write('<br>')
result_real.write('m1A:')
result_real.write(''.join(M1A_seq))
result_real.write('<br>')
result_real.write('m5C:')
result_real.write(''.join(M5C_seq))
result_real.write('<br>')
result_poosi.write('PSE:')
result_poosi.write(mm_line_Pse_pro)
result_poosi.write('<br>')
result_poosi.write('m6A:')
result_poosi.write(mm_line_M6A_pro)
result_poosi.write('<br>')
result_poosi.write('m1A:')
result_poosi.write(mm_line_M1A_pro)
result_poosi.write('<br>')
result_poosi.write('m5C:')
result_poosi.write(mm_line_M5C_pro)
htmlf.close()
result_real.close()
result_poosi.close()