Mercurial > repos > iss > eurl_vtec_wgs_pt

annotate scripts/modules/utils.py @ 3:0506503db01d draft

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planemo upload commit 0708bd0601ac65e8a1c7cdd2504cebdf45755828
author iss
date Thu, 19 Oct 2023 12:31:29 +0000
parents c6bab5103a14
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 import pickle
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2 import traceback
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3 import shlex
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4 import subprocess
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5 from threading import Timer
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6 import shutil
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7 import time
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8 import functools
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9 import os.path
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10 import sys
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11 import argparse
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12
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13
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14 def start_logger(workdir):
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15 time_str = time.strftime("%Y%m%d-%H%M%S")
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16 sys.stdout = Logger(workdir, time_str)
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17 logfile = sys.stdout.getLogFile()
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18 return logfile, time_str
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19
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20
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21 class Logger(object):
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22 def __init__(self, out_directory, time_str):
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23 self.logfile = os.path.join(out_directory, str('run.' + time_str + '.log'))
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24 self.terminal = sys.stdout
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25 self.log = open(self.logfile, "w")
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26
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27 def write(self, message):
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28 self.terminal.write(message)
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29 self.log.write(message)
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30 self.log.flush()
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31
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32 def flush(self):
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33 pass
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34
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35 def getLogFile(self):
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36 return self.logfile
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37
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38
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39 def checkPrograms(programs_version_dictionary):
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40 print('\n' + 'Checking dependencies...')
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41 programs = programs_version_dictionary
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42 which_program = ['which', '']
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43 listMissings = []
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44 for program in programs:
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45 which_program[1] = program
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46 run_successfully, stdout, stderr = runCommandPopenCommunicate(which_program, False, None, False)
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47 if not run_successfully:
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48 listMissings.append(program + ' not found in PATH.')
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49 else:
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50 print(stdout.splitlines()[0])
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51 if programs[program][0] is None:
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52 print(program + ' (impossible to determine programme version) found at: ' + stdout.splitlines()[0])
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53 else:
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54 if program.endswith('.jar'):
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55 check_version = ['java', '-jar', stdout.splitlines()[0], programs[program][0]]
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56 programs[program].append(stdout.splitlines()[0])
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57 else:
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58 check_version = [stdout.splitlines()[0], programs[program][0]]
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59 run_successfully, stdout, stderr = runCommandPopenCommunicate(check_version, False, None, False)
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60 if stdout == '':
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61 stdout = stderr
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62 if program in ['wget', 'awk']:
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63 version_line = stdout.splitlines()[0].split(' ', 3)[2]
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64 elif program in ['prefetch', 'fastq-dump']:
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65 version_line = stdout.splitlines()[1].split(' ')[-1]
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66 else:
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67 version_line = stdout.splitlines()[0].split(' ')[-1]
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68 replace_characters = ['"', 'v', 'V', '+', ',']
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69 for i in replace_characters:
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70 version_line = version_line.replace(i, '')
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71 print(program + ' (' + version_line + ') found')
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72 if programs[program][1] == '>=':
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73 program_found_version = version_line.split('.')
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74 program_version_required = programs[program][2].split('.')
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75 if len(program_version_required) == 3:
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76 if len(program_found_version) == 2:
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77 program_found_version.append(0)
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78 else:
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79 program_found_version[2] = program_found_version[2].split('_')[0]
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80 for i in range(0, len(program_version_required)):
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81 if int(program_found_version[i]) > int(program_version_required[i]):
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82 break
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83 elif int(program_found_version[i]) == int(program_version_required[i]):
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84 continue
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85 else:
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86 listMissings.append('It is required ' + program + ' with version ' +
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87 programs[program][1] + ' ' + programs[program][2])
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88 else:
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89 if version_line != programs[program][2]:
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90 listMissings.append('It is required ' + program + ' with version ' + programs[program][1] +
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91 ' ' + programs[program][2])
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92 return listMissings
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93
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94
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95 def requiredPrograms():
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96 programs_version_dictionary = {}
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97 programs_version_dictionary['rematch.py'] = ['--version', '>=', '4.0']
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98 missingPrograms = checkPrograms(programs_version_dictionary)
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99 if len(missingPrograms) > 0:
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100 sys.exit('\n' + 'Errors:' + '\n' + '\n'.join(missingPrograms))
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101
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102
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103 def general_information(logfile, version, outdir, time_str):
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104 # Check if output directory exists
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105
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106 print('\n' + '==========> patho_typing <==========')
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107 print('\n' + 'Program start: ' + time.ctime())
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108
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109 # Tells where the logfile will be stored
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110 print('\n' + 'LOGFILE:')
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111 print(logfile)
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112
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113 # Print command
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114 print('\n' + 'COMMAND:')
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115 script_path = os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))), 'patho_typing.py')
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116 print(sys.executable + ' ' + ' '.join(sys.argv))
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117
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118 # Print directory where programme was lunch
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119 print('\n' + 'PRESENT DIRECTORY:')
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120 present_directory = os.path.abspath(os.getcwd())
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121 print(present_directory)
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122
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123 # Print program version
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124 print('\n' + 'VERSION:')
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125 script_version_git(version, present_directory, script_path)
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126
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127 # Check programms
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128 requiredPrograms()
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129
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130 return script_path
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131
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132
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133 def setPATHvariable(doNotUseProvidedSoftware, script_path):
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134 path_variable = os.environ['PATH']
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135 script_folder = os.path.dirname(script_path)
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136 # Set path to use provided softwares
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137 if not doNotUseProvidedSoftware:
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138 bowtie2 = os.path.join(script_folder, 'src', 'bowtie2-2.2.9')
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139 samtools = os.path.join(script_folder, 'src', 'samtools-1.3.1', 'bin')
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140 bcftools = os.path.join(script_folder, 'src', 'bcftools-1.3.1', 'bin')
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141
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142 os.environ['PATH'] = str(':'.join([bowtie2, samtools, bcftools, path_variable]))
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143
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144 # Print PATH variable
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145 print('\n' + 'PATH variable:')
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146 print(os.environ['PATH'])
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147
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148
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149 def script_version_git(version, current_directory, script_path, no_git_info=False):
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150 """
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151 Print script version and get GitHub commit information
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152
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153 Parameters
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154 ----------
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155 version : str
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156 Version of the script, e.g. "4.0"
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157 current_directory : str
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158 Path to the directory where the script was start to run
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159 script_path : str
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160 Path to the script running
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161 no_git_info : bool, default False
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162 True if it is not necessary to retreive the GitHub commit information
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163
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164 Returns
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165 -------
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166
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167 """
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168 print('Version {}'.format(version))
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169
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170 if not no_git_info:
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171 try:
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172 os.chdir(os.path.dirname(os.path.dirname(script_path)))
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173 command = ['git', 'log', '-1', '--date=local', '--pretty=format:"%h (%H) - Commit by %cn, %cd) : %s"']
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174 run_successfully, stdout, stderr = runCommandPopenCommunicate(command, False, 15, False)
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175 print(stdout)
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176 command = ['git', 'remote', 'show', 'origin']
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177 run_successfully, stdout, stderr = runCommandPopenCommunicate(command, False, 15, False)
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178 print(stdout)
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179 except:
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180 print('HARMLESS WARNING: git command possibly not found. The GitHub repository information will not be'
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181 ' obtained.')
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182 finally:
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183 os.chdir(current_directory)
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184
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185
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186 def runTime(start_time):
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187 end_time = time.time()
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188 time_taken = end_time - start_time
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189 hours, rest = divmod(time_taken, 3600)
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190 minutes, seconds = divmod(rest, 60)
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191 print('Runtime :' + str(hours) + 'h:' + str(minutes) + 'm:' + str(round(seconds, 2)) + 's')
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192 return round(time_taken, 2)
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193
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194
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195 def timer(function, name):
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196 @functools.wraps(function)
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197 def wrapper(*args, **kwargs):
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198 print('\n' + 'RUNNING {0}\n'.format(name))
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199 start_time = time.time()
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200
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201 results = list(function(*args, **kwargs)) # guarantees return is a list to allow .insert()
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202
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203 time_taken = runTime(start_time)
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204 print('END {0}'.format(name))
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205
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206 results.insert(0, time_taken)
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207 return results
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208 return wrapper
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209
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210
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211 def removeDirectory(directory):
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212 if os.path.isdir(directory):
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213 shutil.rmtree(directory)
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214
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215
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216 def saveVariableToPickle(variableToStore, pickleFile):
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217 with open(pickleFile, 'wb') as writer:
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218 pickle.dump(variableToStore, writer)
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219
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220
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221 def extractVariableFromPickle(pickleFile):
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222 with open(pickleFile, 'rb') as reader:
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223 variable = pickle.load(reader)
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224 return variable
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225
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226
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227 def trace_unhandled_exceptions(func):
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228 @functools.wraps(func)
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229 def wrapped_func(*args, **kwargs):
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230 try:
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231 func(*args, **kwargs)
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232 except:
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233 print('Exception in ' + func.__name__)
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234 traceback.print_exc()
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235 return wrapped_func
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236
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237
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238 def kill_subprocess_Popen(subprocess_Popen, command):
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239 print('Command run out of time: ' + str(command))
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240 subprocess_Popen.kill()
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241
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242
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243 def runCommandPopenCommunicate(command, shell_True, timeout_sec_None, print_comand_True):
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244 run_successfully = False
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245 if not isinstance(command, str):
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246 command = ' '.join(command)
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247 command = shlex.split(command)
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248
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249 if print_comand_True:
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250 print('Running: ' + ' '.join(command))
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251
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252 if shell_True:
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253 command = ' '.join(command)
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254 proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
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255 else:
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256 proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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257
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258 not_killed_by_timer = True
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259 if timeout_sec_None is None:
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260 stdout, stderr = proc.communicate()
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261 else:
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262 time_counter = Timer(timeout_sec_None, kill_subprocess_Popen, args=(proc, command,))
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263 time_counter.start()
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264 stdout, stderr = proc.communicate()
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265 time_counter.cancel()
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266 not_killed_by_timer = time_counter.isAlive()
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267
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268 stdout = stdout.decode("utf-8")
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269 stderr = stderr.decode("utf-8")
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270
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271 if proc.returncode == 0:
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272 run_successfully = True
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273 else:
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274 if not print_comand_True and not_killed_by_timer:
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275 print('Running: ' + str(command))
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276 if len(stdout) > 0:
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277 print('STDOUT')
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278 print(stdout)
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279 if len(stderr) > 0:
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280 print('STDERR')
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281 print(stderr)
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282 return run_successfully, stdout, stderr
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283
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284
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285 def required_length(tuple_length_options, argument_name):
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286 class RequiredLength(argparse.Action):
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287 def __call__(self, parser, args, values, option_string=None):
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288 if len(values) not in tuple_length_options:
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289 msg = 'Option {argument_name} requires one of the following number of' \
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290 ' arguments: {tuple_length_options}'.format(argument_name=self.argument_name,
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291 tuple_length_options=tuple_length_options)
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292 raise argparse.ArgumentTypeError(msg)
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293 setattr(args, self.dest, values)
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294 return RequiredLength
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295
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296
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297 def get_sequence_information(fasta_file, length_extra_seq):
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298 sequence_dict = {}
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299 headers = {}
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300
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301 with open(fasta_file, 'rtU') as reader:
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302 blank_line_found = False
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303 sequence_counter = 0
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304 temp_sequence_dict = {}
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305 for line in reader:
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306 line = line.splitlines()[0]
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307 if len(line) > 0:
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308 if not blank_line_found:
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309 if line.startswith('>'):
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310 if len(temp_sequence_dict) > 0:
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311 if list(temp_sequence_dict.values())[0]['length'] - 2 * length_extra_seq > 0:
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312 sequence_dict[list(temp_sequence_dict.keys())[0]] = list(temp_sequence_dict.values())[0]
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313 headers[list(temp_sequence_dict.values())[0]['header'].lower()] = sequence_counter
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314 else:
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315 print(list(temp_sequence_dict.values())[0]['header'] + ' sequence ignored due to '
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316 'length <= 0')
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317 temp_sequence_dict = {}
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318
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319 if line[1:].lower() in headers:
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320 sys.exit('Found duplicated sequence headers')
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321
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322 sequence_counter += 1
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323 temp_sequence_dict[sequence_counter] = {'header': line[1:].lower(), 'sequence': '', 'length': 0}
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324 else:
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325 temp_sequence_dict[sequence_counter]['sequence'] += line.upper()
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326 temp_sequence_dict[sequence_counter]['length'] += len(line)
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327 else:
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328 sys.exit('It was found a blank line between the fasta file above line ' + line)
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329 else:
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330 blank_line_found = True
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331
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332 if len(temp_sequence_dict) > 0:
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333 if list(temp_sequence_dict.values())[0]['length'] - 2 * length_extra_seq > 0:
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334 sequence_dict[list(temp_sequence_dict.keys())[0]] = list(temp_sequence_dict.values())[0]
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335 headers[list(temp_sequence_dict.values())[0]['header'].lower()] = sequence_counter
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336 else:
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337 print(list(temp_sequence_dict.values())[0]['header'] + ' sequence ignored due to length <= 0')
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338
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339 return sequence_dict, headers
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340
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341
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342 def simplify_sequence_dict(sequence_dict):
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343 simple_sequence_dict = {}
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344 for counter, info in list(sequence_dict.items()):
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345 simple_sequence_dict[info['header']] = info
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346 del simple_sequence_dict[info['header']]['header']
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347 return simple_sequence_dict
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348
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349
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350 def chunkstring(string, length):
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351 return (string[0 + i:length + i] for i in range(0, len(string), length))
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352
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353
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354 def clean_headers_sequences(sequence_dict):
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355 problematic_characters = ["|", " ", ",", ".", "(", ")", "'", "/", ":"]
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356 # print 'Checking if reference sequences contain ' + str(problematic_characters) + '\n'
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357
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358 headers_changed = False
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359 new_headers = {}
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360 for i in sequence_dict:
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361 if any(x in sequence_dict[i]['header'] for x in problematic_characters):
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362 for x in problematic_characters:
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363 sequence_dict[i]['header'] = sequence_dict[i]['header'].replace(x, '_')
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364 headers_changed = True
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365 new_headers[sequence_dict[i]['header'].lower()] = i
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366
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367 if headers_changed:
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368 print('At least one of the those characters was found. Replacing those with _' + '\n')
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369
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370 return sequence_dict, new_headers