Mercurial > repos > iss > eurl_vtec_wgs_pt

annotate scripts/ReMatCh/modules/utils.py @ 0:c6bab5103a14 draft

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"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
author iss
date Mon, 21 Mar 2022 15:23:09 +0000
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0
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1 import pickle
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2 from traceback import format_exception as traceback_format_exception
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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 from functools import wraps as functools_wraps
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9 import os.path
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10 import sys
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11
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12
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13 def start_logger(workdir):
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14 time_str = time.strftime("%Y%m%d-%H%M%S")
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15 sys.stdout = Logger(workdir, time_str)
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16 logfile = sys.stdout.getLogFile()
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17 return logfile, time_str
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18
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19
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20 class Logger(object):
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21 def __init__(self, out_directory, time_str):
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22 self.logfile = os.path.join(out_directory, str('run.' + time_str + '.log'))
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23 self.terminal = sys.stdout
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24 self.log = open(self.logfile, "w")
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25
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26 def write(self, message):
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27 self.terminal.write(message)
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28 self.log.write(message)
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29 self.log.flush()
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30
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31 def flush(self):
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32 pass
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33
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34 def getLogFile(self):
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35 return self.logfile
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36
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37
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38 def get_cpu_information(outdir, time_str):
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39 with open(os.path.join(outdir, 'cpu_information.' + time_str + '.cpu.txt'), 'wt') as writer:
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40 command = ['cat', '/proc/cpuinfo']
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41 run_successfully, stdout, stderr = run_command_popen_communicate(command, False, None, False)
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42 if run_successfully:
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43 writer.write(stdout)
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44
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45 with open(os.path.join(outdir, 'cpu_information.' + time_str + '.slurm.txt'), 'wt') as writer:
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46 for environment in sorted(os.environ):
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47 if environment.startswith('SLURM_'):
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48 writer.write('#' + environment + '\n' + os.environ[environment] + '\n')
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49
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50
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51 def setPATHvariable(doNotUseProvidedSoftware, script_path):
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52 path_variable = os.environ['PATH']
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53 script_folder = os.path.dirname(script_path)
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54 # Set path to use provided softwares
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55 if not doNotUseProvidedSoftware:
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56 bowtie2 = os.path.join(script_folder, 'src', 'bowtie2-2.2.9')
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57 samtools = os.path.join(script_folder, 'src', 'samtools-1.3.1', 'bin')
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58 bcftools = os.path.join(script_folder, 'src', 'bcftools-1.3.1', 'bin')
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59
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60 os.environ['PATH'] = str(':'.join([bowtie2, samtools, bcftools, path_variable]))
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61
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62 # Print PATH variable
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63 print('\n' + 'PATH variable:')
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64 print(os.environ['PATH'])
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65
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66
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67 def checkPrograms(programs_version_dictionary):
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68 print('\n' + 'Checking dependencies...')
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69 programs = programs_version_dictionary
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70 which_program = ['which', '']
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71 listMissings = []
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72 for program in programs:
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73 which_program[1] = program
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74 run_successfully, stdout, stderr = run_command_popen_communicate(which_program, False, None, False)
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75 if not run_successfully:
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76 listMissings.append(program + ' not found in PATH.')
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77 else:
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78 print(stdout.splitlines()[0])
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79 if programs[program][0] is None:
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80 print(program + ' (impossible to determine programme version) found at: ' + stdout.splitlines()[0])
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81 else:
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82 if program.endswith('.jar'):
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83 check_version = ['java', '-jar', stdout.splitlines()[0], programs[program][0]]
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84 programs[program].append(stdout.splitlines()[0])
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85 else:
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86 check_version = [stdout.splitlines()[0], programs[program][0]]
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87 run_successfully, stdout, stderr = run_command_popen_communicate(check_version, False, None, False)
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88 if stdout == '':
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89 stdout = stderr
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90 if program in ['wget', 'awk']:
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91 version_line = stdout.splitlines()[0].split(' ', 3)[2]
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92 elif program in ['prefetch', 'fastq-dump']:
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93 version_line = stdout.splitlines()[1].split(' ')[-1]
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94 else:
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95 version_line = stdout.splitlines()[0].split(' ')[-1]
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96 replace_characters = ['"', 'v', 'V', '+', ',']
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97 for i in replace_characters:
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98 version_line = version_line.replace(i, '')
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99 print(program + ' (' + version_line + ') found')
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100 if programs[program][1] == '>=':
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101 program_found_version = version_line.split('.')
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102 program_version_required = programs[program][2].split('.')
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103 if len(program_version_required) == 3:
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104 if len(program_found_version) == 2:
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105 program_found_version.append(0)
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106 else:
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107 program_found_version[2] = program_found_version[2].split('_')[0]
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108 for i in range(0, len(program_version_required)):
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109 if int(program_found_version[i]) > int(program_version_required[i]):
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110 break
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111 elif int(program_found_version[i]) == int(program_version_required[i]):
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112 continue
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113 else:
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114 listMissings.append('It is required ' + program + ' with version ' +
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115 programs[program][1] + ' ' + programs[program][2])
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116 else:
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117 if version_line != programs[program][2]:
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118 listMissings.append('It is required ' + program + ' with version ' + programs[program][1] +
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119 ' ' + programs[program][2])
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120 return listMissings
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121
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122
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123 def requiredPrograms(asperaKey, downloadCramBam, SRA, SRAopt):
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124 programs_version_dictionary = {}
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125 programs_version_dictionary['wget'] = ['--version', '>=', '1.12']
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126 programs_version_dictionary['gzip'] = ['--version', '>=', '1.6']
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127 programs_version_dictionary['bowtie2'] = ['--version', '>=', '2.2.9']
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128 programs_version_dictionary['samtools'] = ['--version', '==', '1.3.1']
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129 programs_version_dictionary['bcftools'] = ['--version', '==', '1.3.1']
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130 if asperaKey is not None:
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131 programs_version_dictionary['ascp'] = ['--version', '>=', '3.6.1']
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132 if SRA or SRAopt:
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133 programs_version_dictionary['prefetch'] = ['--version', '>=', '2.8.2']
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134 programs_version_dictionary['fastq-dump'] = ['--version', '>=', '2.8.2']
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135 programs_version_dictionary['awk'] = ['--version', '>=', '3.0.4']
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136 missingPrograms = checkPrograms(programs_version_dictionary)
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137 if len(missingPrograms) > 0:
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138 sys.exit('\n' + 'Errors:' + '\n' + '\n'.join(missingPrograms))
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139
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140
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141 def general_information(logfile, version, outdir, time_str, doNotUseProvidedSoftware, asperaKey, downloadCramBam, SRA, SRAopt):
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142 # Check if output directory exists
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143
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144 print('\n' + '==========> ReMatCh <==========')
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145 print('\n' + 'Program start: ' + time.ctime())
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146
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147 # Tells where the logfile will be stored
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148 print('\n' + 'LOGFILE:')
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149 print(logfile)
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150
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151 # Print command
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152 print('\n' + 'COMMAND:')
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153 script_path = os.path.join(os.path.dirname(os.path.dirname(os.path.realpath(__file__))), 'rematch.py')
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154 print(sys.executable + ' ' + ' '.join(sys.argv))
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155
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156 # Print directory where programme was lunch
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157 print('\n' + 'PRESENT DIRECTORY:')
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158 present_directory = os.path.abspath(os.getcwd())
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159 print(present_directory)
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160
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161 # Print program version
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162 print('\n' + 'VERSION:')
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163 script_version_git(version, present_directory, script_path)
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164
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165 # Get CPU information
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166 get_cpu_information(outdir, time_str)
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167
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168 # Set and print PATH variable
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169 setPATHvariable(doNotUseProvidedSoftware, script_path)
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170
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171 # Check programms
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172 requiredPrograms(asperaKey, downloadCramBam, SRA, SRAopt)
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173
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174 return script_path
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175
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176
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177 def script_version_git(version, current_directory, script_path, no_git_info=False):
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178 """
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179 Print script version and get GitHub commit information
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180
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181 Parameters
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182 ----------
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183 version : str
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184 Version of the script, e.g. "4.0"
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185 current_directory : str
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186 Path to the directory where the script was start to run
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187 script_path : str
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188 Path to the script running
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189 no_git_info : bool, default False
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190 True if it is not necessary to retreive the GitHub commit information
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191
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192 Returns
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193 -------
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194
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195 """
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196 print('Version {}'.format(version))
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197
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198 if not no_git_info:
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199 try:
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200 os.chdir(os.path.dirname(os.path.dirname(script_path)))
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201 command = ['git', 'log', '-1', '--date=local', '--pretty=format:"%h (%H) - Commit by %cn, %cd) : %s"']
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202 run_successfully, stdout, stderr = run_command_popen_communicate(command, False, 15, False)
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203 print(stdout)
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204 command = ['git', 'remote', 'show', 'origin']
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205 run_successfully, stdout, stderr = run_command_popen_communicate(command, False, 15, False)
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206 print(stdout)
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207 except:
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208 print('HARMLESS WARNING: git command possibly not found. The GitHub repository information will not be'
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209 ' obtained.')
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210 finally:
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211 os.chdir(current_directory)
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212
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213
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214 def run_time(start_time):
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215 end_time = time.time()
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216 time_taken = end_time - start_time
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217 hours, rest = divmod(time_taken, 3600)
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218 minutes, seconds = divmod(rest, 60)
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219 print('Runtime :' + str(hours) + 'h:' + str(minutes) + 'm:' + str(round(seconds, 2)) + 's')
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220 return round(time_taken, 2)
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221
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222
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223 def timer(function, name):
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224 @functools_wraps(function)
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225 def wrapper(*args, **kwargs):
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226 print('\n' + 'RUNNING {0}\n'.format(name))
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227 start_time = time.time()
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228
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229 results = list(function(*args, **kwargs)) # guarantees return is a list to allow .insert()
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230
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231 time_taken = run_time(start_time)
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232 print('END {0}'.format(name))
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233
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234 results.insert(0, time_taken)
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235 return results
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236 return wrapper
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237
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238
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239 def remove_directory(directory):
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240 if os.path.isdir(directory):
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241 shutil.rmtree(directory)
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242
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243
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244 def save_variable_to_pickle(variableToStore, outdir, prefix):
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245 pickleFile = os.path.join(outdir, str(prefix + '.pkl'))
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246 with open(pickleFile, 'wb') as writer:
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247 pickle.dump(variableToStore, writer)
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248
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249
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250 def extract_variable_from_pickle(pickleFile):
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251 with open(pickleFile, 'rb') as reader:
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252 variable = pickle.load(reader)
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253 return variable
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254
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255
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256 def trace_unhandled_exceptions(func):
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257 @functools_wraps(func)
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258 def wrapped_func(*args, **kwargs):
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259 try:
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260 func(*args, **kwargs)
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261 except Exception as e:
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262 print('Exception in ' + func.__name__)
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263 print(e)
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264
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265 exc_type, exc_value, exc_tb = sys.exc_info()
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266 print(''.join(traceback_format_exception(exc_type, exc_value, exc_tb)))
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267
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268 raise exc_type(exc_value)
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269
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270 return wrapped_func
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271
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272
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273 def kill_subprocess_Popen(subprocess_Popen, command):
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274 print('Command run out of time: ' + str(command))
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275 subprocess_Popen.kill()
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276
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277
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278 def run_command_popen_communicate(command, shell_True, timeout_sec_None, print_comand_True):
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279 run_successfully = False
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280 if not isinstance(command, str):
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281 command = ' '.join(command)
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282 command = shlex.split(command)
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283
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284 if print_comand_True:
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285 print('Running: ' + ' '.join(command))
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286
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287 if shell_True:
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288 command = ' '.join(command)
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289 proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
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290 else:
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291 proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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292
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293 not_killed_by_timer = True
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294 if timeout_sec_None is None:
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295 stdout, stderr = proc.communicate()
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296 else:
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297 time_counter = Timer(timeout_sec_None, kill_subprocess_Popen, args=(proc, command,))
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298 time_counter.start()
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299 stdout, stderr = proc.communicate()
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300 time_counter.cancel()
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301 not_killed_by_timer = time_counter.isAlive()
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302
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303 if proc.returncode == 0:
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304 run_successfully = True
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305 else:
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306 if not print_comand_True and not_killed_by_timer:
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307 print('Running: ' + str(command))
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308 if len(stdout) > 0:
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309 print('STDOUT')
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310 print(stdout.decode("utf-8"))
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311 if len(stderr) > 0:
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312 print('STDERR')
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313 print(stderr.decode("utf-8"))
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314 return run_successfully, stdout.decode("utf-8"), stderr.decode("utf-8")
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315
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316
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317 def rchop(string, ending):
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318 if string.endswith(ending):
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319 string = string[:-len(ending)]
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320 return string
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321
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322
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323 def reverse_complement(seq):
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324 complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N'}
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325
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326 reverse_complement_string = ''
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327
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328 seq = reversed(list(seq.upper()))
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329
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330 for base in seq:
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331 reverse_complement_string += complement[base]
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332
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333 return reverse_complement_string