Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

annotate scripts/modules/utils.py @ 0:965517909457 draft

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Wed, 22 Jan 2020 08:41:44 -0500
parents
children 0cbed1c0a762
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0
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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 == 'wget':
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63 version_line = stdout.splitlines()[0].split(' ', 3)[2]
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64 else:
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65 version_line = stdout.splitlines()[0].split(' ')[-1]
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66 replace_characters = ['"', 'v', 'V', '+']
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67 for i in replace_characters:
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68 version_line = version_line.replace(i, '')
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69 print program + ' (' + version_line + ') found'
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70 if programs[program][1] == '>=':
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71 program_found_version = version_line.split('.')
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72 program_version_required = programs[program][2].split('.')
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73 if len(program_version_required) == 3:
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74 if len(program_found_version) == 2:
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75 program_found_version.append(0)
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76 else:
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77 program_found_version[2] = program_found_version[2].split('_')[0]
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78 for i in range(0, len(program_version_required)):
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79 if isinstance(program_found_version[i], (int, long)):
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80 if int(program_found_version[i]) < int(program_version_required[i]):
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81 listMissings.append('It is required ' + program + ' with version ' + programs[program][1] + ' ' + programs[program][2])
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82 else:
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83 if version_line != programs[program][2]:
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84 listMissings.append('It is required ' + program + ' with version ' + programs[program][1] + ' ' + programs[program][2])
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85 return listMissings
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86
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87
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88 def requiredPrograms():
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89 programs_version_dictionary = {}
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90 programs_version_dictionary['rematch.py'] = ['--version', '>=', '3.2']
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91 missingPrograms = checkPrograms(programs_version_dictionary)
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92 if len(missingPrograms) > 0:
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93 sys.exit('\n' + 'Errors:' + '\n' + '\n'.join(missingPrograms))
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94
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95
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96 def general_information(logfile, version, outdir, time_str):
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97 # Check if output directory exists
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98
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99 print '\n' + '==========> patho_typing <=========='
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100 print '\n' + 'Program start: ' + time.ctime()
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101
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102 # Tells where the logfile will be stored
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103 print '\n' + 'LOGFILE:'
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104 print logfile
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105
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106 # Print command
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107 print '\n' + 'COMMAND:'
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108 script_path = os.path.abspath(sys.argv[0])
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109 print sys.executable + ' ' + script_path + ' ' + ' '.join(sys.argv[1:])
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110
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111 # Print directory where programme was lunch
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112 print '\n' + 'PRESENT DIRECTORY:'
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113 present_directory = os.path.abspath(os.getcwd())
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114 print present_directory
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115
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116 # Print program version
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117 print '\n' + 'VERSION:'
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118 scriptVersionGit(version, present_directory, script_path)
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119
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120 # Check programms
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121 requiredPrograms()
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122
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123 return script_path
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124
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125
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126 def setPATHvariable(doNotUseProvidedSoftware, script_path):
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127 path_variable = os.environ['PATH']
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128 script_folder = os.path.dirname(script_path)
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129 # Set path to use provided softwares
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130 if not doNotUseProvidedSoftware:
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131 bowtie2 = os.path.join(script_folder, 'src', 'bowtie2-2.2.9')
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132 samtools = os.path.join(script_folder, 'src', 'samtools-1.3.1', 'bin')
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133 bcftools = os.path.join(script_folder, 'src', 'bcftools-1.3.1', 'bin')
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134
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135 os.environ['PATH'] = str(':'.join([bowtie2, samtools, bcftools, path_variable]))
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136
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137 # Print PATH variable
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138 print '\n' + 'PATH variable:'
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139 print os.environ['PATH']
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140
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141
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142 def scriptVersionGit(version, directory, script_path):
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143 print 'Version ' + version
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144
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145 try:
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146 os.chdir(os.path.dirname(script_path))
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147 command = ['git', 'log', '-1', '--date=local', '--pretty=format:"%h (%H) - Commit by %cn, %cd) : %s"']
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148 run_successfully, stdout, stderr = runCommandPopenCommunicate(command, False, 15, False)
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149 print stdout
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150 command = ['git', 'remote', 'show', 'origin']
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151 run_successfully, stdout, stderr = runCommandPopenCommunicate(command, False, 15, False)
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152 print stdout
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153 os.chdir(directory)
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154 except:
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155 print 'HARMLESS WARNING: git command possibly not found. The GitHub repository information will not be obtained.'
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156
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157
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158 def runTime(start_time):
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159 end_time = time.time()
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160 time_taken = end_time - start_time
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161 hours, rest = divmod(time_taken, 3600)
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162 minutes, seconds = divmod(rest, 60)
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163 print 'Runtime :' + str(hours) + 'h:' + str(minutes) + 'm:' + str(round(seconds, 2)) + 's'
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164 return round(time_taken, 2)
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165
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166
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167 def timer(function, name):
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168 @functools.wraps(function)
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169 def wrapper(*args, **kwargs):
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170 print('\n' + 'RUNNING {0}\n'.format(name))
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171 start_time = time.time()
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172
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173 results = list(function(*args, **kwargs)) # guarantees return is a list to allow .insert()
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174
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175 time_taken = runTime(start_time)
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176 print('END {0}'.format(name))
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177
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178 results.insert(0, time_taken)
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179 return results
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180 return wrapper
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181
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182
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183 def removeDirectory(directory):
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184 if os.path.isdir(directory):
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185 shutil.rmtree(directory)
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186
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187
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188 def saveVariableToPickle(variableToStore, pickleFile):
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189 with open(pickleFile, 'wb') as writer:
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190 pickle.dump(variableToStore, writer)
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191
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192
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193 def extractVariableFromPickle(pickleFile):
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194 with open(pickleFile, 'rb') as reader:
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195 variable = pickle.load(reader)
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196 return variable
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197
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198
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199 def trace_unhandled_exceptions(func):
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200 @functools.wraps(func)
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201 def wrapped_func(*args, **kwargs):
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202 try:
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203 func(*args, **kwargs)
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204 except:
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205 print 'Exception in ' + func.__name__
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206 traceback.print_exc()
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207 return wrapped_func
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208
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209
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210 def kill_subprocess_Popen(subprocess_Popen, command):
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211 print 'Command run out of time: ' + str(command)
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212 subprocess_Popen.kill()
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213
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214
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215 def runCommandPopenCommunicate(command, shell_True, timeout_sec_None, print_comand_True):
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216 run_successfully = False
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217 if not isinstance(command, basestring):
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218 command = ' '.join(command)
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219 command = shlex.split(command)
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220
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221 if print_comand_True:
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222 print 'Running: ' + ' '.join(command)
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223
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224 if shell_True:
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225 command = ' '.join(command)
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226 proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
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227 else:
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228 proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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229
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230 not_killed_by_timer = True
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231 if timeout_sec_None is None:
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232 stdout, stderr = proc.communicate()
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233 else:
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234 timer = Timer(timeout_sec_None, kill_subprocess_Popen, args=(proc, command,))
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235 timer.start()
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236 stdout, stderr = proc.communicate()
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237 timer.cancel()
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238 not_killed_by_timer = timer.isAlive()
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239
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240 if proc.returncode == 0:
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241 run_successfully = True
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242 else:
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243 if not print_comand_True and not_killed_by_timer:
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244 print 'Running: ' + str(command)
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245 if len(stdout) > 0:
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246 print 'STDOUT'
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247 print stdout.decode("utf-8")
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248 if len(stderr) > 0:
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249 print 'STDERR'
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250 print stderr.decode("utf-8")
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251 return run_successfully, stdout, stderr
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252
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253
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254 def required_length(tuple_length_options, argument_name):
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255 class RequiredLength(argparse.Action):
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256 def __call__(self, parser, args, values, option_string=None):
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257 if len(values) not in tuple_length_options:
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258 msg = 'Option {argument_name} requires one of the following number of arguments: {tuple_length_options}'.format(
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259 argument_name=self.argument_name, tuple_length_options=tuple_length_options)
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260 raise argparse.ArgumentTypeError(msg)
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261 setattr(args, self.dest, values)
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262 return RequiredLength
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263
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264
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265 def get_sequence_information(fasta_file, length_extra_seq):
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266 sequence_dict = {}
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267 headers = {}
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268
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269 with open(fasta_file, 'rtU') as reader:
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270 blank_line_found = False
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271 sequence_counter = 0
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272 temp_sequence_dict = {}
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273 for line in reader:
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274 line = line.splitlines()[0]
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275 if len(line) > 0:
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276 if not blank_line_found:
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277 if line.startswith('>'):
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278 if len(temp_sequence_dict) > 0:
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279 if temp_sequence_dict.values()[0]['length'] - 2 * length_extra_seq > 0:
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280 sequence_dict[temp_sequence_dict.keys()[0]] = temp_sequence_dict.values()[0]
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281 headers[temp_sequence_dict.values()[0]['header'].lower()] = sequence_counter
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282 else:
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283 print temp_sequence_dict.values()[0]['header'] + ' sequence ignored due to length <= 0'
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284 temp_sequence_dict = {}
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285
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286 if line[1:].lower() in headers:
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287 sys.exit('Found duplicated sequence headers')
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288
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289 sequence_counter += 1
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290 temp_sequence_dict[sequence_counter] = {'header': line[1:].lower(), 'sequence': '', 'length': 0}
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291 else:
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292 temp_sequence_dict[sequence_counter]['sequence'] += line.upper()
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293 temp_sequence_dict[sequence_counter]['length'] += len(line)
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294 else:
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295 sys.exit('It was found a blank line between the fasta file above line ' + line)
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296 else:
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297 blank_line_found = True
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298
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299 if len(temp_sequence_dict) > 0:
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300 if temp_sequence_dict.values()[0]['length'] - 2 * length_extra_seq > 0:
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301 sequence_dict[temp_sequence_dict.keys()[0]] = temp_sequence_dict.values()[0]
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302 headers[temp_sequence_dict.values()[0]['header'].lower()] = sequence_counter
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303 else:
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304 print temp_sequence_dict.values()[0]['header'] + ' sequence ignored due to length <= 0'
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305
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306 return sequence_dict, headers
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307
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308
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309 def simplify_sequence_dict(sequence_dict):
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310 simple_sequence_dict = {}
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311 for counter, info in sequence_dict.items():
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312 simple_sequence_dict[info['header']] = info
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313 del simple_sequence_dict[info['header']]['header']
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314 return simple_sequence_dict
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315
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316
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317 def chunkstring(string, length):
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318 return (string[0 + i:length + i] for i in range(0, len(string), length))
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319
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320
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321 def clean_headers_sequences(sequence_dict):
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322 problematic_characters = ["|", " ", ",", ".", "(", ")", "'", "/", ":"]
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323 # print 'Checking if reference sequences contain ' + str(problematic_characters) + '\n'
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324
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325 headers_changed = False
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326 new_headers = {}
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327 for i in sequence_dict:
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328 if any(x in sequence_dict[i]['header'] for x in problematic_characters):
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329 for x in problematic_characters:
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330 sequence_dict[i]['header'] = sequence_dict[i]['header'].replace(x, '_')
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331 headers_changed = True
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332 new_headers[sequence_dict[i]['header'].lower()] = i
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333
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334 if headers_changed:
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335 print 'At least one of the those characters was found. Replacing those with _' + '\n'
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336
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337 return sequence_dict, new_headers