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18
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1 import os, os.path, random, glob, subprocess, threading, time, resource
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2 from optparse import OptionParser
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3 from SMART.Java.Python.misc.Progress import *
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4 from SMART.Java.Python.getRandomRegions import RandomRegionsGenerator
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5 from commons.core.writer.TranscriptWriter import TranscriptWriter
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6 from SMART.Java.Python.structure.Transcript import Transcript
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7 from commons.core.parsing.GffParser import GffParser
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8
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9 #TYPES = ("bin", "has", "seg", "fj", "nc", "new")
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10 TYPES = ("new", )
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11
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12 class RunCmd(threading.Thread):
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13 def __init__(self, cmd, out, err, time, memory):
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14 threading.Thread.__init__(self)
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15 self._cmd = cmd
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16 self._out = out
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17 self._err = err
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18 self._time = time
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19 self._memory = memory
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20 self._id = os.getpid()
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21 self._mem = 0.0
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22 self._outputFileName = "tmp_%d.out" % (self._id)
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23
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24 def run(self):
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25 self._p = subprocess.Popen(self._cmd, stdout = self._out, stderr = self._err, shell = True)
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26 #self._p.wait()
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27
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28 def _runShellCommand(self, command):
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29 p = subprocess.call("%s > %s" % (command, self._outputFileName), shell=True)
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30 handle = open(self._outputFileName)
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31 data = [line.split() for line in handle.readlines()[1:] if line]
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32 handle.close()
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33 os.remove(self._outputFileName)
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34 return data
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35
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36 def _getPid(self):
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37 self._pid = None
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38 cpt = 1
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39 while True:
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40 commandsFound = []
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41 for line in self._runShellCommand("ps -o pid,cmd"):
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42 if line[1:] == self._cmd.split(" "):
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43 self._pid = int(line[0])
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44 commandsFound.append(" ".join(line[1:]))
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45 if self._pid != None:
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46 return True
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47 time.sleep(1)
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48 if cpt % 100 == 0:
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49 print "pid of '%s' not found after %d seconds. Found: %s" % (self._cmd, cpt, " --- ".join(commandsFound))
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50 cpt += 1
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51 if cpt > 300:
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52 return False
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53
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54 def _fetchMemory(self):
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55 lines = self._runShellCommand("ps u -p %d" % (self._pid))
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56 for line in lines:
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57 self._mem = max(self._mem, float(line[3]))
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58 return self._mem >= self._memory
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59 #print "Cannot find the memory of the current PID (%d) in: %s" % (self._pid, " --- ".join([" ".join(line) for line in lines]))
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60 return False
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61
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62 def getMemory(self):
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63 return self._mem
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64
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65 def _abort(self):
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66 try:
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67 self._p.terminate()
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68 except Exception:
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69 pass
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70 self._killSubThreads()
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71
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72 def _killSubThreads(self):
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73 for line in self._runShellCommand("ps --ppid %d -o pid" % (self._pid)):
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74 self._runShellCommand("kill %s" % (line[0]))
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75 self._runShellCommand("kill %s" % (self._pid))
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76
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77 def go(self):
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78 startTime = time.time()
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79 self.run()
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80 #self.start()
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81 while not self._getPid():
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82 #self.start()
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83 self.run()
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84 while True:
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85 if self._time != None and time.time() - startTime > self._time:
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86 print "\nCommand '%s' did not finish in time. Aborting it." % (self._cmd)
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87 self._abort()
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88 break
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89 if self._memory != None and self._fetchMemory():
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90 print "\nCommand '%s' required too much memory (%f). Aborting it." % (self._cmd, self._mem)
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91 self._abort()
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92 break
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93 #self.join(0.1)
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94 time.sleep(0.1)
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95 #if not self.isAlive():
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96 if self._p.poll() != None:
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97 return True
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98 return False
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99
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100
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101 class DataStructure(object):
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102 def __init__(self):
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103 self._structure = {}
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104
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105 def addData(self, data):
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106 if data._nbRefs not in self._structure:
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107 self._structure[data._nbRefs] = {}
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108 if data._nbQueries not in self._structure[data._nbRefs]:
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109 self._structure[data._nbRefs][data._nbQueries] = {}
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110 if data._genomeSize not in self._structure[data._nbRefs][data._nbQueries]:
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111 self._structure[data._nbRefs][data._nbQueries][data._genomeSize] = {}
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112 if data._type not in self._structure[data._nbRefs][data._nbQueries][data._genomeSize]:
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113 self._structure[data._nbRefs][data._nbQueries][data._genomeSize][data._type] = []
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114 self._structure[data._nbRefs][data._nbQueries][data._genomeSize][data._type].append(data._group)
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115
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116 def export(self):
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117 outputString = "#refs\t#queries\tgenome size\ttype\t# written\t# overlaps\tbuild t.\trun t.\tmem\n"
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118 for nbRefs in sorted(self._structure.keys()):
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119 for nbQueries in sorted(self._structure[nbRefs].keys()):
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120 for genomeSize in sorted(self._structure[nbRefs][nbQueries].keys()):
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121 for type in TYPES:
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122 if type not in self._structure[nbRefs][nbQueries][genomeSize]:
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123 outputString += "NA\tNA\tNA\t%s\tNA\tNA\tNA\tNA\tNA\tNA\n" % (type)
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124 else:
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125 for group in self._structure[nbRefs][nbQueries][genomeSize][type]:
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126 outputString += "%d\t%d\t%d\t%s\t%d\t%d\t%f\t%f\t%f\n" % (nbRefs, nbQueries, genomeSize, type, group._nbOutputs, group._nbOverlaps, group._buildTime, group._runTime, group._mem)
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127 return outputString
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128
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129
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130 class Data(object):
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131 def __init__(self, type, buildTime, runTime, mem, nbRefs, nbQueries, nbOutputs, nbOverlaps, genomeSize):
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132 self._type = type
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133 self._nbRefs = nbRefs
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134 self._nbQueries = nbQueries
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135 self._genomeSize = genomeSize
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136 self._group = Group(nbOutputs, nbOverlaps, buildTime, runTime, mem)
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137
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138 def checkConsistency(self, data):
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139 return self._group.checkConsistency(data._group)
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140
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141
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142 class Group(object):
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143 def __init__(self, nbOutputs, nbOverlaps, buildTime, runTime, mem):
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144 self._buildTime = buildTime
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145 self._runTime = runTime
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146 self._mem = mem
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147 self._nbOutputs = nbOutputs
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148 self._nbOverlaps = nbOverlaps
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149
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150 def checkConsistency(self, group):
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151 if (self._buildTime == "NA" or group._buildTime == "NA"):
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152 return True
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153 return (self._nbOutputs == group._nbOutputs and self._nbOverlaps == group._nbOverlaps)
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154
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155
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156 class Benchmark(object):
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157
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158 def __init__(self, verbosity = 1):
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159 self._verbosity = verbosity
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160 self._checkEnvironmentVariable()
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161 self._toolName = {"bin": os.path.join(os.environ["SMARTPATH"], "ncList", "FindOverlapsWithSeveralIntervalsBin.py"), \
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162 "has": os.path.join(os.environ["SMARTPATH"], "ncList", "FindOverlapsWithSeveralIntervalsHashBin.py"), \
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163 "seg": os.path.join(os.environ["SMARTPATH"], "ncList", "FindOverlapsWithSeveralIntervalsBinSegment.py"), \
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164 "fj": os.path.join(os.environ["SMARTPATH"], "ncList", "FindOverlapsFJoin.py"), \
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165 "nc": os.path.join(os.environ["SMARTPATH"], "ncList", "FindOverlapsWithSeveralIntervals.py"), \
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166 "new": os.path.join(os.environ["SMARTPATH"], "FindOverlapsOptim.py")}
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167 self._structure = DataStructure()
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168 self._pid = os.getpid()
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169 self._count = 0
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170 self._time = None
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171 self._memory = None
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172
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173 def _checkEnvironmentVariable(self):
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174 if "SMARTPATH" not in os.environ:
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175 raise Exception("'SMARTPATH' is not set. Please set it to '<installation-direction>/S-mart/Java/Python'.")
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176
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177 def _createTmpFileName(self, name, extension):
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178 self._count += 1
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179 return "tmp_%d_%d_%s.%s" % (self._pid, self._count, name, extension)
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180
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181 def _dumpAndReturn(self, fileName, exception):
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182 handle = open(fileName)
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183 print "Error in parsing file '%s':" % (fileName)
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184 for line in handle:
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185 print line.strip()
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186 print "Command is: '%s'" % (self._command)
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187 raise exception
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188
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189 def setNbReferences(self, nbReferences):
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190 self._nbReferences = nbReferences
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191
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192 def setNbQueries(self, nbQueries):
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193 self._nbQueries = nbQueries
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194
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195 def setGenomeSizes(self, nbGenomeSizes):
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196 self._nbGenomeSizes = nbGenomeSizes
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197
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198 def setNbReplicates(self, nbReplicates):
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199 self._nbReplicates = nbReplicates
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200
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201 def setChromosomeName(self, chromosome):
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202 self._chromosomeName = chromosome
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203
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204 def setSizes(self, minSize, maxSize):
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205 self._minSize = minSize
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206 self._maxSize = maxSize
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207
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208 def setOutputFileName(self, fileName):
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209 self._outputFileName = fileName
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210
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211 def setLimits(self, time, memory):
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212 self._time = time
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213 self._memory = memory
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214
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215 def _generateIntervals(self, nbElements, genomeSize):
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216 fileName = self._createTmpFileName("intervals", "gff3")
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217 iRR = RandomRegionsGenerator(0)
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218 iRR.setMinSize(self._minSize)
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219 iRR.setMaxSize(self._maxSize)
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220 iRR.setGenomeSize(genomeSize)
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221 iRR.setChromosomeName(self._chromosomeName)
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222 iRR.setStrands(False)
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223 iRR.setNumber(nbElements)
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224 iRR.setOutputFile(fileName)
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225 iRR.run()
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226 return fileName
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227
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228 def _startTool(self, type, refFileName, queryFileName, nbReferences, nbQueries, genomeSize):
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229 outputFileName = self._createTmpFileName("output", "gff3")
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230 outFileName = self._createTmpFileName("out", "out")
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231 errFileName = self._createTmpFileName("err", "err")
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232 outHandle = open(outFileName, "w")
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233 errHandle = open(errFileName, "w")
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234 self._command = "python %s -i %s -f gff3 -j %s -g gff3 -o %s -v 3" % (self._toolName[type], queryFileName, refFileName, outputFileName)
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235 thread = RunCmd(self._command, outHandle, errHandle, self._time, self._memory)
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236 over = thread.go()
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237 self._mem = thread.getMemory()
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238 if os.path.exists(outputFileName):
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239 os.remove(outputFileName)
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240 outHandle.close()
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241 errHandle.close()
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242 errData = open(errFileName).readlines()
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243 if errData:
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244 print "Error output: \n%s\n" % ("\n".join(errData))
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245 if not over:
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246 errHandle = open(errFileName, "r")
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247 error = errHandle.readlines()
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248 errHandle.close()
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249 if error:
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250 for line in error:
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251 print line.strip()
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252 print "Previous process failed"
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253 os.remove(errFileName)
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254 if not over:
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255 return False
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256 return outFileName
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257
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258 def _parseTrace(self, type, fileName, genomeSize):
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259 handle = open(fileName)
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260 buildTime = 0
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261 try:
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262 for line in handle:
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263 line = line.strip()
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264 if "time spent" in line:
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265 buildTime += float(line.split()[-1][:-1])
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266 elif "done" in line:
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267 buildTime += float(line.split("(")[1][:-2])
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268 elif "# queries" in line:
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269 nbQueries = int(line.split()[-1])
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270 elif "# refs" in line:
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271 nbRefs = int(line.split()[-1])
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272 elif "# written" in line:
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273 nbOutputs = int(line.split()[2])
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274 nbOverlaps = int(line.split()[3][1:])
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275 elif "time" in line:
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276 runTime = float(line.split()[-1][:-1])
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277 except Exception, e:
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278 handle.close()
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279 self._dumpAndReturn(fileName, e)
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280 handle.close()
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281 try:
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282 return Data(type, buildTime, runTime, self._mem, nbRefs, nbQueries, nbOutputs, nbOverlaps, genomeSize)
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283 except Exception, e:
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284 handle.close()
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285 self._dumpAndReturn(fileName, e)
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286
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287 def _cleanTmpFiles(self, really = False):
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288 files = glob.glob("tmp_%d_*.pkl" % (self._pid)) + glob.glob("tmp_%d_*.bin" % (self._pid))
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289 if really:
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290 files += glob.glob("tmp_%d_*.gff3" % (self._pid)) + glob.glob("tmp_%d_*.out" % (self._pid))
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291 for fileName in files:
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292 os.remove(fileName)
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293
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294 def run(self):
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295 progress = Progress(len(self._nbReferences) * len(self._nbQueries) * len(self._nbGenomeSizes) * self._nbReplicates, "Processing", self._verbosity)
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296 for nbReferences in self._nbReferences:
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297 for queriesRatio in self._nbQueries:
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298 nbQueries = int(nbReferences * queriesRatio)
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299 for genomeSizeRatio in self._nbGenomeSizes:
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300 genomeSize = int(nbReferences * genomeSizeRatio)
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301 for replicate in range(self._nbReplicates):
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302 refFileName = self._generateIntervals(nbReferences, genomeSize)
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303 queryFileName = self._generateIntervals(nbQueries, genomeSize)
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304 data = {}
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305 for type in TYPES:
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306 fileName = self._startTool(type, refFileName, queryFileName, nbReferences, nbQueries, genomeSize)
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307 if not fileName:
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308 data[type] = Data(type, "NA", "NA", "NA", nbReferences, nbQueries, "NA", "NA", genomeSize)
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309 else:
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310 data[type] = self._parseTrace(type, fileName, genomeSize)
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311 self._structure.addData(data[type])
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312 os.remove(fileName)
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313 self._cleanTmpFiles()
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314 self._cleanTmpFiles(True)
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315 firstType = TYPES[0]
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316 for type in TYPES[1:]:
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317 if not data[firstType].checkConsistency(data[type]):
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318 raise Exception("Outputs are not consistent.\n # outputs: %d vs %d.\n # overlaps: %d vs %d.\n %s: %f + %f; %s: %f + %f.\n Files are %s and %s." % (data[firstType]._group._nbOutputs, data[type]._group._nbOutputs, data[firstType]._group._nbOverlaps, data[type]._group._nbOverlaps, firstType, data[firstType]._group._buildTime, data[firstType]._group._runTime, data[firstType]._group._mem, type, data[type]._group._buildTime, data[type]._group._runTime, data[type]._group._mem, refFileName, queryFileName))
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319 for fileName in (queryFileName, refFileName):
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320 if os.path.exists(fileName):
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321 os.remove(fileName)
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322 progress.inc()
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323 progress.done()
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324 handle = open(self._outputFileName, "w")
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325 handle.write(self._structure.export())
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326 handle.close()
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327
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328
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329
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330 if __name__ == "__main__":
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331
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332 description = "Benchmark v1.0.2: Compare NC-List with other tools. Only work under Linux. [Category: Other]"
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333 parser = OptionParser(description = description)
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334 parser.add_option("-r", "--nbReferences", dest="nbReferences", action="store", default=None, type="string", help="number of references (list of integers separated by commas) [compulsory] [format: string]")
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335 parser.add_option("-q", "--nbQueries", dest="nbQueries", action="store", default=None, type="string", help="number of queries as a factor of the number of references (list of floats separated by commas) [compulsory] [format: string]")
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336 parser.add_option("-R", "--nbReplicates", dest="nbReplicates", action="store", default=None, type="int", help="number of replicates [compulsory] [format: int]")
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337 parser.add_option("-s", "--genomeSizes", dest="genomeSizes", action="store", default=None, type="string", help="genome size as a factor of the number of references (list of floats separated by commas) [compulsory] [format: string]")
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338 parser.add_option("-c", "--chromosome", dest="chromosome", action="store", default="chr1", type="string", help="name of the chromosome [default: chr1] [format: string]")
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339 parser.add_option("-z", "--minSize", dest="minSize", action="store", default=None, type="int", help="minimum size of the reads [compulsory] [format: int]")
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340 parser.add_option("-Z", "--maxSize", dest="maxSize", action="store", default=None, type="int", help="maximum size of the reads [compulsory] [format: int]")
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341 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in TXT format]")
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342 parser.add_option("-t", "--time", dest="time", action="store", default=None, type="int", help="maximum time to wait (in seconds) [default: None] [format: int]")
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343 parser.add_option("-m", "--memory", dest="memory", action="store", default=None, type="float", help="maximum memory usage (in %) [default: None] [format: float]")
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344 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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345 (options, args) = parser.parse_args()
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346
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347 benchmark = Benchmark(options.verbosity)
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348 benchmark.setNbReferences(map(int, options.nbReferences.split(",")))
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349 benchmark.setNbQueries(map(float, options.nbQueries.split(",")))
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350 benchmark.setGenomeSizes(map(float, options.genomeSizes.split(",")))
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351 benchmark.setNbReplicates(options.nbReplicates)
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352 benchmark.setChromosomeName(options.chromosome)
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353 benchmark.setSizes(options.minSize, options.maxSize)
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354 benchmark.setLimits(options.time, options.memory)
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355 benchmark.setOutputFileName(options.outputFileName)
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356 benchmark.run()
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357
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