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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 import random, os, glob, subprocess
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32 from commons.core.parsing.ParserChooser import ParserChooser
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33 from commons.core.parsing.GffParser import GffParser
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34 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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35 from SMART.Java.Python.misc.Progress import Progress
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36 from SMART.Java.Python.misc import Utils
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37 from commons.core.LoggerFactory import LoggerFactory
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38 from commons.core.utils.RepetOptionParser import RepetOptionParser
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39
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40 LOG_DEPTH = "smart"
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41 DEFAULT_REGION = "_all_"
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42 MULTIPLE_STR = {1: "", 1000: " (in kbp)", 1000000: " (in Gbp)"}
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43
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44 class GetReadDistribution(object):
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45
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46 def __init__(self, verbosity = 0):
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47 self.xLab = ""
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48 self.yLab = "# reads"
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49 self.verbosity = verbosity
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50 self.number = random.randint(0, 100000)
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51 self.log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
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52 self.parsers = {}
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53 self.distribution = {}
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54 self.factors = {}
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55 self.regions = None
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56 self.tmpDatName = None
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57 self.tmpRName = None
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58 self.quorum = 1
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59 self.strands = False
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60 self.width = 800
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61 self.height = 300
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62 self.arial = False
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63
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64 def setNames(self, names):
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65 self.names = names
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66
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67 def setInputFiles(self, fileNames, format):
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68 chooser = ParserChooser(self.verbosity)
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69 chooser.findFormat(format)
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70 for cpt, fileName in enumerate(fileNames):
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71 self.parsers[self.names[cpt]] = chooser.getParser(fileName)
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72
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73 def setOutputFileName(self, fileName):
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74 self.outputFileName = fileName
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75
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76 def setLabs(self, xLab, yLab):
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77 self.xLab = xLab
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78 self.yLab = yLab
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79
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80 def setBinSize(self, binSize):
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81 self.binSize = binSize
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82
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83 def setColors(self, colors):
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84 self.colors = colors
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85
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86 def setFactors(self, factors):
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87 if factors == None:
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88 self.factors = dict([name, 1.0] for name in self.names)
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89 else:
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90 self.factors = dict(zip(self.names, factors))
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91
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92 def setMultiple(self, boolean):
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93 self.multiple = boolean
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94
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95 def setImageSize(self, width, height):
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96 if width != None:
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97 self.width = width
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98 if height != None:
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99 self.height = height
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100
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101 def setQuorum(self, quorum):
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102 self.quorum = quorum
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103
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104 def setRegionsFile(self, fileName):
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105 if fileName != None:
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106 self._loadRegions(fileName)
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107
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108 def setBothStrands(self, strands):
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109 self.strands = strands
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110
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111 def setArial(self, arial):
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112 self.arial = arial
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113
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114 def _checkOptions(self):
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115 if not self.parsers:
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116 self.logAndRaise("ERROR: Missing input file names")
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117
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118 def _logAndRaise(self, errorMsg):
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119 self.log.error(errorMsg)
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120 raise Exception(errorMsg)
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121
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122 def _loadRegions(self, fileName):
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123 self.regions = {}
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124 parser = GffParser(fileName, self.verbosity)
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125 for transcript in parser.getIterator():
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126 chromosome = transcript.getChromosome()
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127 start = transcript.getStart()
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128 end = transcript.getEnd()
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129 name = transcript.getName()
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130 if chromosome not in self.regions:
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131 self.regions[chromosome] = {}
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132 if start not in self.regions[chromosome]:
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133 self.regions[chromosome][start] = {}
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134 if end not in self.regions[chromosome][start]:
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135 self.regions[chromosome][start][end] = []
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136 self.regions[chromosome][start][end].append(name)
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137
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138 def _getRegions(self, transcript):
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139 if self.regions == None:
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140 return [DEFAULT_REGION]
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141 chromosome = transcript.getChromosome()
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142 start = transcript.getStart()
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143 end = transcript.getEnd()
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144 if chromosome not in self.regions:
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145 return []
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146 names = []
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147 for loadedStart in sorted(self.regions[chromosome].keys()):
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148 if loadedStart > end:
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149 return names
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150 for loadedEnd in reversed(sorted(self.regions[chromosome][loadedStart].keys())):
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151 if loadedEnd < start:
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152 break
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153 names.extend(self.regions[chromosome][loadedStart][loadedEnd])
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154 return names
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155
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156 def _parse(self, name):
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157 progress = UnlimitedProgress(10000, "Reading file '%s'" % (name), self.verbosity)
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158 for transcript in self.parsers[name].getIterator():
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159 if transcript.__class__.__name__ == "Mapping":
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160 transcript = transcript.getTranscript()
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161 regions = self._getRegions(transcript)
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162 for region in regions:
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163 if region not in self.distribution:
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164 self.distribution[region] = {}
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165 if name not in self.distribution[region]:
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166 self.distribution[region][name] = {}
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167 chromosome = transcript.getChromosome()
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168 nbElements = float(transcript.getTagValue("nbElements")) if "nbElements" in transcript.getTagNames() else 1
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169 nbElements *= self.factors.get(name, 1)
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170 strand = transcript.getDirection() if self.strands else 1
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171 if chromosome not in self.distribution[region][name]:
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172 self.distribution[region][name][chromosome] = {}
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173 if strand not in self.distribution[region][name][chromosome]:
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174 self.distribution[region][name][chromosome][strand] = {}
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175 previousBin = None
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176 for exon in transcript.getExons():
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177 for pos in range(exon.getStart(), exon.getEnd()+1):
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178 bin = pos / self.binSize
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179 if bin != previousBin:
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180 self.distribution[region][name][chromosome][strand][bin] = self.distribution[region][name][chromosome][strand].get(bin, 0) + nbElements
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181 previousBin = bin
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182 progress.inc()
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183 progress.done()
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184
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185 def _checkQuorum(self, region):
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186 if self.quorum == None:
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187 return True
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188 return max([max([max([max(self.distribution[region][name][chromosome][strand].values()) for strand in self.distribution[region][name][chromosome]]) for chromosome in self.distribution[region][name]]) for name in self.distribution[region]])
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189
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190 def _writeData(self, region):
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191 self.tmpDatName = "tmpFile%d.dat" % (self.number)
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192 handle = open(self.tmpDatName, "w")
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193 handle.write("Chr\tPos\tStrand\tCount\tSample\n")
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194 for name in self.distribution[region]:
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195 for chromosome in sorted(self.distribution[region][name].keys()):
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196 for strand in sorted(self.distribution[region][name][chromosome].keys()):
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197 for pos in sorted(self.distribution[region][name][chromosome][strand].keys()):
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198 handle.write("%s\t%d\t%d\t%d\t\"%s\"\n" % (chromosome, pos * self.binSize, strand, self.distribution[region][name][chromosome][strand].get(pos, 0) * strand, name))
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199 handle.close()
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200
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201 def _findMultiple(self, region):
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202 if not self.multiple:
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203 return 1
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204 maxPosition = max([max([max([max(self.distribution[region][name][chromosome][strand].keys()) for strand in self.distribution[region][name][chromosome]]) for chromosome in self.distribution[region][name]]) for name in self.distribution[region]]) * self.binSize
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205 if maxPosition > 2000000:
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206 return 1000000
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207 elif maxPosition > 2000:
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208 return 1000
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209 return 1
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210
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211 def _writeScript(self, region):
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212 self.tmpRName = "tmpFile%d.R" % (self.number)
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213 fileName = self.outputFileName if region == DEFAULT_REGION else "%s_%s.png" % (os.path.splitext(self.outputFileName)[0], region)
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214 colors = "scale_fill_brewer(palette=\"Set1\") + scale_color_brewer(palette=\"Set1\")" if self.colors == None else "scale_fill_manual(values = c(%s)) + scale_color_manual(values = c(%s))" % (", ".join(["\"%s\"" % (color) for color in self.colors]), ", ".join(["\"%s\"" % (color) for color in self.colors]))
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215 title = "" if region == DEFAULT_REGION else " + labs(title = \"Distribution of %s\") " % (region)
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216 facet = "Sample ~ Chr" if region == DEFAULT_REGION else "Sample ~ ."
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217 handle = open(self.tmpRName, "w")
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218 multiple = self._findMultiple(region)
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219 arial = ", text = element_text(family=\"Arial\", size=20)" if self.arial else ""
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220 if self.arial:
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221 handle.write("library(extrafont)\nloadfonts()\n")
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222 handle.write("library(ggplot2)\n")
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223 handle.write("data <- read.table(\"%s\", header = T)\n" % (self.tmpDatName))
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224 handle.write("data$Sample <- factor(data$Sample, levels=c(%s))\n" % (", ".join(["\"%s\"" % (name) for name in self.names])))
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225 handle.write("png(\"%s\", width = %d, height = %d)\n" % (fileName, self.width, self.height))
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226 handle.write("ggplot(data, aes(x = Pos/%d, y = Count, fill = Sample, color = Sample)) %s + geom_bar(stat = \"identity\") + facet_grid(%s, space=\"free\") + xlab(\"%s%s\") + ylab(\"%s\") + %s + theme(legend.position = \"none\", panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank()%s)\n" % (multiple, title, facet, self.xLab, MULTIPLE_STR[multiple], self.yLab, colors, arial))
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227 handle.write("dev.off()\n")
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228
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229 def _runR(self):
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230 rCommand = os.environ["SMARTRPATH"] if "SMARTRPATH" in os.environ else "R"
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231 command = "\"%s\" CMD BATCH %s" % (rCommand, self.tmpRName)
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232 status = subprocess.call(command, shell=True)
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233 if status != 0:
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234 raise Exception("Problem with the execution of script file %s, status is: %s" % (self.tmpRName, status))
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235
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236 def _plot(self):
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237 progress = Progress(len(self.distribution), "Plotting data", self.verbosity)
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238 for region in self.distribution:
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239 if not self._checkQuorum(region):
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240 self.log.info("Not displaying '%s' for it contains insufficient data." % (region))
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241 else:
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242 self._writeData(region)
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243 self._writeScript(region)
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244 self._runR()
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245 progress.inc()
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246 progress.done()
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247
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248 def _cleanFiles(self):
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249 for fileName in (self.tmpDatName, self.tmpRName):
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250 if fileName != None and os.path.exists(fileName):
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251 os.remove(fileName)
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252 for otherFileName in glob.glob("%s*" % (fileName)):
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253 os.remove(otherFileName)
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254
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255 def run(self):
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256 LoggerFactory.setLevel(self.log, self.verbosity)
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257 self._checkOptions()
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258 self.log.info("START Get Read Distribution")
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259 for name in self.names:
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260 self._parse(name)
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261 self._plot()
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262 self._cleanFiles()
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263 self.log.info("END Get Read Distribution")
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264
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265
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266 if __name__ == "__main__":
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267 description = "Usage: GetReadDistribution.py [options]\n\nGet Read Distribution v1.0.1: Get the distribution of a set of reads. [Category: Personal]\n"
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268 epilog = ""
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269 parser = RepetOptionParser(description = description, epilog = epilog)
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270 parser.add_option("-i", "--input", dest="inputFileNames", action="store", default=None, type="string", help="input files, separated by commas [compulsory] [format: string]")
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271 parser.add_option("-f", "--format", dest="format", action="store", default=None, type="string", help="format of the input [compulsory] [format: transcript or sequence file format]")
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272 parser.add_option("-n", "--names", dest="names", action="store", default=None, type="string", help="name of the input data, separated by commas [compulsory] [format: string]")
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273 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [format: output file in PNG format]")
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274 parser.add_option("-s", "--binSize", dest="binSize", action="store", default=10000, type="int", help="bin size [format: int] [default: 10000]")
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275 parser.add_option("-l", "--xLabel", dest="xLab", action="store", default="", type="string", help="x-axis label name [format: string]")
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276 parser.add_option("-L", "--yLabel", dest="yLab", action="store", default="# reads", type="string", help="y-axis label name [format: string] [default: Reads]")
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277 parser.add_option("-c", "--colors", dest="colors", action="store", default=None, type="string", help="colors of the bars, separated by commas [format: string]")
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278 parser.add_option("-a", "--factors", dest="factors", action="store", default=None, type="string", help="normalization factors, separated by commas [format: string]")
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279 parser.add_option("-r", "--regions", dest="regionsFileName", action="store", default=None, type="string", help="regions to plot [format: transcript file in GFF format]")
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280 parser.add_option("-2", "--strands", dest="strands", action="store_true", default=False, help="plot negative strands on the negative x-axis [format: boolean] [default: False]")
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281 parser.add_option("-m", "--multiple", dest="multiple", action="store_true", default=False, help="use human readable genomic positions (k, G) [format: boolean] [default: False]")
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282 parser.add_option("-q", "--quorum", dest="quorum", action="store", default=1, type="int", help="minimum number of intervals to plot a region [format: int] [default: 1]")
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283 parser.add_option("-z", "--width", dest="width", action="store", default=800, type="int", help="width of the image [format: int] [default: 800]")
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284 parser.add_option("-Z", "--height", dest="height", action="store", default=300, type="int", help="height of the image [format: int] [default: 300]")
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285 parser.add_option("-A", "--arial", dest="arial", action="store_true", default=False, help="use Arial font [format: boolean] [default: false]")
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286 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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287 options = parser.parse_args()[0]
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288 iGetReadDistribution = GetReadDistribution(options.verbosity)
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289 iGetReadDistribution.setNames(options.names.split(","))
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290 iGetReadDistribution.setInputFiles(options.inputFileNames.split(","), options.format)
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291 iGetReadDistribution.setOutputFileName(options.outputFileName)
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292 iGetReadDistribution.setLabs(options.xLab, options.yLab)
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293 iGetReadDistribution.setBinSize(options.binSize)
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294 iGetReadDistribution.setColors(None if options.colors == None else options.colors.split(","))
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295 iGetReadDistribution.setFactors(None if options.factors == None else map(float, options.factors.split(",")))
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296 iGetReadDistribution.setRegionsFile(options.regionsFileName)
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297 iGetReadDistribution.setMultiple(options.multiple)
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298 iGetReadDistribution.setQuorum(options.quorum)
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299 iGetReadDistribution.setImageSize(options.width, options.height)
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300 iGetReadDistribution.setBothStrands(options.strands)
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301 iGetReadDistribution.setArial(options.arial)
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302 iGetReadDistribution.run()
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303
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