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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 """Get the repartition of some elements in a chromosomes"""
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32
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33 import os
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34 from optparse import OptionParser
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35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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36 from SMART.Java.Python.structure.Transcript import Transcript
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37 from commons.core.writer.Gff3Writer import Gff3Writer
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38 from SMART.Java.Python.misc.RPlotter import RPlotter
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39 from SMART.Java.Python.misc.Progress import Progress
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40 from math import *
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41
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42 def divideKeyDict(dictionary, ratio):
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43 return dict([(key / ratio, dictionary[key]) for key in dictionary])
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44
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45
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46 def setTranscript(chromosome, direction, start, end, name, value):
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47 transcript = Transcript()
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48 transcript.setChromosome(chromosome)
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49 transcript.setDirection(direction)
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50 transcript.setStart(start)
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51 transcript.setEnd(end)
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52 transcript.setName(name)
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53 transcript.setTagValue("nbElements", value)
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54 return transcript
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55
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56
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57
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58 if __name__ == "__main__":
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59
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60 magnifyingFactor = 1000
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61
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62 # parse command line
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63 description = "Get Distribution v1.0.1: Get the distribution of the genomic coordinates on a genome. [Category: Visualization]"
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64
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65 parser = OptionParser(description = description)
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66 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
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67 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]")
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68 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
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69 parser.add_option("-r", "--reference", dest="referenceFileName", action="store", default=None, type="string", help="file containing the genome [compulsory] [format: file in FASTA format]")
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70 parser.add_option("-n", "--nbBins", dest="nbBins", action="store", default=1000, type="int", help="number of bins [default: 1000] [format: int]")
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71 parser.add_option("-2", "--bothStrands", dest="bothStrands", action="store_true", default=False, help="plot one curve per strand [format: bool] [default: false]")
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72 parser.add_option("-w", "--raw", dest="raw", action="store_true", default=False, help="plot raw number of occurrences instead of density [format: bool] [default: false]")
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73 parser.add_option("-x", "--csv", dest="csv", action="store_true", default=False, help="write a .csv file [format: bool]")
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74 parser.add_option("-c", "--chromosome", dest="chromosome", action="store", default=None, type="string", help="plot only a chromosome [format: string]")
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75 parser.add_option("-s", "--start", dest="start", action="store", default=None, type="int", help="start from a given region [format: int]")
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76 parser.add_option("-e", "--end", dest="end", action="store", default=None, type="int", help="end from a given region [format: int]")
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77 parser.add_option("-y", "--yMin", dest="yMin", action="store", default=None, type="int", help="minimum value on the y-axis to plot [format: int]")
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78 parser.add_option("-Y", "--yMax", dest="yMax", action="store", default=None, type="int", help="maximum value on the y-axis to plot [format: int]")
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79 parser.add_option("-g", "--gff", dest="gff", action="store_true", default=False, help="also write GFF3 file [format: bool] [default: false]")
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80 parser.add_option("-H", "--height", dest="height", action="store", default=None, type="int", help="height of the graphics [format: int] [default: 300]")
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81 parser.add_option("-W", "--width", dest="width", action="store", default=None, type="int", help="width of the graphics [format: int] [default: 1000]")
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82 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
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83 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool]")
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84 parser.add_option("-D", "--directory", dest="working_Dir", action="store", default=os.getcwd(), type="string", help="the directory to store the results [format: directory]")
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85 (options, args) = parser.parse_args()
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86
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87 sizes = {}
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88 if options.referenceFileName != None:
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89 # get the sizes of the chromosomes
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90 referenceHandle = open(options.referenceFileName)
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91 name = None
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92 size = 0
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93 maxSize = 0
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94 for line in referenceHandle:
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95 line = line.strip()
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96 if line == "": continue
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97 if line[0] == ">":
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98 if name != None:
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99 if options.verbosity > 10:
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100 print name
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101 sizes[name] = size
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102 maxSize = max(maxSize, size)
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103 size = 0
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104 name = line[1:]
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105 else:
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106 size += len(line)
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107 sizes[name] = size
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108 maxSize = max(maxSize, size)
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109 if options.verbosity > 1:
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110 print "done"
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111 start = 0
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112 end = maxSize
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113 else:
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114 if options.chromosome == None or options.start == None or options.end == None:
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115 raise Exception("Missing chromosome or start and end positions, or reference file")
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116 maxSize = options.end
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117 sizes[options.chromosome] = options.end
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118 start = options.start
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119 end = options.end
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120
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121
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122 tmp1 = int(maxSize / float(options.nbBins))
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123 tmp2 = 10 ** (len("%d" % (tmp1))-2)
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124 sliceSize = int((tmp1 / tmp2) * tmp2)
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125
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126 bins = dict()
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127 binsPlus = dict()
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128 binsMinus = dict()
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129 for chromosome in sizes:
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130 bins[chromosome] = dict([(i * sliceSize + 1, 0) for i in range(start / sliceSize, sizes[chromosome] / sliceSize + 1)])
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131 binsPlus[chromosome] = dict([(i * sliceSize + 1, 0) for i in range(start / sliceSize, sizes[chromosome] / sliceSize + 1)])
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132 binsMinus[chromosome] = dict([(i * sliceSize + 1, 0) for i in range(start / sliceSize, sizes[chromosome] / sliceSize + 1)])
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133
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134 parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
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135 progress = Progress(parser.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
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136 maxSlice = 0
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137 # count the number of reads
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138 for transcript in parser.getIterator():
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139 if options.chromosome == None or (transcript.getChromosome() == options.chromosome and transcript.getStart() >= start and transcript.getStart() <= end):
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140 if transcript.getDirection() == 1:
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141 binsPlus[transcript.getChromosome()][(transcript.getStart() / sliceSize) * sliceSize + 1] += 1
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142 else:
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143 binsMinus[transcript.getChromosome()][(transcript.getStart() / sliceSize) * sliceSize + 1] += 1
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144 bins[transcript.getChromosome()][(transcript.getStart() / sliceSize) * sliceSize + 1] += 1
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145 maxSlice = max(maxSlice, transcript.getStart() / sliceSize)
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146 progress.inc()
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147 progress.done()
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148
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149 # compute densities
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150 densityPlus = dict()
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151 for chromosome in bins:
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152 densityPlus[chromosome] = dict([(bin, 0) for bin in binsPlus[chromosome]])
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153 for bin in binsPlus[chromosome]:
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154 densityPlus[chromosome][bin] = float(binsPlus[chromosome][bin]) / sliceSize * magnifyingFactor
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155 # correct densities for first and last bins
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156 if start % sliceSize != 0:
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157 densityPlus[chromosome][(start / sliceSize) * sliceSize + 1] = float(binsPlus[chromosome][(start / sliceSize) * sliceSize + 1]) / (sliceSize - (start % sliceSize)) * magnifyingFactor
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158 if sizes[chromosome] % sliceSize != 0:
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159 densityPlus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1] = float(binsPlus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1]) / (sizes[chromosome] % sliceSize) * magnifyingFactor
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160 densityMinus = dict()
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161 for chromosome in binsMinus:
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162 densityMinus[chromosome] = dict([(bin, 0) for bin in binsMinus[chromosome]])
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163 for bin in binsMinus[chromosome]:
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164 densityMinus[chromosome][bin] = float(binsMinus[chromosome][bin]) / sliceSize * magnifyingFactor
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165 # correct densities for first and last bins
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166 if start % sliceSize != 0:
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167 densityMinus[chromosome][(start / sliceSize) * sliceSize + 1] = float(binsMinus[chromosome][(start / sliceSize) * sliceSize + 1]) / (sliceSize - (start % sliceSize)) * magnifyingFactor
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168 if sizes[chromosome] % sliceSize != 0:
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169 densityMinus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1] = float(binsMinus[chromosome][(sizes[chromosome] / sliceSize) * sliceSize + 1]) / (sizes[chromosome] % sliceSize) * magnifyingFactor
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170 density = dict()
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171 for chromosome in bins:
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172 density[chromosome] = dict([(bin, 0) for bin in bins[chromosome]])
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173 for bin in bins[chromosome]:
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174 density[chromosome][bin] = densityPlus[chromosome][bin] + densityMinus[chromosome][bin]
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175
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176 for chromosome in densityMinus:
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177 for bin in densityMinus[chromosome]:
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178 densityMinus[chromosome][bin] *= -1
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179 for bin in binsMinus[chromosome]:
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180 binsMinus[chromosome][bin] *= -1
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181
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182 for chromosome in density:
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183 maxX = max(bins[chromosome].keys())
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184 if maxX <= 1000:
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185 unit = "nt."
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186 ratio = 1.0
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187 elif maxX <= 1000000:
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188 unit = "kb"
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189 ratio = 1000.0
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190 else:
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191 unit = "Mb"
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192 ratio = 1000000.0
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193 outputFileName = "%s_%s" % (options.outputFileName, chromosome)
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194 if options.start != None and options.end != None:
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195 outputFileName += ":%d-%d" % (options.start, options.end)
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196 outputFileName += ".png"
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197 plotter = RPlotter(outputFileName, options.verbosity)
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198 plotter.setXLabel("Position on %s (in %s)" % (chromosome.replace("_", " "), unit))
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199 plotter.setYLabel("# reads")
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200 if options.bothStrands:
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201 plotter.setImageSize(1000, 300)
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202 else:
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203 plotter.setImageSize(1000, 200)
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204 if options.height != None:
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205 plotter.setHeight(options.height)
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206 if options.width != None:
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207 plotter.setWidth(options.width)
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208 if options.yMax != None:
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209 plotter.setMinimumY(options.yMin)
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210 if options.yMax != None:
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211 plotter.setMaximumY(options.yMax)
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212 if options.bothStrands :
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213 if options.raw:
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214 plotter.addLine(divideKeyDict(binsPlus[chromosome], ratio))
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215 else:
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216 plotter.addLine(divideKeyDict(densityPlus[chromosome], ratio))
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217 if options.raw:
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218 plotter.addLine(divideKeyDict(binsMinus[chromosome], ratio))
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219 else:
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220 plotter.addLine(divideKeyDict(densityMinus[chromosome], ratio))
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221 else:
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222 if options.raw:
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223 plotter.addLine(divideKeyDict(bins[chromosome], ratio))
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224 else:
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225 plotter.addLine(divideKeyDict(density[chromosome], ratio))
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226 plotter.plot()
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227
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228 if options.csv:
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229 outputFileName = "%s" % (options.outputFileName)
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230 if options.chromosome != None:
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231 outputFileName += "_%s" % (options.chromosome)
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232 if options.start != None and options.end != None:
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233 outputFileName += ":%d-%d" % (options.start, options.end)
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234 outputFileName += ".csv"
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235 csvHandle = open(outputFileName, "w")
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236 for slice in range(start / sliceSize, maxSlice + 1):
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237 csvHandle.write(";%d-%d" % (slice * sliceSize + 1, (slice+1) * sliceSize))
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238 csvHandle.write("\n")
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239 if options.bothStrands:
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240 for chromosome in densityPlus:
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241 if len(densityPlus[chromosome]) > 0:
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242 csvHandle.write("%s [+]" % (chromosome))
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243 for slice in sorted(densityPlus[chromosome].keys()):
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244 csvHandle.write(";%.2f" % (densityPlus[chromosome][slice]))
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245 csvHandle.write("\n")
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246 if len(densityMinus[chromosome]) > 0:
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247 csvHandle.write("%s [-]" % (chromosome))
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248 for slice in sorted(densityPlus[chromosome].keys()):
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249 csvHandle.write(";%.2f" % (-densityMinus[chromosome][slice]))
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250 csvHandle.write("\n")
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251 else:
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252 for chromosome in density:
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253 if len(density[chromosome]) > 0:
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254 csvHandle.write(chromosome)
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255 for slice in sorted(density[chromosome].keys()):
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256 csvHandle.write(";%.2f" % (density[chromosome][slice]))
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257 csvHandle.write("\n")
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258 csvHandle.close()
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259
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260 if options.gff:
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261 chromosome = "" if options.chromosome == None else options.chromosome.capitalize()
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262 start = "" if options.start == None else "%d" % (options.start)
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263 end = "" if options.end == None else "%d" % (options.end)
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264 link1 = "" if options.start == None and options.end == None else ":"
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265 link2 = "" if options.start == None and options.end == None else "-"
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266 writer = Gff3Writer("%s%s%s%s%s.gff3" % (options.outputFileName, link1, start, link2, end), options.verbosity)
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267 cpt = 1
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268 if options.raw:
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269 valuesPlus = binsPlus
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270 valuesMinus = binsMinus
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271 values = bins
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272 else:
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273 valuesPlus = densityPlus
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274 valuesMinus = densityMinus
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275 values = density
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276 if options.bothStrands:
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277 for chromosome in values:
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278 for slice in valuesPlus[chromosome]:
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279 writer.addTranscript(setTranscript(chromosome, 1, slice, slice + sliceSize, "region%d" % (cpt), valuesPlus[chromosome][slice]))
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280 cpt += 1
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281 for slice in valuesMinus[chromosome]:
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282 writer.addTranscript(setTranscript(chromosome, -1, slice, slice + sliceSize, "region%d" % (cpt), - valuesMinus[chromosome][slice]))
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283 cpt += 1
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284 else:
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285 for chromosome in values:
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286 for slice in values[chromosome]:
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287 writer.addTranscript(setTranscript(chromosome, 1, slice, slice + sliceSize, "region%d" % (cpt), values[chromosome][slice]))
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288 cpt += 1
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289 writer.write()
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290
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291
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