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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 os, sys
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32 from optparse import OptionParser
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33 from commons.core.parsing.FastaParser import FastaParser
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34 from commons.core.parsing.FastqParser import FastqParser
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35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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36 from commons.core.parsing.GffParser import GffParser
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37 from SMART.Java.Python.misc.Progress import Progress
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38 from SMART.Java.Python.misc.RPlotter import RPlotter
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39 from SMART.Java.Python.misc import Utils
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40
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41 from commons.core.LoggerFactory import LoggerFactory
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42 from commons.core.utils.RepetOptionParser import RepetOptionParser
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43
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44 LOG_DEPTH = "smart"
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45
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46 class GetSizes(object):
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47
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48 def __init__(self, inFileName = None, inFormat=None, outFileName = None, query=None,xMax=None, xMin=None, csv=False, verbosity = 0):
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49 self.inFileName = inFileName
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50 self.inFormat= inFormat
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51 self.outFileName = outFileName
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52 self.query = query
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53 self.xMax = xMax
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54 self.xMin = xMin
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55 self.xLab = "Size"
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56 self.yLab = "# reads"
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57 self.barplot = False
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58 self.csv = csv
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59 self._verbosity = verbosity
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60 self.parser = None
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61 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
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62
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63 def setAttributesFromCmdLine(self):
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64 description = "Usage: getSizes.py [options]\n\nGet Sizes v1.0.2: Get the sizes of a set of genomic coordinates. [Category: Visualization]\n"
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65 epilog = ""
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66 parser = RepetOptionParser(description = description, epilog = epilog)
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67 parser.add_option("-i", "--input", dest="inputFileName", action="store", default=None, type="string", help="input file [compulsory] [format: file in transcript or sequence format given by -f]")
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68 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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69 parser.add_option("-q", "--query", dest="query", action="store", default=None, type="string", help="type to mesure [default: size] [format: choice (size, intron size, exon size, 1st exon size)]")
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70 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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71 parser.add_option("-x", "--xMax", dest="xMax", action="store", default=None, type="int", help="maximum value on the x-axis to plot [format: int]")
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72 parser.add_option("-X", "--xMin", dest="xMin", action="store", default=None, type="int", help="minimum value on the x-axis to plot [format: int]")
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73 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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74 parser.add_option("-c", "--csv", dest="csv", action="store", type="string", help="write a .csv file [format: bool] [default: false]")
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75 parser.add_option("-a", "--xLabel", dest="xLab", action="store", default="Size", type="string", help="x absis label name [format: string] [default: Size]")
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76 parser.add_option("-b", "--yLabel", dest="yLab", action="store", default="# reads", type="string", help="y absis label name [format: string] [default: Reads]")
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77 parser.add_option("-B", "--barplot", dest="barplot", action="store_true", default=False, help="use barplot representation [format: bool] [default: false]")
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78 options = parser.parse_args()[0]
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79 self._setAttributesFromOptions(options)
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80
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81 def _setAttributesFromOptions(self, options):
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82 self.setInFileName(options.inputFileName)
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83 self.setInFormat(options.format)
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84 self.setQuery(options.query)
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85 self.setOutFileName(options.outputFileName)
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86 self.setXMax(options.xMax)
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87 self.setXMin(options.xMin)
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88 self.setxLab(options.xLab)
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89 self.setyLab(options.yLab)
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90 self.setBarplot(options.barplot)
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91 self.setVerbosity(options.verbosity)
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92
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93 def setInFileName(self, inputFileName):
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94 self.inFileName = inputFileName
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95
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96 def setInFormat(self, inFormat):
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97 self.inFormat = inFormat
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98
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99 def setQuery(self, query):
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100 self.query = query
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101
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102 def setOutFileName(self, outFileName):
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103 self.outFileName = outFileName
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104
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105 def setXMax(self, xMax):
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106 self.xMax = xMax
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107
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108 def setXMin(self, xMin):
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109 self.xMin = xMin
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110
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111 def setxLab(self, xLab):
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112 self.xLab = xLab
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113
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114 def setyLab(self, yLab):
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115 self.yLab = yLab
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116
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117 def setBarplot(self, barplot):
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118 self.barplot = barplot
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119
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120 def setCsv(self, csv):
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121 self.csv = csv
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122
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123 def setVerbosity(self, verbosity):
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124 self._verbosity = verbosity
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125
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126 def _checkOptions(self):
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127 if self.inFileName == None:
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128 self._logAndRaise("ERROR: Missing input file name")
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129 if self.inFormat == "fasta":
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130 self.parser = FastaParser(self.inFileName, self._verbosity)
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131 elif self.inFormat == "fastq":
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132 self.parser = FastqParser(self.inFileName, self._verbosity)
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133 else:
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134 self.parser = TranscriptContainer(self.inFileName, self.inFormat, self._verbosity)
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135
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136 def _logAndRaise(self, errorMsg):
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137 self._log.error(errorMsg)
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138 raise Exception(errorMsg)
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139
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140 def run(self):
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141 LoggerFactory.setLevel(self._log, self._verbosity)
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142 self._checkOptions()
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143 self._log.info("START getsizes")
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144 self._log.debug("Input file name: %s" % self.inFileName)
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145
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146 nbItems = self.parser.getNbItems()
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147 self._log.info( "%i items found" % (nbItems))
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148
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149 # treat items
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150 progress = Progress(nbItems, "Analyzing sequences of %s" % (self.inFileName), self._verbosity)
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151 sizes = {}
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152 names = {}
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153 minimum = 1000000000000
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154 maximum = 0
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155 sum = 0
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156 number = 0
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157 nbSubItems = 0
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158 for item in self.parser.getIterator():
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159 items = []
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160 if self.query == "exon":
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161 items = item.getExons()
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162 elif self.query == "exon1":
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163 if len(item.getExons()) > 1:
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164 item.sortExons()
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165 items = [item.getExons()[0]]
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166 elif self.query == "intron":
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167 items = item.getIntrons()
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168 else:
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169 items = [item, ]
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170
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171 for thisItem in items:
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172 try:
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173 nbElements = int(float(thisItem.getTagValue("nbElements")))
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174 if nbElements == None:
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175 nbElements = 1
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176 except:
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177 nbElements = 1
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178 size = thisItem.getSize()
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179 minimum = min(minimum, size)
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180 maximum = max(maximum, size)
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181 name = thisItem.name.split()[0]
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182
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183 if size not in sizes:
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184 sizes[size] = nbElements
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185 if self.csv:
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186 names[size] = [name, ]
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187 else:
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188 sizes[size] += nbElements
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189 if self.csv:
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190 names[size].append(name)
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191 sum += size
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192 nbSubItems += nbElements
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193 number += 1
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194 progress.inc()
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195 progress.done()
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196
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197 if self.outFileName != None:
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198 plotter = RPlotter(self.outFileName, self._verbosity)
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199 plotter.setFill(0)
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200 plotter.setMinimumX(self.xMin)
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201 plotter.setMaximumX(self.xMax)
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202 plotter.setXLabel(self.xLab)
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203 plotter.setYLabel(self.yLab)
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204 plotter.setBarplot(self.barplot)
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205 plotter.addLine(sizes)
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206 plotter.plot()
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207
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208 if nbSubItems == 0:
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209 self._logAndRaise("No item found")
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210
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211 if self.csv:
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212 csvHandle = open(self.csv, "w")
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213 for size in range(min(sizes.keys()), max(sizes.keys())+1):
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214 if size not in sizes:
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215 csvHandle.write("%d,0,\n" % (size))
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216 else:
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217 csvHandle.write("%d,%d,%s\n" % (size, sizes[size], ";".join(names[size])))
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218 csvHandle.close()
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219
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220 self.items = number
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221 self.subItems = nbSubItems
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222 self.nucleotides = sum
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223 self.minAvgMedMax = Utils.getMinAvgMedMax(sizes)
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224
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225 print "%d items" % (number)
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226 print "%d sub-items" % (nbSubItems)
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227 print "%d nucleotides" % (sum)
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228 print "min/avg/med/max transcripts: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(sizes)
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229
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230 self._log.info("END getsizes")
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231
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232
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233 if __name__ == "__main__":
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234 iGetSizes = GetSizes()
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235 iGetSizes.setAttributesFromCmdLine()
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236 iGetSizes.run()
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237
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238 #TODO: add two more options!!!!!!
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