Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/plotCsv.py @ 1:30c5431d8ce4

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Uploaded
author yufei-luo
date Thu, 17 Jan 2013 11:01:51 -0500
parents e0f8dcca02ed
children
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rev   line source
0
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #! /usr/bin/env python
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 # Copyright INRA-URGI 2009-2010
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4 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 # "http://www.cecill.info".
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10 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 # same conditions as regards security.
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27 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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30 #
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31 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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32 Plot the data from the data files
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33 """
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34
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35 import os
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36 import re
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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37 from optparse import OptionParser
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38 from SMART.Java.Python.misc.RPlotter import *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 from SMART.Java.Python.misc.Progress import *
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40
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41
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42 def mergeData(line1, line2):
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43 if line1.keys() != line2.keys():
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44 sys.exit("Error! Input files do not correspond to each other! Aborting...")
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45 mergedData = {}
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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46 for key in line1:
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47 mergedData[key] = (line1[key], line2[key])
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48 return mergedData
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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49
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50
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51
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52 if __name__ == "__main__":
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53
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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54 # parse command line
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55 description = "Plot CSV v1.0.1: Plot the content of a CSV file. [Category: Personnal]"
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56
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57 parser = OptionParser(description = description)
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58 parser.add_option("-i", "--input", dest="inputFileNames", action="store", type="string", help="input file [compulsory] [format: file in CSV format]")
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59 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]")
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60 parser.add_option("-s", "--shape", dest="shape", action="store", type="string", help="shape of the plot [format: choice (line, bar, points, heatPoints)]")
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61 parser.add_option("-l", "--log", dest="log", action="store", default="", type="string", help="use log on x- or y-axis (write 'x', 'y' or 'xy') [format: string] [default: ]")
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62 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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63 (options, args) = parser.parse_args()
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64
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65 plotter = RPlotter(options.outputFileName, options.verbosity)
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66 if options.shape == "bar":
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67 plotter.setBarplot(True)
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68 elif options.shape == "points":
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69 plotter.setPoints(True)
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70 elif options.shape == "heatPoints":
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71 plotter.setHeatPoints(True)
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72
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73 plotter.setLog(options.log)
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74
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75 lines = []
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76 nbsColumns = []
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77 for inputFileName in options.inputFileNames.split(","):
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78 inputFile = open(inputFileName)
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79 line = {}
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80 nbColumns = None
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81
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82 for point in inputFile:
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83 point = point.strip()
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84
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85 m = re.search(r"^\s*(\S+)\s+(\d+\.?\d*)\s+(\d+\.?\d*)\s*$", point)
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86 if m != None:
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87 line[m.group(1)] = (float(m.group(2)), float(m.group(3)))
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88 if nbColumns == None:
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89 nbColumns = 3
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90 nbsColumns.append(nbColumns)
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91 elif nbColumns != 3:
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92 sys.exit("Number of columns changed around line '%s' of file '%s'! Aborting..." % (point, inputFileName))
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93 else:
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94 m = re.search(r"^\s*(\d+\.?\d*)\s+(\d+\.?\d*)\s*$", point)
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95 if m != None:
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96 line[float(m.group(1))] = float(m.group(2))
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97 if nbColumns == None:
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98 nbColumns = 2
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99 nbsColumns.append(nbColumns)
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100 if nbColumns != 2:
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101 sys.exit("Number of columns changed around line '%s' of file '%s'! Aborting..." % (point, inputFileName))
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102 else:
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103 m = re.search(r"^\s*(\S+)\s+(\d+\.?\d*)\s*$", point)
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104 if m != None:
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105 line[m.group(1)] = float(m.group(2))
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106 if nbColumns == None:
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107 nbColumns = 1
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108 nbsColumns.append(nbColumns)
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109 if nbColumns != 1:
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110 sys.exit("Number of columns changed around line '%s' of file '%s'! Aborting..." % (point, inputFileName))
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111 else:
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112 sys.exit("Do not understand line '%s' of file '%s'! Aborting..." % (point, inputFileName))
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113
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114 lines.append(line)
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115
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116 if len(lines) != len(nbsColumns):
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117 sys.exit("Something is wrong in the input files! Aborting...")
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118
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119 if options.shape == "bar":
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120 if len(lines) != 1:
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121 sys.exit("Error! Bar plot should have exactly one input file! Aborting...")
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122 if nbsColumns[0] != 2:
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123 sys.exit("Error! Bar plot input file should have exactly two columns! Aborting...")
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124 plotter.addLine(lines[0])
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125 elif options.shape == "points":
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126 if len(lines) != 2:
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127 sys.exit("Error! Points cloud should have exactly two input file! Aborting...")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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128 if nbsColumns[0] != 2 or nbsColumns[1] != 2:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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129 sys.exit("Error! Points cloud plot input file should have exactly two columns! Aborting...")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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130 plotter.addLine(mergedData(lines[0], lines[1]))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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131 elif options.shape == "heatPoints":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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132 if len(lines) != 3:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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133 sys.exit("Error! Heat points cloud should have exactly three input file! Aborting...")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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134 plotter.addLine(mergeData(lines[0], lines[1]))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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135 plotter.addHeatLine(lines[2])
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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136 elif options.shape == "line":
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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137 for i in range(0, len(lines)):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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138 if (nbsColumns[i] != 2):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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139 sys.exit("Error! Curve plot input file should have exactly two columns! Aborting...")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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140 plotter.addLine(lines[i])
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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141 else:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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142 sys.exit("Do not understand shape '%s'" % (options.shape))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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143
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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144
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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145 plotter.plot()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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146