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comparison smart_toolShed/SMART/Java/Python/plotCsv.py @ 0:e0f8dcca02ed

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