Mercurial > repos > yufei-luo > s_mart
view smart_toolShed/SMART/Java/Python/plotCsv.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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#! /usr/bin/env python # # Copyright INRA-URGI 2009-2010 # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. # """ Plot the data from the data files """ import os import re from optparse import OptionParser from SMART.Java.Python.misc.RPlotter import * from SMART.Java.Python.misc.Progress import * def mergeData(line1, line2): if line1.keys() != line2.keys(): sys.exit("Error! Input files do not correspond to each other! Aborting...") mergedData = {} for key in line1: mergedData[key] = (line1[key], line2[key]) return mergedData if __name__ == "__main__": # parse command line description = "Plot CSV v1.0.1: Plot the content of a CSV file. [Category: Personnal]" parser = OptionParser(description = description) parser.add_option("-i", "--input", dest="inputFileNames", action="store", type="string", help="input file [compulsory] [format: file in CSV format]") parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in PNG format]") parser.add_option("-s", "--shape", dest="shape", action="store", type="string", help="shape of the plot [format: choice (line, bar, points, heatPoints)]") 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: ]") parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") (options, args) = parser.parse_args() plotter = RPlotter(options.outputFileName, options.verbosity) if options.shape == "bar": plotter.setBarplot(True) elif options.shape == "points": plotter.setPoints(True) elif options.shape == "heatPoints": plotter.setHeatPoints(True) plotter.setLog(options.log) lines = [] nbsColumns = [] for inputFileName in options.inputFileNames.split(","): inputFile = open(inputFileName) line = {} nbColumns = None for point in inputFile: point = point.strip() m = re.search(r"^\s*(\S+)\s+(\d+\.?\d*)\s+(\d+\.?\d*)\s*$", point) if m != None: line[m.group(1)] = (float(m.group(2)), float(m.group(3))) if nbColumns == None: nbColumns = 3 nbsColumns.append(nbColumns) elif nbColumns != 3: sys.exit("Number of columns changed around line '%s' of file '%s'! Aborting..." % (point, inputFileName)) else: m = re.search(r"^\s*(\d+\.?\d*)\s+(\d+\.?\d*)\s*$", point) if m != None: line[float(m.group(1))] = float(m.group(2)) if nbColumns == None: nbColumns = 2 nbsColumns.append(nbColumns) if nbColumns != 2: sys.exit("Number of columns changed around line '%s' of file '%s'! Aborting..." % (point, inputFileName)) else: m = re.search(r"^\s*(\S+)\s+(\d+\.?\d*)\s*$", point) if m != None: line[m.group(1)] = float(m.group(2)) if nbColumns == None: nbColumns = 1 nbsColumns.append(nbColumns) if nbColumns != 1: sys.exit("Number of columns changed around line '%s' of file '%s'! Aborting..." % (point, inputFileName)) else: sys.exit("Do not understand line '%s' of file '%s'! Aborting..." % (point, inputFileName)) lines.append(line) if len(lines) != len(nbsColumns): sys.exit("Something is wrong in the input files! Aborting...") if options.shape == "bar": if len(lines) != 1: sys.exit("Error! Bar plot should have exactly one input file! Aborting...") if nbsColumns[0] != 2: sys.exit("Error! Bar plot input file should have exactly two columns! Aborting...") plotter.addLine(lines[0]) elif options.shape == "points": if len(lines) != 2: sys.exit("Error! Points cloud should have exactly two input file! Aborting...") if nbsColumns[0] != 2 or nbsColumns[1] != 2: sys.exit("Error! Points cloud plot input file should have exactly two columns! Aborting...") plotter.addLine(mergedData(lines[0], lines[1])) elif options.shape == "heatPoints": if len(lines) != 3: sys.exit("Error! Heat points cloud should have exactly three input file! Aborting...") plotter.addLine(mergeData(lines[0], lines[1])) plotter.addHeatLine(lines[2]) elif options.shape == "line": for i in range(0, len(lines)): if (nbsColumns[i] != 2): sys.exit("Error! Curve plot input file should have exactly two columns! Aborting...") plotter.addLine(lines[i]) else: sys.exit("Do not understand shape '%s'" % (options.shape)) plotter.plot()