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

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/plotCsv.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,146 @@
+#! /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()
+