update normalization thershold. update browser list widget

rjdkmr · Mar 20, 2017 · 313ade5 · 313ade5
1 parent 346b68e
commit 313ade5
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Showing 17 changed files with 949 additions and 70 deletions.
diff --git a/docs/apidoc/genomicsDataHandler/hdf5handler.rst b/docs/apidoc/genomicsDataHandler/hdf5handler.rst
@@ -6,6 +6,7 @@
 
 .. autosummary::
 		HDF5Handler
+		HDF5Handler.setTitle
 		HDF5Handler.getChromList
 		HDF5Handler.getResolutionList
 		HDF5Handler.getDataNameList

diff --git a/docs/apidoc/summary.rst b/docs/apidoc/summary.rst
@@ -105,6 +105,7 @@ genomicsDataHandler module
 
 .. autosummary::
 		genomicsDataHandler.HDF5Handler
+		genomicsDataHandler.HDF5Handler.setTitle
 		genomicsDataHandler.HDF5Handler.getChromList
 		genomicsDataHandler.HDF5Handler.getResolutionList
 		genomicsDataHandler.HDF5Handler.getDataNameList

diff --git a/gcMapExplorer/clui/normIC.py b/gcMapExplorer/clui/normIC.py
@@ -77,6 +77,20 @@
 
 """
 
+vminHelp = \
+""" Minimum thershold value for normalization.
+If contact frequency is less than or equal to this thershold value,
+this value is discarded during normalization.
+
+"""
+
+vmaxHelp = \
+""" Maximum thershold value for normalization.
+If contact frequency is greater than or equal to this thershold value,
+this value is discarded during normalization.
+
+"""
+
 tolHelp = \
 """ Tolerance for matrix balancing.
 Smaller tolreance increases accuracy in sums of rows and columns.
@@ -161,13 +175,14 @@ def main():
 
     if args.outputFileFormat == 'ccmap' and args.inputFileFormat == 'ccmap':
         gmlib.normalizer.normalizeCCMapByIC(args.inputFile, tol=args.tol, iteration=args.iteration,
-                                            outFile=args.outputFile,
+                                            outFile=args.outputFile, vmin=args.vmin, vmax=args.vmax,
                                             percentile_thershold_no_data=args.percentile_thershold_no_data,
                                             thershold_data_occup=args.thershold_data_occup,
                                             workDir=args.workDir)
 
     if args.outputFileFormat == 'gcmap' and args.inputFileFormat == 'ccmap':
         norm_ccmap = gmlib.normalizer.normalizeCCMapByIC(args.inputFile, tol=args.tol,  iteration=args.iteration,
+                                            vmin=args.vmin, vmax=args.vmax,
                                             percentile_thershold_no_data=args.percentile_thershold_no_data,
                                             thershold_data_occup=args.thershold_data_occup,
                                             workDir=args.workDir)
@@ -177,6 +192,7 @@ def main():
     if args.outputFileFormat == 'gcmap' and args.inputFileFormat == 'gcmap':
         gmlib.normalizer.normalizeGCMapByIC(args.inputFile, args.outputFile,
                                             tol=args.tol,  iteration=args.iteration,
+                                            vmin=args.vmin, vmax=args.vmax, 
                                             percentile_thershold_no_data=args.percentile_thershold_no_data,
                                             thershold_data_occup=args.thershold_data_occup,
                                             workDir=args.workDir)
@@ -212,6 +228,14 @@ def parseArguments():
                         type = float, default=1e-4,
                         help=tolHelp)
 
+    parser.add_argument('-vmax', '--maximum-value', action='store',
+                        dest='vmax', type=float, metavar=None,
+                        help=vminHelp)
+
+    parser.add_argument('-vmin', '--minimum-value', action='store',
+                        dest='vmin', metavar=None, type=float,
+                        help=vmaxHelp)
+
     parser.add_argument('-c', '--iteration', action='store',
                         dest='iteration', metavar=500,
                         type = int, default=500,

diff --git a/gcMapExplorer/clui/normKR.py b/gcMapExplorer/clui/normKR.py
@@ -87,6 +87,20 @@
 
 """
 
+vminHelp = \
+""" Minimum thershold value for normalization.
+If contact frequency is less than or equal to this thershold value,
+this value is discarded during normalization.
+
+"""
+
+vmaxHelp = \
+""" Maximum thershold value for normalization.
+If contact frequency is greater than or equal to this thershold value,
+this value is discarded during normalization.
+
+"""
+
 mapSizeCeilingForMemoryHelp = \
 """ Maximum size of contact map allowed for calculation using RAM.
 If map size or shape is larger than this value, normalization will be
@@ -177,13 +191,15 @@ def main():
         showErrorAndExit(parser, msg)
 
     if args.outputFileFormat == 'ccmap' and args.inputFileFormat == 'ccmap':
-        gmlib.normalizer.normalizeCCMapByKR(args.inputFile, memory=args.memory, tol=args.tol, outFile=args.outputFile,
+        gmlib.normalizer.normalizeCCMapByKR(args.inputFile, memory=args.memory, tol=args.tol,
+                                            vmin=args.vmin, vmax=args.vmax, outFile=args.outputFile,
                                             percentile_thershold_no_data=args.percentile_thershold_no_data,
                                             thershold_data_occup=args.thershold_data_occup,
                                             workDir=args.workDir)
 
     if args.outputFileFormat == 'gcmap' and args.inputFileFormat == 'ccmap':
         norm_ccmap = gmlib.normalizer.normalizeCCMapByKR(args.inputFile, memory=args.memory, tol=args.tol,
+                                            vmin=args.vmin, vmax=args.vmax,
                                             percentile_thershold_no_data=args.percentile_thershold_no_data,
                                             thershold_data_occup=args.thershold_data_occup,
                                             workDir=args.workDir)
@@ -193,7 +209,7 @@ def main():
     if args.outputFileFormat == 'gcmap' and args.inputFileFormat == 'gcmap':
         gmlib.normalizer.normalizeGCMapByKR(args.inputFile, args.outputFile,
                                             mapSizeCeilingForMemory=args.mapSizeCeilingForMemory,
-                                            tol=args.tol,
+                                            tol=args.tol, vmin=args.vmin, vmax=args.vmax,
                                             percentile_thershold_no_data=args.percentile_thershold_no_data,
                                             thershold_data_occup=args.thershold_data_occup,
                                             workDir=args.workDir)
@@ -234,6 +250,14 @@ def parseArguments():
                         choices=['RAM', 'HDD'], default='RAM',
                         help=memoryHelp)
 
+    parser.add_argument('-vmax', '--maximum-value', action='store',
+                        dest='vmax', type=float, metavar=None,
+                        help=vminHelp)
+
+    parser.add_argument('-vmin', '--minimum-value', action='store',
+                        dest='vmin', metavar=None, type=float,
+                        help=vmaxHelp)
+
     parser.add_argument('-mscm', '--map-size-ceiling-for-memory', action='store',
                         dest='mapSizeCeilingForMemory', metavar='20000',
                         type = int,

diff --git a/gcMapExplorer/clui/normMCFS.py b/gcMapExplorer/clui/normMCFS.py
@@ -79,6 +79,20 @@
 
 """
 
+vminHelp = \
+""" Minimum thershold value for normalization.
+If contact frequency is less than or equal to this thershold value,
+this value is discarded during normalization.
+
+"""
+
+vmaxHelp = \
+""" Maximum thershold value for normalization.
+If contact frequency is greater than or equal to this thershold value,
+this value is discarded during normalization.
+
+"""
+
 percentile_thershold_no_data_help = \
 """ It can be used to filter the map, where rows/columns with largest numbers
 of missing data can be discarded. Its value should be between 1 and 100.
@@ -142,12 +156,14 @@ def main():
 
     if args.outputFileFormat == 'ccmap' and args.inputFileFormat == 'ccmap':
         gmlib.normalizer.normalizeCCMapByMCFS(args.inputFile, stats=args.stats, outFile=args.outputFile,
+                                            vmin=args.vmin, vmax=args.vmax,
                                             percentile_thershold_no_data=args.percentile_thershold_no_data,
                                             thershold_data_occup=args.thershold_data_occup,
                                             workDir=args.workDir)
 
     if args.outputFileFormat == 'gcmap' and args.inputFileFormat == 'ccmap':
         norm_ccmap = gmlib.normalizer.normalizeCCMapByMCFS(args.inputFile, stats=args.stats,
+                                            vmin=args.vmin, vmax=args.vmax,
                                             percentile_thershold_no_data=args.percentile_thershold_no_data,
                                             thershold_data_occup=args.thershold_data_occup,
                                             workDir=args.workDir)
@@ -156,7 +172,7 @@ def main():
 
     if args.outputFileFormat == 'gcmap' and args.inputFileFormat == 'gcmap':
         gmlib.normalizer.normalizeGCMapByMCFS(args.inputFile, args.outputFile,
-                                            stats=args.stats,
+                                            stats=args.stats, vmin=args.vmin, vmax=args.vmax, 
                                             percentile_thershold_no_data=args.percentile_thershold_no_data,
                                             thershold_data_occup=args.thershold_data_occup,
                                             compression=args.compression,
@@ -190,6 +206,13 @@ def parseArguments():
                         dest='stats', metavar='median',
                         choices=['median', 'mean'], default='median',
                         help=statsHelp)
+    parser.add_argument('-vmax', '--maximum-value', action='store',
+                        dest='vmax', type=float, metavar=None,
+                        help=vminHelp)
+
+    parser.add_argument('-vmin', '--minimum-value', action='store',
+                        dest='vmin', metavar=None, type=float,
+                        help=vmaxHelp)
 
     parser.add_argument('-ptnd', '--percentile-thershold-no-data', action='store',
                         dest='percentile_thershold_no_data', metavar=99,