fix #969 (#970)

* fix #969

* PEP8

* updated changes.txt

* fixed a little bug in parseCommon.py which caused flake8 failure.

* [WIP] added auto to plotheatmap #908 (#982)

* added auto to plotheatmap

* fixed lint, added warning message, updated the help for zmin, zmax

* galaxy test plotPCA

* lower down the delat for potPCA galaxy test

Co-authored-by: Leily Rabbani <rabbani@pc390.ie-freiburg.mpg.de>

* updated version and changes

* removed alpha from plotPCA test

* removed compare="sim_size"

Co-authored-by: Devon Ryan <devon.ryan@genedata.com>
Co-authored-by: Leily Rabbani <rabbani@pc390.ie-freiburg.mpg.de>
Co-authored-by: LeilyR <leila.rabbani@gmail.com>

CHANGES.txt

@@ -1,3 +1,12 @@
+3.5.0
+
+ * Fixed a small issue in computeGCBias (issue #969)
+ * Added dataRange to computeMatricOperation to return min,max,median and 10th and 90th percentile.
+ * Fixed a small typo in bamCompare. (issue #966)
+ * Save the output matrix of the plotheatmap in a format to be compatible with running plotheatmap on it again.(issue #953)
+ * Different colors can now be set by user for plotProfile --plotType heatmap (issue #956)
+ * `auto` option now has been added to the zMin and zMax of plotHeatmap. (issue #908)
+
 3.4.3
 
  * Changed iteritems() in estimateEscaleFactor to its python3 compatible items().

deeptools/_version.py

@@ -2,4 +2,4 @@
 # This file is originally generated from Git information by running 'setup.py
 # version'. Distribution tarballs contain a pre-generated copy of this file.
 
-__version__ = '3.4.3'
+__version__ = '3.5.0'

deeptools/computeGCBias.py

@@ -604,7 +604,7 @@ def plotGCbias(file_name, frequencies, reads_per_gc, region_size, image_format=N
     plt.setp(bp['whiskers'], color='black', linestyle='dashed')
     plt.setp(bp['fliers'], marker='None')
     # get the whisker that spands the most
-    y_max = max([x.get_data()[1][1] for x in bp['whiskers']])
+    y_max = np.nanmax([x.get_data()[1][1] for x in bp['whiskers']])
     ax1.set_ylim(0 - (y_max * 0.05), y_max * 1.05)
     ax1.set_ylabel('Number of reads')
     ax1.set_xlabel('GC fraction')

deeptools/parserCommon.py

@@ -361,8 +361,7 @@ def numberOfProcessors(string):
             raise argparse.ArgumentTypeError("the given value {} is not valid. "
                                              "Error message: {}\nThe number of "
                                              "available processors in your "
-                                             "computer is {}.".format(string, e,
-                                                                      availProc))
+                                             "computer is {}.".format(string, e, availProc))
 
         if numberOfProcessors > availProc:
             numberOfProcessors = availProc

galaxy/wrapper/deepTools_macros.xml

@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.4.3.0</token>
+    <token name="@WRAPPER_VERSION@">3.5.0.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.4.3">deeptools</requirement>
+            <requirement type="package" version="3.5.0">deeptools</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
         <expand macro="stdio" />

galaxy/wrapper/plotPCA.xml

@@ -78,7 +78,7 @@
             <param name="outFileFormat" value="png" />
             <param name="outFileNameData" value="True" />
             <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="12000" />
-            <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" compare="sim_size" delta="12000" />
+            <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" />
         </test>
     </tests>
     <help>