Merge pull request #30 from DRL/hotfix

hotfix

Author: DRL

bloblib/BtPlot.py

@@ -547,7 +547,7 @@ def plotScatter(self, cov_lib, info_flag, out_f):
                     group_y_array = array(self.stats[group]['covs'][cov_lib])
                 elif self.plot == 'covplot':
                     group_x_array = array(self.stats[group]['covs'][cov_lib])
-                    group_y_array = array([self.cov_y_dict.get(name, 0.02) for name in self.stats[group]['name']])
+                    group_y_array = array([self.cov_y_dict[name] if self.cov_y_dict[name] > 0.02 else 0.02 for name in self.stats[group]['name']])
                 else:
                     BtLog.error('34', self.plot)
                 marker_size_array = []

bloblib/covplot.py

@@ -128,7 +128,10 @@ def main():
     plotObj.exclude_groups = exclude_groups
     plotObj.version = blobDb.version
     plotObj.format = format
-    plotObj.max_cov = axis_max
+    if max_cov <= axis_max:
+        plotObj.max_cov = max_cov
+    else:
+        plotObj.max_cov = axis_max
     plotObj.no_title = no_title
     plotObj.multiplot = multiplot
     plotObj.hist_type = hist_type
@@ -159,7 +162,7 @@ def main():
             plotObj.ylabel = ylabel
         if (xlabel):
             plotObj.xlabel = xlabel
-        out_f = "%s.%s.%s.p%s.%s.%s" % (blobDb.title, taxrule, rank, max_group_plot, hist_type, min_length)
+        out_f = "%s.%s.%s.p%s.%s.%s.%s" % (blobDb.title, taxrule, rank, max_group_plot, hist_type, min_length, cov_f.replace(".","_"))
         if catcolour_dict:
             out_f = "%s.%s" % (out_f, "catcolour")
         if ignore_contig_length:

blobtools

@@ -43,7 +43,7 @@ except ImportError:
     sys.exit("[ERROR]\t: The module docopt is not installed. \n \tPlease run : pip install docopt")
 
 
-__version__ = "blobtools v0.9.19.2"
+__version__ = "blobtools v0.9.19.3"
 MAINDIR = join(dirname(__file__), '')
 DATADIR = join(MAINDIR, 'data/')
 LIBDIR = join(MAINDIR, 'bloblib/')
@@ -71,5 +71,5 @@ if __name__ == '__main__':
     elif args['<command>'] == 'taxify':
         exit(call(['python', LIBDIR + 'taxify.py'] + argv))
     else:
-        exit(call(['./blobtools', '--help']))
+        exit(call(['python', MAINDIR + 'blobtools.py', '--help']))
 

blobtools.py

@@ -43,7 +43,7 @@
     sys.exit("[ERROR]\t: The module docopt is not installed. \n \tPlease run : pip install docopt")
 
 
-__version__ = "blobtools v0.9.19"
+__version__ = "blobtools v0.9.19.3"
 MAINDIR = join(dirname(__file__), '')
 DATADIR = join(MAINDIR, 'data/')
 LIBDIR = join(MAINDIR, 'bloblib/')
@@ -71,5 +71,5 @@
     elif args['<command>'] == 'taxify':
         exit(call(['python', LIBDIR + 'taxify.py'] + argv))
     else:
-        exit(call(['./blobtools', '--help']))
+        exit(call(['python', MAINDIR + 'blobtools.py', '--help']))