diff cpo_galaxy_tree.py @ 12:4b2738bc81ed draft

planemo upload

--- a/cpo_galaxy_tree.py	Fri Aug 24 16:54:25 2018 -0400
+++ b/cpo_galaxy_tree.py	Fri Aug 24 19:10:42 2018 -0400
@@ -18,6 +18,7 @@
 #		<requirement type="package" version="3.6">python</requirement>
 #       <requirement type="package" version="3.1.1">ete3</requirement>
 #		<requirement type="package" version="5.6.0">pyqt</requirement>
+#		<requirement type="package" version="5.6.2">qt</requirement>
 #  </requirements>
 
 import subprocess
@@ -53,17 +54,17 @@
 class workflowResult(object):
     def __init__(self):
         self.new = False
-        self.ID	= "" 
-        self.ExpectedSpecies = ""
-        self.MLSTSpecies = ""
-        self.SequenceType = ""
-        self.MLSTScheme = ""
-        self.CarbapenemResistanceGenes =""
-        self.OtherAMRGenes=""
-        self.TotalPlasmids = 0
+        self.ID	= "?" 
+        self.ExpectedSpecies = "?"
+        self.MLSTSpecies = "?"
+        self.SequenceType = "?"
+        self.MLSTScheme = "?"
+        self.CarbapenemResistanceGenes ="?"
+        self.OtherAMRGenes="?"
+        self.TotalPlasmids = -1
         self.plasmids = []
-        self.DefinitelyPlasmidContigs =""
-        self.LikelyPlasmidContigs=""
+        self.DefinitelyPlasmidContigs ="?"
+        self.LikelyPlasmidContigs="?"
         self.row = ""
 class plasmidObj(object):
     def __init__(self):
@@ -128,13 +129,15 @@
     _worflowResult = {}
     r = pandas.read_csv(pathToResult, delimiter='\t', header=0) 
     r = r.replace(numpy.nan, '', regex=True)
+    _naResult = workflowResult()
+    _worflowResult["na"] = _naResult
     for i in range(len(r.index)):  
         _results = workflowResult()
         if(str(r.loc[r.index[i], 'new']).lower() == "new"):
             _results.new = True
         else:
             _results.new = False        
-        _results.ID = str(r.loc[r.index[i], 'ID'])
+        _results.ID = str(r.loc[r.index[i], 'ID']).replace(".fa","")
         _results.ExpectedSpecies = str(r.loc[r.index[i], 'Expected Species'])
         _results.MLSTSpecies = str(r.loc[r.index[i], 'MLST Species'])
         _results.SequenceType = str(r.loc[r.index[i], 'Sequence Type'])
@@ -177,7 +180,7 @@
 
     #set the tree style
     ts = e.TreeStyle()
-    ts.show_leaf_name = False
+    ts.show_leaf_name = True
     ts.show_branch_length = True
     ts.scale = 2000 #pixel per branch length unit
     ts.branch_vertical_margin = 15 #pixel between branches
@@ -228,10 +231,13 @@
         elif (n.is_leaf() and not n.name == "Reference"): 
             #not reference branches, populate with metadata
             index = 0
-            mData = metadata[n.name.replace(".fa","")]
+            if (n.name.replace(".fa","") in metadata.keys()):
+                mData = metadata[n.name.replace(".fa","")]
+            else:
+                mData = metadata["na"]
             n.add_face(addFace(mData.ID), index, "aligned")
             index = index + 1
-            if (metadata[n.name.replace(".fa","")].new == True): #new column
+            if (mData.new == True): #new column
                 face = e.RectFace(30,30,"green","green") # TextFace("Y",fsize=10,tight_text=True)
                 face.border.margin = 5
                 face.margin_right = 5
@@ -271,4 +277,4 @@
 Main()
 
 end = time.time()
-print("Finished!\nThe analysis used: " + str(end-start) + " seconds")
+print("Finished!\nThe analysis used: " + str(end-start) + " seconds")
\ No newline at end of file