--- a/cpo_galaxy_tree.py	Thu Aug 23 18:35:54 2018 -0400
+++ b/cpo_galaxy_tree.py	Thu Aug 23 19:40:12 2018 -0400
@@ -17,13 +17,14 @@
 #		<requirement type="package" version="0.23.4">pandas</requirement>
 #		<requirement type="package" version="3.6">python</requirement>
 #       <requirement type="package" version="3.1.1">ete3</requirement>
-#		<requirement type="package" version="5.9.3">pyqt</requirement>
+#		<requirement type="package" version="5.6.0">pyqt</requirement>
 #  </requirements>
 
 import subprocess
 import pandas #conda pandas
 import optparse
 import os
+os.environ['QT_QPA_PLATFORM']='offscreen' 
 import datetime
 import sys
 import time
@@ -167,73 +168,7 @@
     for i in range(len(distance)):
         temp = distance[i].split("\t")
         distanceDict[temp[0]] = temp[1:]
-    #region step5: tree construction
 
-    '''
-    #region create detailed tree
-    
-    plasmidCount = 0
-    for n in t.traverse():
-        if (n.is_leaf() and not n.name == "Reference"):
-            mData = metadata[n.name.replace(".fa","")]
-            face = faces.TextFace(mData.MLSTSpecies,fsize=10,tight_text=True)
-            face.border.margin = 5
-            face.margin_left = 10
-            face.margin_right = 10
-            n.add_face(face, 0, "aligned")
-            face = faces.TextFace(mData.SequenceType,fsize=10,tight_text=True)
-            face.border.margin = 5
-            face.margin_right = 10
-            n.add_face(face, 1, "aligned")
-            face = faces.TextFace(mData.CarbapenemResistanceGenes,fsize=10,tight_text=True)
-            face.border.margin = 5
-            face.margin_right = 10
-            n.add_face(face, 2, "aligned")
-            index = 3
-            if (mData.TotalPlasmids > plasmidCount):
-                plasmidCount = mData.TotalPlasmids
-            for i in range(0, mData.TotalPlasmids):
-                face = faces.TextFace(mData.plasmids[i].PlasmidRepType,fsize=10,tight_text=True)
-                face.border.margin = 5
-                face.margin_right = 10
-                n.add_face(face, index, "aligned")
-                index+=1
-                face = faces.TextFace(mData.plasmids[i].PlasmidMobility,fsize=10,tight_text=True)
-                face.border.margin = 5
-                face.margin_right = 10
-                n.add_face(face, index, "aligned")
-                index+=1
-
-    face = faces.TextFace("Species",fsize=10,tight_text=True)
-    face.border.margin = 5
-    face.margin_right = 10
-    face.margin_left = 10
-    (t&"Reference").add_face(face, 0, "aligned")
-    face = faces.TextFace("Sequence Type",fsize=10,tight_text=True)
-    face.border.margin = 5
-    face.margin_right = 10
-    (t&"Reference").add_face(face, 1, "aligned")
-    face = faces.TextFace("Carbapenamases",fsize=10,tight_text=True)
-    face.border.margin = 5
-    face.margin_right = 10
-    (t&"Reference").add_face(face, 2, "aligned")
-    index = 3
-    for i in range(0, plasmidCount):
-        face = faces.TextFace("plasmid " + str(i) + " replicons",fsize=10,tight_text=True)
-        face.border.margin = 5
-        face.margin_right = 10
-        (t&"Reference").add_face(face, index, "aligned")
-        index+=1
-        face = faces.TextFace("plasmid " + str(i) + " mobility",fsize=10,tight_text=True)
-        face.border.margin = 5
-        face.margin_right = 10
-        (t&"Reference").add_face(face, index, "aligned")
-        index+=1
-
-    t.render("./pipelineTest/tree.png", w=5000,units="mm", tree_style=ts)
-    
-    #endregion
-    '''
     #region create box tree
     #region step5: tree construction
     treeFile = "".join(read(treePath))
@@ -324,7 +259,7 @@
             for i in range(len(distanceDict[list(distanceDict.keys())[0]])): #this loop adds distance matrix
                 n.add_face(addFace(list(distanceDict[n.name])[i]), index + i, "aligned")
                 
-    t.render("./tree.png", w=5000,units="mm", tree_style=ts) #save it as a png. or an phyloxml
+    t.render("./tree.pdf", w=5000,units="mm", tree_style=ts) #save it as a png. or an phyloxml
 
     #endregion
 #endregion