Updating from ETE2 to ETE3

checkForDependencies.sh

@@ -55,16 +55,16 @@ python -c 'import Bio'
 if [ $? -ne 0 ]; then
     echo ""
     echo "ERROR: Unable to find required package Biopython (Bio). This package is needed for many IO and graphics operations in ITEP"
-    echo "It can be downloaded from http://biopython.org or installed (via setuptools) with sudo easy_install -f http://biopython.org/DIST/ biopython"
+    echo "It can be downloaded from http://biopython.org or installed (via setuptools) with sudo pip install biopython"
     echo ""
     $STATUS=1;
 fi
 
-python -c 'import ete2'
+python -c 'import ete3'
 if [ $? -ne 0 ]; then
     echo ""
-    echo "ERROR: Unable to find required package ETE (ete2). This package is needed for any tree manipulation in ITEP"
-    echo "It can be downloaded at http://ete.cgenomics.org/ or installed (via setuptools) with sudo easy_install -U ete2"
+    echo "ERROR: Unable to find required package ETE (ete3). This package is needed for any tree manipulation in ITEP"
+    echo "It can be downloaded at http://etetoolkit.org/ or installed (via setuptools) with sudo pip install ete3"
     echo ""
     $STATUS=1;
 fi
@@ -73,7 +73,7 @@ python -c 'import ruffus'
 if [ $? -ne 0 ]; then
     echo ""
     echo "ERROR: Unable to find required package ruffus (ruffus). This package is needed for parallelizing BLAST and RPSBlast calls"
-    echo "It can be downlaoded at http://www.ruffus.org.uk/ or installed (via setuptools) with sudo easy_install -U ruffus"
+    echo "It can be downlaoded at http://www.ruffus.org.uk/ or installed (via setuptools) with sudo pip install ruffus"
     echo ""
     $STATUS=1;
 fi

lib/CoreGeneFunctions.py

@@ -13,7 +13,7 @@
 # import errors (e.g. if you're missing mysql interfaces for phylomedb)
 tmp = sys.stdout
 sys.stdout = sys.stderr
-from ete2 import TextFace
+from ete3.treeview import TextFace
 sys.stdout = tmp
 
 def addCoreDataToTree(ete_tree, runid, sanitized = False, any_org = False, all_org = False, only_org = False, none_org = False, uniq_org = False, color = "Black", compare_to_adj_clade = False):
@@ -23,7 +23,7 @@ def addCoreDataToTree(ete_tree, runid, sanitized = False, any_org = False, all_o
     Optionally (with compare_to_adj_clade) instead of comparing to the organisms in the whole tree,
     we compare to only the organisms in the sister clade at each node.
 
-    See http://packages.python.org/ete2/reference/reference_treeview.html#color-names for a list
+    See http://etetoolkit.org/docs/latest/reference/reference_treeview.html#color-names for a list
     of valid color names.'''
 
     cl = getClusterOrgsByRun(runid)

lib/TreeFuncs.py

@@ -4,7 +4,8 @@
 (common operations used by our scripts)'''
 
 from __future__ import print_function
-from ete2 import Tree, faces, TreeStyle, NodeStyle, AttrFace, TextFace
+from ete3 import Tree 
+from ete3.treeview import faces, TreeStyle, NodeStyle, AttrFace, TextFace
 from sanitizeString import *
 import re
 import sys

lib/sanitizeString.py

@@ -44,7 +44,7 @@ def sanitizeByType(container, sanitizeby='tsv', onlycolumns=False):
                 newline=[sanitizeString(item.strip("\r\n"), False) for item in line.split("\t")]
             print("\t".join(newline))
     if sanitizeby=='newick':
-        from ete2 import Tree
+        from ete3 import Tree
         t=Tree("".join(container))
         for l in t:
             l.name=sanitizeString(l.name, False)

src/db_displayTree.py

@@ -82,7 +82,9 @@
 # Import lots of stuff for drawing...
 ####################################
 
-from ete2 import Tree, faces, TreeStyle, NodeStyle, AttrFace, ClusterTree, ProfileFace
+from ete3 import Tree
+from ete3.treeview import faces, TreeStyle, NodeStyle, AttrFace, ProfileFace
+from ete3.clustering import ClusterTree
 import fileinput
 import sqlite3
 from TreeFuncs import *
@@ -150,7 +152,7 @@
     # I could generate this in situ... for now I just have a file I like and run with it.
     # This doesn't match exactlty becuase I don't have the time or motivation now to mess with QT to do it.
     # It should be pretty close though...
-    from ete2 import ImgFace
+    from ete3 import ImgFace
     imgloc = os.path.join(locateRootDirectory(), "src", "internal", "Colormap.png")
     F1 = faces.TextFace("Minimum: %1.1f" %(matrix_min), ftype="Times", fsize=32 )
     F2 = faces.ImgFace(imgloc)

src/db_getPresenceAbsenceTable.py

@@ -32,7 +32,8 @@
 (options,args) = parser.parse_args()
 
 def treeorder(treefile):
-    from ete2 import Tree, faces, TreeStyle, NodeStyle, AttrFace
+    from ete3 import Tree
+    from ete3.treeview import faces, TreeStyle, NodeStyle, AttrFace
     t = Tree(treefile)
     rt = t.get_tree_root()
     nameorder = []

src/db_makeClusterComparisonTable.py

@@ -66,7 +66,7 @@
         geneids += list(clusterrun_to_genes[clusterrun])
     geneids = set(geneids)
 elif options.newick:
-    from ete2 import Tree
+    from ete3 import Tree
     from TreeFuncs import *
     newick_str = "".join( [ line.strip("\r\n") for line in fileinput.input("-") ] )
     t = Tree(newick_str)

src/db_makeNeighborhoodTree.py

@@ -50,8 +50,9 @@
 from sanitizeString import *
 
 import numpy
-from ete2 import Tree, faces, TreeStyle, TextFace, PhyloTree
-from ete2 import Phyloxml, phyloxml
+from ete3 import Tree, PhyloTree
+from ete3.treeview import faces, TreeStyle, TextFace
+from ete3 import Phyloxml, phyloxml
 
 
 def regionlength(genelocs):
@@ -131,7 +132,7 @@ def draw_tree_regions(clusterrunid, t, ts, cur, greyout=3, tempdir=None, label=F
         sys.stderr.write("Making region drawing for gene ID %s...\n" %(newname))
         imgfileloc = make_region_drawing(genelocs, getcolor, newname, maxwidth, tempdir=tempdir, label=label)
         imageFace = faces.ImgFace(imgfileloc)
-        leaf.add_face(imageFace, column=2, position = 'aligned')
+        leaf.add_face(imageFace, column=1, position = 'aligned')
 
     #add legend for clusters
     ts = treelegend(ts, getcolor, greyout, clusterrunid, cur)
@@ -171,7 +172,7 @@ def treelegend(ts, getcolor, greyout, clusterrunid, cur):
         #drop grey ones
         if color == '#7f7f7f': 
             #offset the greys
-            col = (gnum%greycols) + colorcols + 1 + 1 #offset from colors and grey def
+            col = (gnum%greycols) + colorcols + 1 #offset from colors and grey def
             gnum += 1
             # For gray boxes we don't care what the function is.
             text = treelegendtext(cluster, color)
@@ -182,7 +183,7 @@ def treelegend(ts, getcolor, greyout, clusterrunid, cur):
             text = treelegendtext(str(cluster) + ": " + samplefunc[0:63], color)
         #placement of this legend
         ts.legend.add_face(text, column=col)
-    ts.legend.add_face(treelegendtext("> %s occurrences        < or = %s occurrences " % (greyout, greyout),'#FFFFFF'), column=colorcols + 1)
+    ts.legend.add_face(treelegendtext("> %s occurrences        < or = %s occurrences " % (greyout, greyout),'#FFFFFF'), column=colorcols)
     return ts
 
 if __name__ == "__main__":

src/getTreeLeafNames.py

@@ -5,7 +5,7 @@
 import optparse
 import sys
 
-from ete2 import Tree
+from ete3 import Tree
 from TreeFuncs import *
 
 usage = "%prog < tree.nwk > list_of_leaf_names"

src/makeCoreClusterAnalysisTree.py

@@ -7,7 +7,7 @@
 import sys
 import csv
 
-from ete2 import Tree, TextFace, CircleFace
+from ete3 import Tree, TextFace, CircleFace
 
 from CoreGeneFunctions import *
 from ClusterFuncs import *

src/rerootTree.py

@@ -5,7 +5,7 @@
 import optparse
 import sys
 
-from ete2 import Tree
+from ete3 import Tree
 
 from TreeFuncs import *
 

test/TestCore.t

@@ -5,7 +5,7 @@
 import unittest
 from CoreGeneFunctions import *
 from TreeFuncs import *
-from ete2 import Tree
+from ete3 import Tree
 
 class CoreTester(unittest.TestCase):
     def setUp(self):

test/TestTree.t

@@ -4,7 +4,7 @@
 '''Test suite for tree functions'''
 import unittest
 from TreeFuncs import *
-from ete2 import Tree, PhyloTree
+from ete3 import Tree, PhyloTree
 
 class RerootTreeTester(unittest.TestCase):
     def setUp(self):