Update manual

davidemms · Jun 14, 2017 · 0a83f97 · 0a83f97
1 parent 0628290
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Showing 6 changed files with 6 additions and 6 deletions.
diff --git a/OrthoFinder-manual.pdf b/OrthoFinder-manual.pdf
diff --git a/OrthoFinder-options.pdf b/OrthoFinder-options.pdf
diff --git a/Tests/test_orthofinder.py b/Tests/test_orthofinder.py
@@ -35,7 +35,7 @@
 goldResultsDir_smallExample = baseDir + "ExpectedOutput/SmallExampleDataset/"
 goldPrepareBlastDir = baseDir + "ExpectedOutput/SmallExampleDataset_PreparedForBlast/"
 
-version = "1.1.7"
+version = "1.1.8"
 requiredBlastVersion = "2.2.28+"
 
 citation = """When publishing work that uses OrthoFinder please cite:
@@ -109,7 +109,7 @@
 
 -T tree_program, --alignment tree_program
     Use tree_program for tree inference from multiple sequence alignments (requires '-M msa' option). [Default in fasttree]
-    Options: fasttree, iqtree, raxmlAVX.
+    Options: fasttree, iqtree, raxml.
 
 -I inflation_parameter, --inflation inflation_parameter
     Specify a non-default inflation parameter for MCL. Not recommended. [Default is 1.5]
@@ -745,7 +745,7 @@ def test_msa_tree_methods(self):
         self.assertTrue("mafft" in self.stdout)
         self.assertTrue("muscle" in self.stdout)
         self.assertTrue("fasttree" in self.stdout)
-        self.assertTrue("raxmlAVX" in self.stdout)
+        self.assertTrue("raxml" in self.stdout)
         self.assertTrue("iqtree" in self.stdout)
 
 

diff --git a/orthofinder/config.json b/orthofinder/config.json
@@ -12,7 +12,7 @@
     "cmd_line": "muscle -in INPUT -out OUTPUT"
     },
 
-    "raxmlAVX":{ 
+    "raxml":{ 
     "program_type": "tree",
     "cmd_line": "raxmlHPC-AVX -m PROTGAMMALG -p 12345 -s INPUT -n IDENTIFIER",
     "ouput_filename": "PATH/RAxML_bestTree_IDENTIFIER"

diff --git a/orthofinder/scripts/orthologues_from_recon_trees.py b/orthofinder/scripts/orthologues_from_recon_trees.py
@@ -55,7 +55,7 @@ def make_dicts(dlcparResultsDir, outputDir):
             for line in rec:
                 reconlist.append(line.split())
         speclist = [x[0] for x in reconlist if 'spec' == x[2]]
-        speclist = [t&n for n in speclist]
+        speclist = [t&n if n in t else t for n in speclist]
         for node in speclist:
             c1, c2 = node.get_children()
             for leaf1 in c1.get_leaf_names():

diff --git a/orthofinder/scripts/util.py b/orthofinder/scripts/util.py
@@ -47,7 +47,7 @@
 FileInfo = namedtuple("FileInfo", "workingDir graphFilename")     
 
 picProtocol = 1
-version = "1.1.7"
+version = "1.1.8"
 
 # Fix LD_LIBRARY_PATH when using pyinstaller 
 my_env = os.environ.copy()