fix bug

zhangrengang · Sep 18, 2023 · 959d119 · 959d119
1 parent 126e241
commit 959d119
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Showing 2 changed files with 10 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -2,7 +2,13 @@
 ```
 git clone https://github.com/zhangrengang/orthoindex.git
 cd orthoindex
+
+# install
+conda env create -f orthoindex.yaml
+conda activate orthoindex
 python3 setup.py install
+
+# test
 cd example_data/
 sh example.sh
 
@@ -292,8 +298,8 @@ ploidy plot:
   --edgecolor COLOR     bar edge color. [default=None]
 ```
 
-Usage examples: see [Quick Start](#Quick-Start)
+Usage examples: see [Quick Start](#Quick-Start).
 
 ### Phylogenomics pipeline ###
 
-Refer to [evolution_example](https://github.com/zhangrengang/evolution_example/) for a pipeline of phylogenomics analyses based on Orthology Index.
+See [evolution_example](https://github.com/zhangrengang/evolution_example/) for a pipeline of phylogenomics analyses based on Orthology Index.
diff --git a/soi/mcscan.py b/soi/mcscan.py
@@ -217,7 +217,8 @@ def _parse(self):
 					if self.homo_class is not None:
 						rc.intersect = intersect
 						rc.substract = pairs - ortholog_pairs
-				rc.ton = len(ortholog_pairs)	# all syntenic orthologs
+				if self.orthologs is not None:
+					rc.ton = len(ortholog_pairs)	# all syntenic orthologs
 				yield rc
 class XOrthology:
 	def __init__(self, orthologs, **kargs):