From 3ee204a1c7aa5d4203cf7826d5c2b7675f0e7852 Mon Sep 17 00:00:00 2001
From: Leiting Li <lileiting@gmail.com>
Date: Wed, 8 Nov 2017 16:51:10 +0800
Subject: [PATCH 1/2] Update run.py

---
 sharepathway/run.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sharepathway/run.py b/sharepathway/run.py
index e5ccae7..bd34979 100644
--- a/sharepathway/run.py
+++ b/sharepathway/run.py
@@ -54,6 +54,6 @@ def Run(*args, **kwargs):
     # parse KEGG into matrix
     [Pathways, pathwaycount, pathwayMat] = linkpath2mat(Genes, data)
     enrich = enrichment(GenesMat, pathwayMat)
-    result = out2html(GenesMat, pathwayMat,enrich,Genes,Pathways,genelists,pathwaycount,ratio,fileout, pwid2name)
+    result = out2html(GenesMat, pathwayMat,enrich,Genes,Pathways,genelists,pathwaycount,ratio,fileout, pwid2name, species)
     return(result)
 

From aef75b028791e60a95cec81f3c0c5d422670bad8 Mon Sep 17 00:00:00 2001
From: Leiting Li <lileiting@gmail.com>
Date: Wed, 8 Nov 2017 16:51:55 +0800
Subject: [PATCH 2/2] Update out2html.py

---
 sharepathway/out2html.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sharepathway/out2html.py b/sharepathway/out2html.py
index 69c2f77..b2ad87a 100644
--- a/sharepathway/out2html.py
+++ b/sharepathway/out2html.py
@@ -22,6 +22,7 @@ def out2html(*args, **kwargs):
     rr = kwargs.get('ratio',args[7])
     outfilename = kwargs.get('output', args[8])
     pwid2name = dict(kwargs.get('pwid2name', args[9]))
+    species = kwargs.get('species', args[10])
     snum = GenesMat.shape[1]
     pnum = pathwayMat.shape[1]
     gnum = GenesMat.shape[0]
@@ -102,7 +103,7 @@ def out2html(*args, **kwargs):
 </ul>
 </h2>
 </div>
-""" %('hsa',pnum,snum,str(genelistscount),gnum, localtime))
+""" %(species,pnum,snum,str(genelistscount),gnum, localtime))
 
 
     outfile.write("""