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): -""" %('hsa',pnum,snum,str(genelistscount),gnum, localtime)) +""" %(species,pnum,snum,str(genelistscount),gnum, localtime)) outfile.write(""" 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)