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Update species name in the html file #2

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Update species name in the html file #2

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3ee204a
Update run.py
lileiting Nov 8, 2017
aef75b0
Update out2html.py
lileiting Nov 8, 2017
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3 changes: 2 additions & 1 deletion sharepathway/out2html.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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]
Expand Down Expand Up @@ -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("""
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2 changes: 1 addition & 1 deletion sharepathway/run.py
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Expand Up @@ -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)