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Change '=' to '==' in wrapGSEA() #3

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Change '=' to '==' in wrapGSEA() #3

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Change '=' to '==' in wrapGSEA()
konbarsukov Dec 17, 2018
c0c1bb2
Add to geneMapper _AllEnhancers.table.txt
konbarsukov Dec 27, 2018
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7 changes: 4 additions & 3 deletions ROSE2_META.py
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Original file line number Diff line number Diff line change
Expand Up @@ -748,9 +748,10 @@ def main():
cmd = "python %sROSE2_geneMapper.py -g %s -i %s%s -f" % (pipeline_dir,genome, outFolder, superStretchTableFile)
os.system(cmd)




allEnhancersTableFile = "%s_AllEnhancers.table.txt" % (inputName)
cmd = "python %sROSE2_geneMapper.py -g %s -i %s%s -f" % (pipeline_dir, genome, outFolder, allEnhancersTableFile)
print(cmd)
os.system(cmd)

if __name__ == "__main__":
main()
4 changes: 2 additions & 2 deletions pipeline_dfci.py
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Expand Up @@ -5585,10 +5585,10 @@ def wrapGSEA(gctPath,clsPath,sample_1,sample_2,analysis_name,output_folder,metri

IF YOU GET A STRANGE ERROR, MAKE SURE THE GENES IN YOUR GCT FILE ARE CAPITALIZED.
'''
if gmxPath='':
if gmxPath=='':
#default curated gene set
gmxPath='/storage/cylin/grail/annotations/gsea/c2.all.v5.1.symbols.gmt'
if gseaPath='':
if gseaPath=='':
#default gsea version
gseaPath = '/storage/cylin/home/cl6/gsea2-3.0_beta_2.jar'

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