ROSE_geneMapper.py

[Tingfen Yan]

when I run ROSE_geneMapper.py using HG18_MM1S_MED1_SuperEnhancers.table.txt or HG18_MM1S_MED1_AllEnhancers.table.txt, from the output of ROSE_main.py. I got the following error message: MAKING TSS COLLECTION Traceback (most recent call last): File "ROSE_geneMapper.py", line 322, in <module> main() File "ROSE_geneMapper.py", line 299, in main enhancerToGeneTable,geneToEnhancerTable = mapEnhancerToGene(annotFile,enhancerFile,transcribedFile,True,window,noFormatTable) File "ROSE_geneMapper.py", line 171, in mapEnhancerToGene superDict[refID].append(int(line[-1])) ValueError: invalid literal for int() with base 10: ''

It will be really appreciated if you could help me out here.

Best regards, Tingfen Yan

[chazlin]

Hi Tingfen,

Sorry for the bug. In order to help you, could you please provide the exact command that you used to call ROSE_geneMapper.py.

Could you also provide the HG18_MM1S_MED1_AllEnhancers.table.txt output that you are getting from ROSE_main.py?

You can email these to [e-mail].

Thanks!

[Tingfen Yan]

I found out that is because I used python 2.6. after I used python 2.7.3, then I did not have the problem. however, I have to use sudo, otherwise I got message: IOError: [Errno 13] Permission denied. my command is: sudo python ROSE_geneMapper.py -g HG18 -i HG18_MM1S_MED1_SuperEnhancers.table.txt -o result