DANPOS profile does not work --> IndexError: list index out of range

[Gatti_E]

dear all,

I am trying to use DANPOS on my MNAse-Seq data. Unofrtunately, I am not familiar with python; despite this, I was able to run danpos.py wiq in order to normalize wig files from two different samples.
I then started to use the other commands of danpos using your example input files.

my command:

danpos-2.2.2/danpos.py profile sampleB.wig --genefile_paths geneGroup1.xls

DANPOS starts to processes the wig file and when it starts to profile for TSS it stops giving the following error:

File "danpos-2.2.2/lib.py", line 250, in occAroundPoints
    chr,name,stra=col[chrColID],col[nameColID],col[straColID]
IndexError: list index out of range

Any idea why is not working?

Thanks in advance
E.

[Kaifu]

It seems likely that the format of your gene file geneGroup1.xls is not correct, see https://sites.google.com/site/danposdoc/home/profile/input-files

[Gatti_E]

I am using the example files provided by DANPOS (sampleB.wig and geneGroup1.xls)
Unfortunately the error message now is

File "danpos-2.2.2/lib.py", line 293, in occAroundPoints
    v=s/(num-num*excludeP*2)#len(vec)
ZeroDivisionError: float division by zero

To me it makes no sense since I am using example input files.

Any other suggestion?

thanks
E.

[Kaifu]

Did you ever edit the gene file? 

I just downloaded the latest version again and run it with the same command line, but didn't get any error message:

python danpos.py profile sampleB.wig  --genefile_paths geneGroup1.xls

[Gatti_E]

Thanks,

now it works.
Now I will try on my MNAse-seq data paying attention on the correct format of the input files.
Thnaks again for the short and efficient feedback

EG