error in running danpos3_MNase-seq

[sdhur...@gmail.com]

Hi,

I am getting following error while running dnapos3 for my MNase -seq data -

Traceback (most recent call last):
  File "danpos.py", line 1365, in <module>
    if sys.argv[1]=='dpos':runDANPOS(command='dpos')
  File "danpos.py", line 396, in runDANPOS
    danpos(\
  File "/Users/dsaha/DANPOS3/functions.py", line 126, in danpos
    groups[groupname]=loadinput(groups[groupname], fs=fs, cut=cut, save=False,
  File "/Users/dsaha/DANPOS3/functions.py", line 1019, in loadinput
    else:wigs[fname[:-4]+'.wig']=rd.toWig(fs=fs,extend=extend,mifrsz=mifrsz,mafrsz=mafrsz)#,fdrwigs=fdrwigs,fdrflag=fdrflag)
  File "/Users/dsaha/DANPOS3/reads.py", line 848, in toWig
    if fs==None:fs=self.fragSizeDis(minsize=mifrsz,maxsize=mafrsz)
  File "/Users/dsaha/DANPOS3/reads.py", line 114, in fragSizeDis
    while(0-(functions.div(float(str(functions.ppois(cut,avg.item(),lower_tail=False, log_bool = True)).split()[-1]),log(10)))<lgpcut):cut+=1
TypeError: ppois() got an unexpected keyword argument 'lower_tail'

I was using sorted bam file as input file to run dpos.

Kindly suggest!

Best

-Dhurjhoti

[simon holzinger]

Hi Dhurjhoti, 

I fixed this bugs quite some time ago, unfortunately the maintainer of the GitHub repo hasn't accepted the pull request yet. 

In the mean time you could use my fork (https://github.com/SimHolz/DANPOS3/tree/master) where everything should work. 

Let me know if you encounter any issues. 

Best wishes 

Simon