error while running command from testRun.sh

[alishka1988]

Hello,

I'm having some issues running the arc plotting command. I've tried it with my own files, then tried it with the files in the HiCPlotter/data folder and I get the same error in both cases.

Here's the command from testRun.sh that fails:

python HiCPlotter.py -f data/HiC/Mouse/mES.chr3 -n mES -chr chr3 -o Bhlhe22 -r 40000 -s 400 -e 475 -a data/HiC/Mouse/mESC_SMC_ChIPPet.bed -al SMC -hist data/HiC/Mouse/GSM747534_chr3.bedGraph,data/HiC/Mouse/wgEncodeLicrHistoneEsb4H3k27me3ME0C57bl6StdSig.chr3.bedGraph -hl CTCF,H3K27me3 -pi 0 -ptr 0 -t data/HiC/Mouse/mm9_Polycomb_domains.bed -tl Polycomb -tc 00CCFF -ac B4B4B4 -fh 0

This is the error I'm getting:
File "HiCPlotter.py", line 2045, in
HiCplotter(**args)
File "HiCPlotter.py", line 1203, in HiCplotter
pts = get_ellipse_coords(a=rad, b=1.0, x=center, k=1./8)
File "HiCPlotter.py", line 413, in get_ellipse_coords
pts = np.zeros((360*k+1, 2))
TypeError: 'float' object cannot be interpreted as an index

Can you please look into it?

Thanks,

Alina

[akdemirlab]

Hi,

Thanks for using HiCPlotter! Do you mind checking what is the version of your python/matplotlib?
(http://stackoverflow.com/questions/1093322/how-do-i-check-what-version-of-python-is-running-my-script)

The same command is working well on my computer.

Kadir

[alishka1988]

I'm running Python 2.7.11 and matplotlib 2.0.0. I just realized that in the manual it says matplotlib 1.31 and 1.4.3 have been tested successfully. Perhaps, my version of matplotlib is too new.

[akdemirlab]

can you try changing line 413 with below and try again:

pts = np.zeros((int(360*k+1), 2))

[alishka1988]

Looks like the fix worked! Thank you.

Alina