seqcode/miniMDS

example is not run

Closed this issue · 10 comments

zhixuqiu commented

bash fig10.sh
usage: normalize.py [-h] [--chrom2 CHROM2] hic_id res chrom1 norm
normalize.py: error: the following arguments are required: norm

zhixuqiu commented

I added this arguments in your python script normalize.py. it was also not run.

File "/home/qiuzx/software/installed_dir/miniconda2/envs/py36/lib/python3.6/site-packages/numpy/lib/npyio.py", line 860, in loadtxt
    fh = iter(open(fname))
FileNotFoundError: [Errno 2] No such file or directory: 'GM12878_combined/10.0kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_10.0kb.KRnorm'
Lila14 commented

Sorry, I've fixed the scripts now. Many still had old parameters. Let me know if there are further issues.

zhixuqiu commented

Sorry, I've fixed the scripts now. Many still had old parameters. Let me know if there are further issues.

OK, thanks. But I tried again. The script fig10.sh was also not implemented.

FileNotFoundError: [Errno 2] No such file or directory: GM12878_combined/10.0kb_resolution_intrachromosomal/chr1/MAPQGE30/chr1_10.0kb.KRnorm

This error also existed in script "minimds_inter.py" . The error was from the function "get_res_string" in script "tools.py". I have change it.

res_kb = round(res/1000) if res_kb < 1000: return str(res_kb) + "kb" else: return str(round(res_kb/1000)) + "mb"

But a new bug occured. I don't know how to correct it.

File "../normalize.py", line 26, in normalize norm1 = kr1[int(loc1)/res] IndexError: only integers, slices (:), ellipsis (...), numpy.newaxis (None) and integer or boolean arrays are valid indices

Lila14 commented

It looks the res variable in normalize.py is a float in your example. I'm not sure why this would happen, because the res argument is read as an int. Can you make sure you have the current version of normalize.py?

zhixuqiu commented

It looks the res variable in normalize.py is a float in your example. I'm not sure why this would happen, because the res argument is read as an int. Can you make sure you have the current version of normalize.py?

Yes, I used the new normalize.py. To correct res argument, I changed the tools.py.

ahorvath commented

Hi @Lila14,

I'd like to infer interchromosomal interactions. When running sh fig10.sh I got this error:

python ../minimds_inter.py --partitioned -l 100000 -p 0.01 -m 0.01 -o hic_data/GM12878_combined hic_data/GM12878_combined_interchromosomal hic_data/GM12878_combined 1000000 10000

usage: minimds_inter.py [-h] [--partitioned] [-c C] [-C C] [-l L] [-p P]
[-m M] [-o O] [-r R] [-n N] [-a A] [-a2 A2]
prefix inter_res intra_res
....
minimds_inter.py: error: argument inter_res: invalid int value: 'hic_data/GM12878_combined'
[ahorvath@admin scripts]$ ls hic_data/GM12878_combined

Can you help me, please?

Bests,
Attila

Lila14 commented
ahorvath commented

Can you provide an example, please?

This was from fig10.sh

set -e

bash get_gm12878.sh 10000 0
bash get_gm12878.sh 100000 0
bash get_gm12878.sh 1000000 0
bash get_gm12878_inter.sh 1000000

python ../minimds_inter.py --partitioned -l 100000 -p 0.01 -m 0.01 -o hic_data/GM12878_combined hic_data/GM12878_combined_interchromosomal hic_data/GM12878_combined 1000000 10000
python fig10.py

Thanks in advance.

Lila14 commented

Sorry for the late reply. I've pushed some changes that should fix fig10.sh. I haven't fully tested them, so let me know if there are any issues.

Lila14 commented

fig10.sh seems to be working now. Please make sure you pull the latest code.