TADbit model

[yangqihang1230]

"I installed TADbit but couldn't export the model function. I can run the test set normally."

optional arguments:
-h, --help show this help message and exit

AVAILABLE PROGRAMS:
{map,parse,filter,describe,clean,normalize,bin,export,import,merge,segment}
map Map Hi-C reads and organize results in an output
working directory
parse Parse mapped Hi-C reads and get the intersection
filter Filter parsed Hi-C reads and get valid pair of reads
to work with
describe Describe jobs and results in a given working directory
clean Delete jobs and results of a given list of jobids in a
given directories
normalize normalize Hi-C data and generates array of biases
bin bin Hi-C data into matrices
export export Hi-C data to other formats
import import Hi-C data to TADbit toy BAM
merge load two working directories with different Hi-C data
samples and merges them into a new working directory
generating some statistics
segment Finds TAD or compartment segmentation in Hi-C data.

[fransua]

Hi,
the most probable cause for this issue is that you have not installed the IMP library: https://github.com/salilab/imp

[yangqihang1230]

Thank you very much for your reply. The model is now displaying correctly, but a new error has occurred. I'm not sure if it's caused by the format of my input file.

(py37) mawei@bioinformatics:/home/Mawei/yqh/3Dgenome/TADbit$ tadbit model --workdir model__test1 --input_matrix 500.abc --noX --optimize --reso 20000 --nmodels 5 --nkeep 5 --exp_type Hi-C --force --matrix_beg 1
o Loading Hi-C matrix
o WARNING: reusing existing folder, please check if you need to remove
Traceback (most recent call last):
File "/home/data2/yqh/conda/envs/py37/bin/tadbit", line 170, in
main(sys.argv)
File "/home/data2/yqh/conda/envs/py37/bin/tadbit", line 167, in main
args.func(args)
File "/home/data2/yqh/conda/envs/py37/lib/python3.7/site-packages/pytadbit/tools/tadbit_model.py", line 738, in run
opts.end - opts.beg))
TypeError: %d format: a number is required, not NoneType

This is the sample format of my input file.

CRM chr1 64444167

chr1:1-10 resolution:20000

MASKED

1 1 93.282519
2 2 73.714816
2 3 36.596588
2 4 33.871353
3 5 21.741614
3 6 17.209513
3 7 16.437257
3 8 15.460301
3 9 11.267053
3 10 15.363264

[fransua]

hi,
sorry for the late reply. Perhaps just add the end coordinate too (which would be, I guess, the size of you matrix).