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3DGenomes / TADbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
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TADbit model #394

Open yangqihang1230 opened 2 months ago

yangqihang1230 commented 2 months ago

"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 commented 2 months ago

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

yangqihang1230 commented 2 months ago

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 commented 1 month ago

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