mbensouda
commented
1 month ago same here:
Generate trans-regulatory netowrk ...
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Traceback (most recent call last):
File "/weka/mbensouda/autumn-hack-cracking-grn-partial-reprogramming/linger/tutorial_PBMCs_GRN_linger_corrected.py", line 114, in
LL_net.trans_reg(GRNdir,method,outdir)TypeError Traceback (most recent call last) Cell In[42], line 4 1 # trans-regulatory network 2 # The output is 'cell_population_trans_regulatory.txt', a matrix of the trans-regulatory score. ----> 4 LL_net.trans_reg(GRNdir,method,outdir)
TypeError: trans_reg() missing 1 required positional argument: 'genome'
LL_net.trans_reg(GRNdir,method,genome,outdir)Generate trans-regulatory netowrk ... 0%| | 0/23 [00:00<?, ?it/s]
FileNotFoundError Traceback (most recent call last) Cell In[43], line 1 ----> 1 LL_net.trans_reg(GRNdir,method,genome,outdir)
File ~/miniconda3/envs/LINGER/lib/python3.10/site-packages/LingerGRN/LL_net.py:1093, in trans_reg(GRNdir, method, outdir, genome) 1091 for i in tqdm(range(23)): 1092 chrN=chrom[i] -> 1093 temp=trans_shap(chrN,outdir) 1094 S=pd.concat([S,temp],axis=0,join='outer') 1095 elif method=='scNN':
File ~/miniconda3/envs/LINGER/lib/python3.10/site-packages/LingerGRN/LL_net.py:646, in trans_shap(chr, outdir) 644 TF_1=[] 645 score_1=[] --> 646 data_merge_temp,geneName,REindex,TFindex,shap_all,TFName,REName=load_shap(chr,outdir) 647 from tqdm import tqdm 648 for j in tqdm(range(data_merge_temp.shape[0])):
File ~/miniconda3/envs/LINGER/lib/python3.10/site-packages/LingerGRN/LL_net.py:582, in load_shap(chr, outdir) 580 import csv 581 #print('loading shapley value '+chr+' ...') --> 582 shapall=torch.load(outdir+"shap"+chr+".pt") 583 import pandas as pd 584 idx_file=outdir+'index.txt'
File ~/miniconda3/envs/LINGER/lib/python3.10/site-packages/torch/serialization.py:986, in load(f, map_location, pickle_module, weights_only, mmap, **pickle_load_args) 983 if 'encoding' not in pickle_load_args.keys(): 984 pickle_load_args['encoding'] = 'utf-8' --> 986 with _open_file_like(f, 'rb') as opened_file: 987 if _is_zipfile(opened_file): 988 # The zipfile reader is going to advance the current file position. 989 # If we want to actually tail call to torch.jit.load, we need to 990 # reset back to the original position. 991 orig_position = opened_file.tell()
File ~/miniconda3/envs/LINGER/lib/python3.10/site-packages/torch/serialization.py:435, in _open_file_like(name_or_buffer, mode) 433 def _open_file_like(name_or_buffer, mode): 434 if _is_path(name_or_buffer): --> 435 return _open_file(name_or_buffer, mode) 436 else: 437 if 'w' in mode:
File ~/miniconda3/envs/LINGER/lib/python3.10/site-packages/torch/serialization.py:416, in _open_file.init(self, name, mode) 415 def init(self, name, mode): --> 416 super().init(open(name, mode))
FileNotFoundError: [Errno 2] No such file or directory: 'hg38shap_chr1.pt'