%load_ext autoreload
%autoreload 2
import sys
import importlib
import pandas as pd
import time
import os
from IPython.display import Image, display
pd.set_option('mode.chained_assignment', None)
import matplotlib.pyplot as plt
from itables import init_notebook_mode
init_notebook_mode(all_interactive=True)
import warnings
import session_info
# Suppress FutureWarnings
warnings.simplefilter(action='ignore', category=FutureWarning)
import sys
import tqdm
from importlib import reload
print(os.getcwd())
sys.path.append('/path/to/verkko_assembly/assemblies/verkko_v2_3_2_hifi/draft_assembly')
import verkkofillet as vf
vf = reload(vf)
```
```
/users/kmcinga1
verkko-fillet version:0.1.20
verkko-fillet version:0.1.20
```
```
import verkkofillet as vf
importlib.reload(vf) and it yielded: verkko-fillet version:0.1.20
```
It yielded:
`<module 'verkkofillet' from '/users/kmcinga1/.mamba/envs/verkko-fillet/lib/python3.9/site-packages/verkkofillet/__init__.py'>` but now when I try to load the verkko ouput directory using these commands : ```
verkkoDir = 'path/to/verkko_assembly/assemblies/verkko_v2_3_2_hifi/draft_assembly'
obj = vf.pp.read_Verkko(verkkoDir)
print(obj.draft_assembly_verkko_fillet)
os.chdir(obj.draft_assembly_verkko_fillet)
```
```
The Verkko fillet target directory already exists: /path/to/verkko_assembly/assemblies/verkko_v2_3_2_hifi/draft_assembly_verkko_fillet
If you didn't mean this, please set another directory or for overwirting, please use force= True
Lock the original Verkko folder to prevent it from being modified.
[lock_original_folder] Command executed successfully!
change working directory: /path/to/verkko_assembly/assemblies/verkko_v2_3_2_hifi/draft_assembly_verkko_fillet
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[4], line 2
1 verkkoDir = '/path/to/verkko_assembly/assemblies/verkko_v2_3_2_hifi/draft_assembly'
----> 2 obj = vf.pp.read_Verkko(verkkoDir)
3 print(obj.draft_assembly_verkko_fillet)
4 os.chdir(obj.draft_assembly_verkko_fillet)
File [~/.mamba/envs/verkko-fillet/lib/python3.9/site-packages/verkkofillet/preprocessing/_read_wirte.py:229](https://jupyter.ilifu.ac.za/user/kmcinga1/lab/tree/~/.mamba/envs/verkko-fillet/lib/python3.9/site-packages/verkkofillet/preprocessing/_read_wirte.py#line=228), in read_Verkko(verkkoDir, verkko_fillet_dir, paths_path, force, scfmap_path, version, species, graph, color, lock_original_folder, showOnly, longLog)
227 # read Path file
228 if paths_path != None:
--> 229 obj = readPath(obj, paths_path)
231 # read scfmap file
232 if scfmap_path != None:
File [~/.mamba/envs/verkko-fillet/lib/python3.9/site-packages/verkkofillet/preprocessing/_read_wirte.py:121](https://jupyter.ilifu.ac.za/user/kmcinga1/lab/tree/~/.mamba/envs/verkko-fillet/lib/python3.9/site-packages/verkkofillet/preprocessing/_read_wirte.py#line=120), in readPath(obj, paths_path)
118 """
119 """
120 if not os.path.exists(paths_path):
--> 121 raise FileNotFoundError(f"File {paths_path}")
123 obj = copy.deepcopy(obj)
125 # Load paths file if it exist
FileNotFoundError: File assembly.paths.tsv
```
Hi there,
I have recently generated assemblies using the latest version of Verkko 2.3.2. I am attempting to use Verkko-fillet to assess my assemblies but I'm struggling to load the Verkko output directory. The error says it cannot find the assembly.paths.tsv and the verkko-fillet directory has directories that are empty.
I followed the following prompts: