rnaglib issues
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues
2023-02-27T14:31:53Z
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/14
`graph_from_pdbid` add automatic download if pdb missing
2023-02-27T14:31:53Z
Carlos GO
`graph_from_pdbid` add automatic download if pdb missing
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/13
Include necessary download calls for examples to work
2023-01-12T15:23:34Z
Carlos GO
Include necessary download calls for examples to work
Example 2 doesn't work if you don't pass the right flags to `rnaglib_download`
Example 2 doesn't work if you don't pass the right flags to `rnaglib_download`
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/12
rna_draw save option sends file to path in site-packages
2022-07-25T14:13:48Z
Carlos GO
rna_draw save option sends file to path in site-packages
See line https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/blob/main/rnaglib/drawing/rna_draw.py#L157
Should just accept the value of `save` e.g.
```python
rna_draw(g, save='/my/path.pdf')
```
See line https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/blob/main/rnaglib/drawing/rna_draw.py#L157
Should just accept the value of `save` e.g.
```python
rna_draw(g, save='/my/path.pdf')
```
Carlos GO
Carlos GO
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/11
wrong edge key in drawing
2022-07-15T14:54:06Z
Carlos GO
wrong edge key in drawing
```python
[ins] In [7]: from rnaglib.drawing.rna_draw import rna_draw
[ins] In [8]: rna_draw(g)
---------------------------------------------------------------------------
KeyError Traceback (most recent...
```python
[ins] In [7]: from rnaglib.drawing.rna_draw import rna_draw
[ins] In [8]: rna_draw(g)
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
File ~/anaconda3/envs/biographs/lib/python3.9/site-packages/rnaglib/drawing/rna_draw.py:89, in process_axis(axis, g, subtitle, highlight_edges, node_color, node_labels, node_ids, label)
88 try:
---> 89 symbol = make_label(d[label])
90 edge_labels[(n1, n2)] = symbol
KeyError: 'LW'
```
Carlos GO
Carlos GO
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/10
learn.pretrained_unsupervised has problems with non-standard data
2022-03-16T17:06:28Z
Seraphin Bassas
learn.pretrained_unsupervised has problems with non-standard data
Hi,
I am running a script in which I try to train a model in the same fashion as is done in the second example given in the rnaglib examples. The steps are as follows:
1. Firstly, I transform each graph in a repository of .cif files into...
Hi,
I am running a script in which I try to train a model in the same fashion as is done in the second example given in the rnaglib examples. The steps are as follows:
1. Firstly, I transform each graph in a repository of .cif files into a new annotated graph in .json format and transfer the .json files into their own repository. The transformation is accomplished using the `do_one()` method in the `rnaglib.prepare_data.main.py` file.
2. Then, I create a GraphDataset object from this repository of .json files and a Loader object from the GraphDataset.
3. Finally, I create an embedder and classifier model from the `model.py` script and make it go through unsupervised and supervised training phases. However, I cannot make it through the unsupervised phase because the graph loader cannot do the node comparison operation because of the following error:
![Screen_Shot_2022-01-12_at_3.06.39_PM](/uploads/ad0caed90b659e4a7ff671c9dd08bdd3/Screen_Shot_2022-01-12_at_3.06.39_PM.png)
Looking into the problem, inside the `compare` method in the `rnaglib.kernels.node_sim.py` file, I print out the rings passed as input to this function and find out they are always `None`, instead of being a list (as is the case for the preinstalled dataset). I don't know if it's an issue with the initial annotation, the transformation of the dataset into a data loader, or something else...
Any help is appreciated, notably an explanation about what the rings are and what they accomplish on a conceptual level.
Thank you, Séraphin
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/9
Testing issue creation with fresh profile
2021-11-30T15:18:12Z
Vincent MALLET
Testing issue creation with fresh profile
Hello, this is Vincent trying to submit an issue with a fresh profile
Hello, this is Vincent trying to submit an issue with a fresh profile
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/8
Set a reachable download path
2021-11-24T17:23:38Z
Carlos GO
Set a reachable download path
Vincent Mallet
Vincent Mallet
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/7
Make tutorial for building graphs from one local PDB
2021-11-24T17:23:30Z
Carlos GO
Make tutorial for building graphs from one local PDB
Carlos GO
Carlos GO
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/6
Linkify missing with docs build
2021-11-24T10:31:55Z
Carlos GO
Linkify missing with docs build
It seems 'linkify' was enabled in the conf.py. After I `pip install linkify` I still get the error:
```
/anaconda3/envs/rnaglib/lib/python3.9/site-packages/markdown_it/rules_core/linkify.py", line 31, in linkify
raise ModuleNotFoun...
It seems 'linkify' was enabled in the conf.py. After I `pip install linkify` I still get the error:
```
/anaconda3/envs/rnaglib/lib/python3.9/site-packages/markdown_it/rules_core/linkify.py", line 31, in linkify
raise ModuleNotFoundError("Linkify enabled but not installed.")
ModuleNotFoundError: Linkify enabled but not installed.
```
Is this module necessary or am i doing something wrong to build the docs?
```
make html
```
Jonathan Broadbent
Jonathan Broadbent
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/5
Add walkthrough for basic data manipulations in docs
2021-11-24T17:23:22Z
Carlos GO
Add walkthrough for basic data manipulations in docs
Carlos GO
Carlos GO
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/4
Access denied to datasets page
2021-11-24T16:02:20Z
Carlos GO
Access denied to datasets page
https://rnaglib.cs.mcgill.ca/static/datasets/iguana/
Giving a 403 error. Could be that it only works through the webserver.
https://rnaglib.cs.mcgill.ca/static/datasets/iguana/
Giving a 403 error. Could be that it only works through the webserver.
Carlos GO
Carlos GO
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/3
Examples page in docs code snippets missing imports
2021-11-24T09:56:33Z
Carlos GO
Examples page in docs code snippets missing imports
Update the code snippets in the examples page to include imports so that it can work on a copy paste.
Update the code snippets in the examples page to include imports so that it can work on a copy paste.
Carlos GO
Carlos GO
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/2
Import error in loader
2021-11-24T10:46:34Z
Carlos GO
Import error in loader
Did a clean pip install from Linux and tried to run the code in the first example and I get an import error with the loader import.
```
File "ex.py", line 11, in <module>
from rnaglib.data_loading import graphloader
ImportError: c...
Did a clean pip install from Linux and tried to run the code in the first example and I get an import error with the loader import.
```
File "ex.py", line 11, in <module>
from rnaglib.data_loading import graphloader
ImportError: cannot import name 'graphloader' from 'rnaglib.data_loading' (/home/carlosoliver/anaconda3/lib/python3.8/site-packages/rnaglib/data_loading/__init__.py)
```
Vincent Mallet
Vincent Mallet
https://jwgitlab.cs.mcgill.ca/cgoliver/rnaglib/-/issues/1
error when running main.py in prepare_data
2022-01-12T16:47:53Z
Seraphin Bassas
error when running main.py in prepare_data
Hi,
I've been following the instructions to prepare PDB data as indicated in the README.md in rnaglib/rnaglib/prepare_data and I've been running into a few errors:
1. for main.py and the first example I was trying to run from rnaglib, I...
Hi,
I've been following the instructions to prepare PDB data as indicated in the README.md in rnaglib/rnaglib/prepare_data and I've been running into a few errors:
1. for main.py and the first example I was trying to run from rnaglib, I was denied access when trying to run the scripts and have to run the `chmod` command to get permission to access the files
2. once this is done, the files are not executable as python files on my machine and I have to shebang them to get them to recognize the import statements being used. But once I do this it seems like things work.
3. when running main.py in prepare_data, I keep running into two problems: either the options mentioned in the README.md and in the argparser in the main.py file are not recognized:
![Screen_Shot_2021-10-07_at_8.05.45_PM](/uploads/20618b83769f1a1a300d6ba3abf3e4a5/Screen_Shot_2021-10-07_at_8.05.45_PM.png)
or I get the following error message:
![Screen_Shot_2021-10-07_at_8.09.28_PM](/uploads/d619c5f403f3759f744c682fc2ea98f7/Screen_Shot_2021-10-07_at_8.09.28_PM.png)
I'm running on IOS with Python 3.8.8
Thank you,
Séraphin
Carlos GO
Carlos GO