shamir-lab / domino Goto Github PK

Hi!
Is seems like the package pcst-fast is not available anymore.
After running python setup.py install I get an error:

error: Could not find suitable distribution for Requirement.parse('pcst-fast==1.0.7')

And just running pip install pcst_fast does not go either:

ERROR: Could not find a version that satisfies the requirement pcst_fast (from versions: none)
ERROR: No matching distribution found for pcst_fast

Best,
Olga

I attempted to install DOMINO through conda with

conda create --name domino
conda activate domino
conda install domino -c conda-forge -c bioconda

On Windows 10 this failed with

UnsatisfiableError: The following specifications were found to be incompatible with each other:
Package numpy conflicts for:
domino -> numpy=1.18.1
Package networkx conflicts for:
domino -> networkx=2.4
Package statsmodels conflicts for:
domino -> statsmodels=0.11.0
Package python conflicts for:
domino -> python[version='>=3.6,<3.8']
Package pandas conflicts for:
domino -> pandas=1.0.1
Package scipy conflicts for:
domino -> scipy=1.4.1
Package matplotlib-base conflicts for:
domino -> matplotlib-base
Package pcst-fast conflicts for:
domino -> pcst-fast=1.0.7
Package python-louvain conflicts for:
domino -> python-louvain=0.14

I assume it is because pcst-fast is not available for Windows. It would be helpful to note in the DOMINO readme that the conda install option (and perhaps the entire domino package?) is not Windows-compatible.

Those three conda commands worked on a Linux server.

Hi,
For slicer method README suggest to use --output_dir parameter, while in the code itself the parameter is called --output_file.

I am testing DOMINO with very small input networks and active gene lists. I get an error message:

line 36, in main_domino
G_final_modules=domino_main(active_genes_file=cur_ag, network_file=network_file, slices_file=slices_file, slice_threshold=slice_threshold, module_threshold=module_threshold)
File "/usr/local/lib/python3.7/site-packages/src/core/domino.py", line 349, in main
".")[0] + ".pkl"))
File "/usr/local/lib/python3.7/site-packages/src/core/domino.py", line 83, in prune_network_by_modularity
G_modularity = nx.algorithms.operators.union_all(G_modules)
File "/usr/local/lib/python3.7/site-packages/networkx/algorithms/operators/all.py", line 61, in union_all
raise ValueError(\'cannot apply union_all to an empty list\')

union_all returns the ValueError if G_modules is an empty list, which seems like the expected behavior for my small inputs.

The ArgumentParser shows the argument name is --slice_threshold but the readme lists it as --slices_threshold

I attempted to execute Domino for my weight list (generated in Genie3), but my output file in Domino is empty. Should my input file in Domino include EnsembleID instead of Gene Symbol?

Hi!

I run DOMINO consecutively with the same imputs (same network and active genes list) and get different module numbers and sizes. What is the reason behind of this situation?
When I check the intersection of union of these modules that are produced by seperate run , they have ~80% common genes but the rest of them are different. Which result can we choose or trust in this case?

Thanks,
Betul

Hi!
Could you please provide an example of the network file or clarify the format here?
Judging from the error I'm getting the file should have 3 columns: ["node_1", "edge_type", "node_2"]. What exactly is the edge_type?

Olga

Hello iam hack hacker

If I'm reading the source code correctly, generate_report_from_template calls format_script and writes to a file path relative to where DOMINO is installed:

I'm attempting to run DOMINO inside a Singularity container where I don't have write permission to create files at that location. The package was installed by root when the image was created, and now I am running as my user.

Making the file paths configurable or using Python's temporary directories would avoid this problem.

Hi, I found that there's an error in the main domino.py code.

I used dip.sif in the examples file for the input, and executed the domino command.

it popped out the following message:

File "c:\users\\appdata\local\programs\python\python38\lib\site-packages\domino_python-0.1.1-py3.8.egg\src\core\domino.py",line 59, in create_subgraph
    res = G_modularity.subgraph(list(nodes))
AttributeError: 'NoneType' object has no attribute 'subgraph'

How can I solve this problem? thanks!