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mmsplice_paper's Introduction

Analysis code MMSplice manuscript

MMSplice predict variant effect on PSI, PSI5, PSI3, splicing efficiency and pathogenicity. This repository contains analysis code for MMSplice manuscript. MMSplice version mmsplice==0.2.0.

Software dependencies

The analysis was done with python and ploting was done with R. Required packages are listed in env.yaml.

  1. Install miniconda or anaconda.
  2. Run: conda env create -f env.yaml. This will install a new conda environment mmaplice-manuscript.
  3. Activate the environment: source activate mmaplice-manuscript. Run the analysis code (in jupyter-notebooks) in this environment.
  4. Install COSSMO from https://github.com/PSI-Lab/COSSMO

Folder structure

In general, the jupyter-notebooks were used to process, analysis the data and perform predictions. The result table are saved and read by R scripts for plotting.

  • script/Figure2: Code to generate figure for the Vex-seq and MFASS data.
  • script/Figure3: Code to generate figure for GTEx A5SS amd A3SS variants.
  • script/Figure4: Code to generate figure for MaPSy data.
  • script/Figure5: Code to generate figure for ClinVar data. Result table of other models were obtained from [Kipoi manuscript] (https://github.com/kipoi/manuscript)
  • data/: contains raw and processed data

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mmsplice_paper's Issues

Issue with Loading Models mmsplice.EXON and EXON3 in /Figure2/VexSeq.ipynb

Hello,

I am currently using MMSplice for my research and encountered an issue when loading the models. My MMSplice version matches the one specified in the env.yaml file in the repository.

I tried to run the following code:

exonM5 = load_model(mmsplice.EXON) exonM3 = load_model(mmsplice.EXON3)

However, I encountered the following errors:

AttributeError Traceback (most recent call last) <ipython-input-53-08118d5956f3> in <module>() 1 exonM5 = load_model(mmsplice.EXON) ----> 2 exonM3 = load_model(mmsplice.EXON3) AttributeError: module 'mmsplice' has no attribute 'EXON3'

Additionally, when I tried to get help on mmsplice.EXON, I received a message indicating that no Python documentation was found for the '/opt/conda/lib/python3.6/site-packages/mmsplice/models/Exon.h5' file.

Steps to Reproduce:

Use the MMSplice version specified in env.yaml.
Run the code provided above.

Environment:

Python version: 3.6
TensorFlow version: 1.11.0
MMSplice version: as specified in env.yaml

Screenshots:
image

Request:

Could you please provide guidance on resolving this issue? Is there a specific version of TensorFlow or other dependencies that I should be using to avoid this error?

Thank you for your assistance.

Best regards,

Shanshuimei

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