MPRA-DragoNN/ConvModel

Authors: Rajiv Movva, Surag Nair

License: MIT

Contributed by: Rajiv Movva, Surag Nair

Cite as: https://doi.org/10.1101/393926

Type: None

Postprocessing: variant_effects

Trained on: Sharpr-MPRA dataset. chr8 validation, chr18 test. other chromosomes train.

Source files

Three-layer convolutional neural network for predicting Sharpr-MPRA activity of arbitrary 145bp sequences.

Create a new conda environment with all dependencies installed
kipoi env create MPRA-DragoNN/ConvModel
source activate kipoi-MPRA-DragoNN__ConvModel
Test the model
kipoi test MPRA-DragoNN/ConvModel --source=kipoi
Make a prediction
kipoi get-example MPRA-DragoNN/ConvModel -o example
kipoi predict MPRA-DragoNN/ConvModel \
  --dataloader_args='{"intervals_file": "example/intervals_file", "fasta_file": "example/fasta_file"}' \
  -o '/tmp/MPRA-DragoNN|ConvModel.example_pred.tsv'
# check the results
head '/tmp/MPRA-DragoNN|ConvModel.example_pred.tsv'
Create a new conda environment with all dependencies installed
kipoi env create MPRA-DragoNN/ConvModel
source activate kipoi-MPRA-DragoNN__ConvModel
Get the model
import kipoi
model = kipoi.get_model('MPRA-DragoNN/ConvModel')
Make a prediction for example files
pred = model.pipeline.predict_example(batch_size=4)
Use dataloader and model separately
# Download example dataloader kwargs
dl_kwargs = model.default_dataloader.download_example('example')
# Get the dataloader and instantiate it
dl = model.default_dataloader(**dl_kwargs)
# get a batch iterator
batch_iterator = dl.batch_iter(batch_size=4)
for batch in batch_iterator:
    # predict for a batch
    batch_pred = model.predict_on_batch(batch['inputs'])
Make predictions for custom files directly
pred = model.pipeline.predict(dl_kwargs, batch_size=4)
Get the model
library(reticulate)
kipoi <- import('kipoi')
model <- kipoi$get_model('MPRA-DragoNN/ConvModel')
Make a prediction for example files
predictions <- model$pipeline$predict_example()
Use dataloader and model separately
# Download example dataloader kwargs
dl_kwargs <- model$default_dataloader$download_example('example')
# Get the dataloader
dl <- model$default_dataloader(dl_kwargs)
# get a batch iterator
it <- dl$batch_iter(batch_size=4)
# predict for a batch
batch <- iter_next(it)
model$predict_on_batch(batch$inputs)
Make predictions for custom files directly
pred <- model$pipeline$predict(dl_kwargs, batch_size=4)
Get the docker image
docker pull kipoi/kipoi-docker:mpra-dragonn-slim
Get the full sized docker image
docker pull kipoi/kipoi-docker:mpra-dragonn
Get the activated conda environment inside the container
docker run -it kipoi/kipoi-docker:mpra-dragonn-slim
Test the model
docker run kipoi/kipoi-docker:mpra-dragonn-slim kipoi test MPRA-DragoNN/ConvModel --source=kipoi
Make prediction for custom files directly
# Create an example directory containing the data
mkdir -p $PWD/kipoi-example 
# You can replace $PWD/kipoi-example with a different absolute path containing the data 
docker run -v $PWD/kipoi-example:/app/ kipoi/kipoi-docker:mpra-dragonn-slim \
kipoi get-example MPRA-DragoNN/ConvModel -o /app/example 
docker run -v $PWD/kipoi-example:/app/ kipoi/kipoi-docker:mpra-dragonn-slim \
kipoi predict MPRA-DragoNN/ConvModel \
--dataloader_args='{'intervals_file': '/app/example/intervals_file', 'fasta_file': '/app/example/fasta_file'}' \
-o '/app/MPRA-DragoNN_ConvModel.example_pred.tsv' 
# check the results
head $PWD/kipoi-example/MPRA-DragoNN_ConvModel.example_pred.tsv
    
Install apptainer
https://apptainer.org/docs/user/main/quick_start.html#quick-installation-steps
Make prediction for custom files directly
kipoi get-example MPRA-DragoNN/ConvModel -o example
kipoi predict MPRA-DragoNN/ConvModel \
--dataloader_args='{"intervals_file": "example/intervals_file", "fasta_file": "example/fasta_file"}' \
-o 'MPRA-DragoNN_ConvModel.example_pred.tsv' \
--singularity 
# check the results
head MPRA-DragoNN_ConvModel.example_pred.tsv

Schema

Inputs

Single numpy array

Name: None

    Shape: (145, 4) 

    Doc: 145bp one-hot encoded ACGT sequences (e.g. [1,0,0,0] = 'A')


Targets

Single numpy array

Name: None

    Shape: (12,) 

    Doc: predicts 12 tasks: k562 minP replicate 1, k562 minP replicate 2, k562 minP pooled, k562 sv40p replicate 1, k562 sv40p replicate 2, k562 sv40p pooled, hepg2 minP replicate 1, hepg2 minP replicate 2, hepg2 minP pooled, hepg2 sv40p replicate 1, hepg2 sv40p replicate 2, hepg2 sv40p pooled.


Dataloader

Defined as: kipoiseq.dataloaders.SeqIntervalDl

Doc: Dataloader for a combination of fasta and tab-delimited input files such as bed files. The dataloader extracts regions from the fasta file as defined in the tab-delimited `intervals_file` and converts them into one-hot encoded format. Returned sequences are of the type np.array with the shape inferred from the arguments: `alphabet_axis` and `dummy_axis`.

Authors: Ziga Avsec , Roman Kreuzhuber

Type: Dataset

License: MIT


Arguments

intervals_file : bed3+<columns> file path containing intervals + (optionally) labels

fasta_file : Reference genome FASTA file path.

num_chr_fasta (optional): True, the the dataloader will make sure that the chromosomes don't start with chr.

label_dtype (optional): None, datatype of the task labels taken from the intervals_file. Example: str, int, float, np.float32

use_strand (optional): reverse-complement fasta sequence if bed file defines negative strand. Requires a bed6 file


Model dependencies
conda:
  • cython=0.28.5
  • h5py=2.8.0
  • python=3.7
  • pip=20.3.3
  • keras=2.3
  • tensorflow=1.14

pip:
  • protobuf==3.20

Dataloader dependencies
conda:
  • bioconda::pybedtools
  • bioconda::pyfaidx
  • bioconda::pyranges
  • numpy
  • pandas

pip:
  • kipoiseq