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Orca

This repository contains code for Orca, a deep learning sequence modeling framework for multiscale genome structure prediction. Orca can predict genome interactions from kilobase to whole-chromosome-scales using only genomic sequence as input. The manuscript is available here.

This is our main repository for Orca, including code for applying Orca models or training new models. For reproducing the analyses in our manuscript, please visit our manuscript repository. A GPU-backed webserver for running the core functionalities of Orca is also available at: orca.zhoulab.io.

What can I use Orca for?

  • Predict the genome structural impacts of any genome variant, including large structural variants of almost any size (the maximum input size 256Mb, which is larger than the largest human chromosome).
  • Predict the genome 3D structure from any human genome sequence, which means you can introduce multiple variants, haplotypes, an entire assembled genome, or any sequence you wish to perform an in silico Hi-C experiment on.
  • Analyze sequence dependencies of genome 3D structure by performing virtual genetic screens. Orca sequence models can serve as an “in silico genome observatory” that allows designing and performing virtual genetic screens to probe the sequence basis of genome 3D organization.

What is Orca?

Orca is a deep learning sequence modeling framework for multiscale genome interaction prediction. Orca models are trained on high-resolution micro-C datasets for H1-ESC and HFF cell lines (and a cohesin-depleted HCT116 Hi-C model for the analysis of sequence dependencies of chromatin compartments). If you have sufficient computational resources including GPUs, you can also train your own models on Hi-C type data given any cooler format input following our examples (see the training section).

Get started

If you just need predictions for one or a handful of variants, we have provided the core functionalities on a web server: orca.zhoulab.io.

Installation

For running Orca locally, clone this repository with the following command.

git clone https://github.com/jzhoulab/orca.git
cd orca

Install python dependencies of Orca and Selene. You can set up a conda env with conda env create -f orca_env.yml or install these packages manually to your environment. Then, install pytorch(>=1.7.0) according to here. Finally, install Selene with the commands below - right now we depend on a development branch of Selene with added support for custom targets:

git clone https://github.com/kathyxchen/selene.git
cd selene
git checkout custom_target_support
python setup.py build_ext --inplace
python setup.py install 

Download model and relevant resource files

Next, download the model and other resource files needed by Orca. Because these files are large and some are optional, we packaged into several files and you can download what you need (some functionalities may not be available if the relevant files are not downloaded).

The minimal resource package for running Orca are packaged here (1.3G), which includes the Orca models and the hg38 reference genome. It is also recommended to download the preprocessed micro-C datasets binned to the resolutions that Orca use, which will allow for comparisons with observed data, from here (34G). In addition, if you would like to generate chromatin tracks visualizations, you can download these files here (15G). To download and extract all resource files, you can run the following commands under the orca directory.

wget https://zenodo.org/record/6234936/files/resources_core.tar.gz
wget https://zenodo.org/record/6234936/files/resources_mcools.tar.gz
wget https://zenodo.org/record/4594676/files/resources_extra.tar.gz
tar xf resources_core.tar.gz
tar xf resources_mcools.tar.gz
tar xf resources_extra.tar.gz

Basic Usage

You can use Orca through either the command-line-interface (CLI) which supports most of the core functionalities or access the full capabilities through python. You can jump to the CLI if you wish to just use the CLI.

For using Orca from python, you can just add the directory you cloned to your python PATH sys.path.append(ORCA_PATH) and use it (for now we haven't made Orca a python package, because most of its functionalities depends on the resource files which is rather large). The full API documentation is available here.

import orca_predict
#Default is using GPU. Set use_cuda = False in load_resources to use CPU.
orca_predict.load_resources(models=['32M', '256M'])
#import loaded resources
from orca_predict import *

#duplication variant
outputs = process_dup('chr17', 70845859, 71884859, hg38, file='./chr17_70845859_71884859_RevSex_dup_maximum_Sox9', show_genes=True)

#deletion variant
outputs = process_del('chr2', 220295000, 222000000, hg38, file='./chr2_220295000_222000000_del_Brachydactyly_Pax3', show_genes=True)

#inversion variant
outputs = process_inv('chr2', 218875000, 220155000, hg38, file='./chr2_218875000_220155000_inv_FsyndromeF1_Wnt6', show_genes=True)

#insertion variant, where ins_seq is the inserted sequence string
outputs = process_ins('chr6', 74353593, ins_seq, hg38, strand='+', file='./chr6_74353593_ins', show_genes=True)

#translocation variant, see docs for how such variant is expressed
outputs = process_single_breakpoint('chr5', 89411065, 'chr7', 94378248,'+','-', hg38, target=True, file='./chr5_89411065_chr7_94378248_+-', show_genes=True)

#Default is using the 1-32Mb models. To use the 256Mb models, just add window_radius=128000000
outputs = process_dup('chr17', 70845859, 71884859, hg38, window_radius=128000000, file='./chr17_70845859_71884859_RevSex_dup_maximum_Sox9')

#of course you can also predict any genomic region
outputs = process_region('chr9', 110404000, 111404000, hg38, window_radius=16000000, file='./chr17_110404000_111404000')

Usage - complex variants

You can also specify more complex variants than the above types, using the custom variant function (here we specify a simple two-segment variant, but it can be used to specify complex variants with an arbitrary number of segments)

_ = process_custom([['chr5', 89411065, 89411065+16000000, '-'],
                ['chr7', 94378248, 94378248+16000000,'+']],
              [['chr5', 89411065-16000000, 89411065+16000000],
               ['chr7', 94378248-16000000, 94378248+16000000]],
              16000000, hg38, anno_list=[[16000000,'double']],
              ref_anno_list=[[16000000,32000000,'black'],[16000000,32000000,'black']], target=False, file='./custom_variant')

For even more flexibility, you can just generate the sequence and give it to Orca to predict. This gives you the full control for introducing any variant, haplotype, or even an individual genome, and predict the multiscale genome organization.

from selene_sdk.sequences import Genome
#sequence: 32Mb sequence
#mpos: specifies the coordinate to zoom into for multiscale prediction
#wpos: specifies the coordinate of the center position of the sequence. 
#chrom: chromosome name
outputs = genomepredict(Genome.sequence_to_encoding(sequence)[None,:,:], chrom, mpos=pos, wpos=wpos, use_cuda=True)

#For 256Mb sequence. See the docs for details of the input 
outputs = genomepredict_256Mb(Genome.sequence_to_encoding(sequence)[None,:,:], chrom, normmats, chrlen, mpos=pos, wpos=wpos, use_cuda=True)

For full information about using Orca, you may visit our API documentation page (http://jzhoulab.github.io/orca-docs/).

Orca Command-line Interface (CLI)

For prediction of multiscale interactions for genomic regions, structural variant of deletion, duplication, inversion, and translocation with single junctions, you can use the command line interface orca_predict.py and the output includes graphical visualizations in pdf format and numerical results saved in pytorch serialization format.

    Orca multiscale genome interaction sequence model prediction tool.

    Usage:
    orca_predict region [options] <coordinate> <output_dir>
    orca_predict del [options] <coordinate> <output_dir>
    orca_predict dup [options] <coordinate> <output_dir>
    orca_predict inv [options] <coordinate> <output_dir>
    orca_predict break [options] <coordinate> <output_dir>

    Options:
    -h --help       Show this screen.
    --show_genes    Show gene annotation (only supported for 32Mb models).
    --show_tracks   Show chromatin tracks (only supported for 32Mb models).
    --256m          Use 256Mb models (default is 32Mb).
    --nocuda        Use CPU implementation. 
    --version       Show version.

For input, a <coordinate> argument and an output directory <output_dir> are required. Most prediction modes except for break requires specifying a region as input in the format like chr9:94904000-126904000.

The break mode is used for predicting the effect of an translocation that connects two chromosomal breakpoints. An example <coordinate> input is chr1:85691449 chr5:89533745 +/+. Specifically, two breakpoint positions and the corresponding two orientations are needed. The orientations decide how the breakpoints are connected. The ‘+’ or ‘-’ sign indicate whether the left or right side of the breakpoint is used (not forward and reverse strands). For example ‘+/+’ indicates connecting chr1:0-85691449 with chr5:0-89533745 at the breakpoints, while ‘+/-’ indicates connecting chr1:0-85691449 with chr5:89533745-chromosome end.

If the function that you needed is not available from the CLI, you can use the python interface as introduced in the previous section and detailed in the Orca API documentation.

Example output

As an example output, here we showed visualizations generated for the predictions of a duplication variant. For structural variant prediction, Orca generates multiple files that each contains a series of multi-level predictions zooming into a breakpoint of the variant, or the corresponding position(s) of the breakpoint in the reference sequence.

The positions of the variant boundaries are be annotated on the left side of each plot. For reference sequence, we also show the micro-C data for comparison.

Example reference sequence predictions for duplication variant (breakpoint):

Example alternative sequence predictions for duplication variant (right boundary):

If you ask Orca to generate gene annotations or chromatin tracks, you will also find annotation pdf outputs files which correspond to the same multi-level regions the genome interaction predictions are made on.

Besides graphical output, we also save the numerical predictions in PyTorch serialization format (pickle) with extension '.pth'. The .pth file can be loaded with torch.load or other pickle file loading function. Each file contains a python dictionary. If the prediction mode is one of the structural variant prediction modes, the dictionary stores multiple dictionaries each corresponding to an output file as described above. The dictionary includes:

predictions - Multi-level predictions for H1-ESC and HFF cell types.

experiments - Observations for H1-ESC and HFF cell types that matches the predictions (only available for reference allele).

chr - The chromosome name

start_coords - Start coordinates for the prediction at each level.

end_coords - End coordinates for the prediction at each level.

annos - Annotation information. A list indicating the relative variant positions for each interaction matrix, saved for plotting purpose.

Train Orca models

If you have set up Orca with its dependencies and has the necessary GPU resources (we have only done training on 4x V100 32Gb servers), you can train new models following the example code under the train directory to train new Orca models.

For training Orca models, you will need at minimum only a mcool file processed to multiple resolutions including at least 1000, 4000, and, 32000; you can use cooler zoomify). Each model is trained in three stages (1Mb module, 1-32Mb module, 32-256Mb module), corresponding to the three python files. You can refer to the train/README.md file for more details of training. Note that the training process does require significant computing resources and time.

Q&A

  • Error when running the code in CPU mode? If you have a cuda-capable device but choose to run in the CPU mode, this can generate a error from torch.DataParallel module. You can fix this by running the code with CUDA_VISIBLE_DEVICES= python ...

  • Which datasets are Orca trained on? You can access these datasets with 4DN accession IDs 4DNFI9GMP2J8 (H1-ESC; Krietenstein et al. 2020), 4DNFI643OYP9 (HFF; Krietenstein et al. 2020), 4DNFILP99QJS (cohesin-depleted HCT116; Rao et al. 2017). We thank the authors of these high-quality datasets.

  • How much resource do I need to run the model locally? It depends on your application. If you only need predictions for a few variants, or if you only need the 1Mb model, CPU may be enough. If you need to predict more than a couple dozens of variants, then GPU is highly recommended (>8GB RAM needed).

Questions and feedbacks

Thank you very much for using Orca. If you have any question or feedback, you can let us know at orca-user@googlegroups.com. If you found a bug, you can file a Github issue with details for reproducing the bug. Orca is completely free for any non-commercial and academic use, please contact us for other applications.

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sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale

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