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GenomeLoader

Table of Contents

Design philosophy

GenomeLoader is a library for loading genomic data for deep learning applications. It is designed to be fast, convenient, and minimalistic. To achieve this goal, I tried my best to adhere to the following rules:

  • Up-to-date. GenomeLoader depends on several libraries. These libraries are sometimes updated without backwards compatibility. I will update GenomeLoader to always be compatible with the latest versions of all dependencies.

  • Minimize memory and processing footprint. Batch data are efficiently loaded from hard drive into memory as needed, with as little effect on training/testing times as possible. In benchmark tests, I typically need less than 2GB of system RAM to train deep learning models with GenomeLoader. To meet this goal, I exclusively developed/tested on the following systems:

    MacBook Pro 15-inch w/ Touch Bar (2017)
    MacOs High Sierra
    2.8GHz quad-core 7th-generation Intel Core i7 processor
    16GB 2133MHz LPDDR3 memory
    256GB SSD storage

    Thinkmate VSX R5 340V7
    Ubuntu 18.04
    Quad-Core Intel Core i7-7700K 4.20GHz 8MB Cache 2 x Crucial 16GB PC4-19200 2400MHz DDR4 Non-ECC UDIMM 2 x Titan Xp GPU 500GB Samsung 960 EVO M.2 PCIe 3.0 x4 NVMe SSD

  • No intermediate files. We all hate running out of space on our hard drives.

  • Use only standardized data formats. In order to make the libraries compatible with other datasets, GenomeLoader only supports st

  • Reproducibility. Random seeds ensures multiple runs of the program yield the same results. However, Tensorflow-GPU always has some element of randomness, so perfect reproducibility in deep learning applications is difficult, if not impossible.

Citation

Coming soon

Installation

Clone the repository and run:

python setup.py develop

develop is preferred over install because I will be constantly updating this repository.

The best and easiest way to install all dependencies is with Anaconda (5.1, Python 3.6 version). Anaconda uses pre-built binaries for specific operating systems to allow simple installation of Python and non-Python software packages. macOS High Sierra or Ubuntu 18.04 is recommended.

Required dependencies

  • pyfaidx (0.5.2). Python wrapper module for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index. Easily installed in Anaconda with the following command line:
pip install pyfaidx
  • [py2bit] . Preferred over genome FASTA files, due to its faster data retrieval and smaller file size footprint.
  • pyBigWig (0.3.11). A python extension for quick access to bigWig and bigBed files: Easily installed in Anaconda with the following command line:
pip install pyBigWig
  • pybedtools (0.7.10). BEDTools wrapper and extension that offers feature-level manipulations from within Python.
  • [quicksect]
  • [keras]
  • [tqdm]
  • [pandas]
  • [scikit-learn]
  • [numpy]

Optional dependencies

  • biopython (1.7.0). Required to read bgzipped FASTA files. Convenient for large genome files.
conda install -c anaconda biopython

Examples

BedGraph

This is an example of loading a BedGraph file for training a simple keras model. It uses the same files and follows the same format from the genomelake repository. You will need to first download the following files:

from genomeloader.wrapper import TwoBitWrapper, BedGraphWrapper
from genomeloader.generator import BedGraphGenerator
from keras.models import Sequential
from keras.layers import Conv1D, Flatten, Dense

t = TwoBitWrapper('hg19.2bit')
bg = BedGraphWrapper('JUND.HepG2.chr22.101bp_intervals.tsv.gz')
datagen = BedGraphGenerator(bg, t, seq_len=None) # The bedGraph file is already pre-sized to contain 101 bp intervals

model = Sequential()
model.add(Conv1D(15, 25, input_shape=(101, 4)))
model.add(Flatten())
model.add(Dense(1, activation='sigmoid'))

model.compile(loss='binary_crossentropy', optimizer='adam', metrics=['accuracy'])
model.fit_generator(datagen, steps_per_epoch=100)

Here is the the expected result:

100/100 [==============================] - 1s 10ms/step - loss: 0.1575 - acc: 0.9887

To-Do

Here is a list of features I plan to add. They will be added according to demand.

  • Multi-task loading