pycorearray: Python Interface to CoreArray Genomic Data Structure (GDS) Files
pre-release version: v0.2, renamed from pygds in Oct 2026 (v0.1 was pygds, from 2017)
Features
This package provides a high-level Python interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The pycorearray package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. GDS files on cloud storage (HTTP/HTTPS, Amazon S3, Google Cloud Storage, Azure Blob Storage) can be opened directly, read-only, without downloading the whole file.
Package Maintainer
Dr. Xiuwen Zheng (zhengxwen@gmail.com)
Prerequisites
Python 3.10 or later
NumPy 1.25 or later
liblzma in xz utilities (for XZ/LZMA compression).
The bundled CoreArray sources also build in ZLIB and LZ4, so the supported
compression methods are: ZIP/ZIP_RA (zlib), LZMA/LZMA_RA (xz), and
LZ4/LZ4_RA.
On macOS with Homebrew, install xz with brew install xz; the build probes
/opt/homebrew/opt/xz and /usr/local/opt/xz automatically, or set the
LZMA_PREFIX environment variable to point at a custom prefix.
For cloud storage access: libcurl, and on Linux also
OpenSSL (libcrypto) to sign S3 and Azure requests; macOS uses its system
libcurl and CommonCrypto. On Debian/Ubuntu: sudo apt-get install libcurl4-openssl-dev libssl-dev. Without them, or with the environment
variable PYCOREARRAY_NO_CLOUD=1, pycorearray is built without cloud access.
Installation
pip install git+https://github.com/CoreArray/pycorearray.git
Or, from a checkout, build the extension in place:
python3 setup.py build_ext --inplace
python3 -m pytest tests/ # run the tests and the examples in the docstrings
Citation
Original papers (implemented in R/Bioconductor):
Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS (2012). A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. Bioinformatics. DOI: 10.1093/bioinformatics/bts606.
Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir BS, Laurie C, Levine D (2017). SeqArray -- A storage-efficient high-performance data format for WGS variant calls. Bioinformatics. DOI: 10.1093/bioinformatics/btx145.
Examples
Open an existing file
gdsfile.open() opens a file read-only by default. An example file comes
with the package:
import pycorearray as gds
f = gds.gdsfile()
f.open(gds.get_example_path('ceu_exon.gds'))
f.show()
File: /.../pycorearray/data/ceu_exon.gds (32.5K)
+ [ ] *
|--+ description [ ] *
|--+ sample.id { Str8 90 LZMA_ra(35.8%), 258B } *
|--+ variant.id { Int32 1348 LZMA_ra(16.8%), 906B } *
|--+ position { Int32 1348 LZMA_ra(64.6%), 3.4K } *
|--+ chromosome { Str8 1348 LZMA_ra(4.63%), 158B } *
|--+ allele { Str8 1348 LZMA_ra(16.7%), 902B } *
|--+ genotype [ ] *
| |--+ data { Bit2 1348x90x2 LZMA_ra(26.3%), 15.6K } *
| |--+ extra.index { Int32 0x3 LZMA_ra, 19B } *
| \--+ extra { Int16 0 LZMA_ra, 19B }
|--+ phase [ ]
| |--+ data { Bit1 1348x90 LZMA_ra(0.91%), 138B } *
| |--+ extra.index { Int32 0x3 LZMA_ra, 19B } *
| \--+ extra { Bit1 0 LZMA_ra, 19B }
|--+ annotation [ ]
| |--+ id { Str8 1348 LZMA_ra(38.4%), 5.5K } *
| |--+ qual { Float32 1348 LZMA_ra(2.26%), 122B } *
| \--+ filter { Int32,factor 1348 LZMA_ra(2.26%), 122B } *
\--+ sample.annotation [ ]
\--+ family { Str8 90 LZMA_ra(57.1%), 222B }
f.index('sample.id').read(start=[0], count=[3])
## array(['NA06984', 'NA06985', 'NA06986'], dtype=object)
f.index('position').read(start=[0], count=[5])
## array([1105366, 1105411, 1110294, 3537996, 3538692], dtype=int32)
g = f.index('genotype/data').read() # variant x sample x allele
g.shape
## (1348, 90, 2)
f.close()
Cloud Storage
A GDS file on cloud storage can be opened directly, read-only, without
downloading the whole file: only the blocks that are read are fetched.
http:// and https:// URLs, Amazon S3 (s3://, also S3-compatible
services), Google Cloud Storage (gs://) and Azure Blob Storage (az://) are
supported. For example, a public file on Amazon S3:
import pycorearray as gds
f = gds.gdsfile()
f.open('s3://gds-stat/download/hapmap/hapmap_r23a.gds')
f.show()
File: s3://gds-stat/download/hapmap/hapmap_r23a.gds (86.5M)
+ [ ] *
|--+ description [ ] *
|--+ sample.id { Str8 270 LZMA_ra(17.3%), 381B } *
|--+ variant.id { Int32 4098136 LZMA_ra(3.19%), 511.4K } *
|--+ position { Int32 4098136 LZMA_ra(48.2%), 7.5M } *
|--+ chromosome { Str8 4098136 LZMA_ra(0.02%), 1.7K } *
|--+ allele { Str8 4098136 LZMA_ra(12.8%), 2.0M } *
|--+ genotype [ ] *
| |--+ data { Bit2 4098136x270x2 LZMA_ra(12.4%), 65.4M } *
| |--+ extra.index { Int32 0x3 LZMA_ra, 18B } *
| \--+ extra { Int16 0 LZMA_ra, 18B }
|--+ phase [ ]
| |--+ data { Bit1 4098136x270 LZMA_ra(0.01%), 19.8K } *
| |--+ extra.index { Int32 0x3 LZMA_ra, 18B } *
| \--+ extra { Bit1 0 LZMA_ra, 18B }
|--+ annotation [ ]
| |--+ id { Str8 4098136 LZMA_ra(27.7%), 11.1M } *
| |--+ qual { Float32 4098136 LZMA_ra(0.02%), 2.5K } *
| |--+ filter { Int32,factor 4098136 LZMA_ra(0.02%), 2.5K } *
| |--+ info [ ]
| \--+ format [ ]
\--+ sample.annotation [ ]
|--+ family { Str8 270 LZMA_ra(17.3%), 381B } *
|--+ father { Str8 270 LZMA_ra(28.2%), 261B } *
|--+ mother { Str8 270 LZMA_ra(28.2%), 261B } *
|--+ sex { Str8 270 LZMA_ra(27.0%), 153B } *
\--+ phenotype { Int32 270 LZMA_ra(8.70%), 101B } *
f.index('position').read(start=[1000], count=[5])
## array([2409958, 2410723, 2410773, 2412474, 2413426], dtype=int32)
f.close()
Credentials for private files are taken from the usual environment variables
of each service, or set with pycorearray.cloud; see help(pycorearray.cloud).
1 maintainer
Metadata
1 maintainer
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