Methods and functions that support the overall operations of code based on Hail Batch.

Project description

batchutils

Overview

Main Features

Installation

Usage

Use the following function as is. Replace the paths with [j1.ofile, j2.ofile, ...]

b = hb.Batch(
    default_image='hailgenetics/hail:0.2.77,
    backend=service_backend,
    name=f'combine-tsvs'
)
combined = batch_combine2(
    combine_tsvs_with_headers,
    combine_compressed_tsvs_with_headers,
    b,
    'combine-tsvs-with-headers',
    ['gs://bucket/input1.tsv', ...],
    final_location='gs://bucket/final-file.tsv.gz',
    branching_factor=25,
    suffix='.tsv.bgz')

final_location is where the output file is.

Cite

Maintainer

Tarjinder Singh @ tsingh@broadinstitute.org

Acknowledgements

Release Notes

Project details

Release history Release notifications | RSS feed

0.1.5.1

Mar 24, 2022

This version

0.1.5

Mar 24, 2022

0.1.3

Mar 9, 2022

0.1.2

Feb 19, 2022

0.1.1

Feb 1, 2022

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

batchutils-0.1.5.tar.gz (22.6 kB view details)

Uploaded Mar 24, 2022 Source

Built Distribution

batchutils-0.1.5-py3-none-any.whl (6.9 kB view details)

Uploaded Mar 24, 2022 Python 3

File details

Details for the file batchutils-0.1.5.tar.gz.

File metadata

Download URL: batchutils-0.1.5.tar.gz
Upload date: Mar 24, 2022
Size: 22.6 kB
Tags: Source
Uploaded using Trusted Publishing? No
Uploaded via: twine/3.8.0 pkginfo/1.8.2 readme-renderer/32.0 requests/2.25.1 requests-toolbelt/0.9.1 urllib3/1.26.8 tqdm/4.62.3 importlib-metadata/4.8.2 keyring/23.5.0 rfc3986/2.0.0 colorama/0.4.4 CPython/3.7.4

File hashes

Hashes for batchutils-0.1.5.tar.gz
Algorithm	Hash digest
SHA256	`79f155614b6c7b740b096d22bc11c2ce3565f9f49c9e015f72e3f8accfadd70e`
MD5	`209a46f63ab742e50e14ff1855d754ad`
BLAKE2b-256	`d78b51aef4573ef721abacdbdf6984ce288f9bef0323ca78777abd627f81e7aa`

See more details on using hashes here.

File details

Details for the file batchutils-0.1.5-py3-none-any.whl.

File metadata

Download URL: batchutils-0.1.5-py3-none-any.whl
Upload date: Mar 24, 2022
Size: 6.9 kB
Tags: Python 3
Uploaded using Trusted Publishing? No
Uploaded via: twine/3.8.0 pkginfo/1.8.2 readme-renderer/32.0 requests/2.25.1 requests-toolbelt/0.9.1 urllib3/1.26.8 tqdm/4.62.3 importlib-metadata/4.8.2 keyring/23.5.0 rfc3986/2.0.0 colorama/0.4.4 CPython/3.7.4

File hashes

Hashes for batchutils-0.1.5-py3-none-any.whl
Algorithm	Hash digest
SHA256	`3bfec92555cba8def70569a0f240bc11ae51e4168e50a6dfd3a56bc53a6297a5`
MD5	`868615bc387c5ae6d05cf61365918e8d`
BLAKE2b-256	`55e303a9cc463e74b4b2a0a9f23937bd50c5dc81498c13d281e132fa762ba964`