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Download your RNA data from HuggingFace with rouskinhf!

A wrapper around Huggingface the load data for eFold. You can:

pull datasets from the Rouskinlab's HuggingFace
create datasets from local files

Installation

To download data

pip install rouskinhf

To push data to huggingface (optional)

get a token access from the rouskilab huggingface's page
add this token to your environment

export HUGGINGFACE_TOKEN="hf_yourtokenhere"

To predict structures from rouskinhf (optional)

You'll need to install D. Mathew's RNAstructure Fold (also available on Rouskinlab GitHub).

Check your RNAstructure Fold installation in a terminal:

Fold --version

How to use

Download a dataset

import rouskinhf

rouskinhf.get_dataset(
    name='bpRNA-1m', # the name of a dataset from huggingface/rouskinlab
    force_download = False # use a local copy of the data if it exists
)

Convert whatever format to rouskinhf format

import rouskinhf

rouskinhf.convert(
    format = 'ct', # can be ct, seismic, bpseq, fasta or json (rouskinhf output data structure)
    file_or_folder = 'path/to/my/ct/folder',
    predict_structure = False, # Add structure from RNAstructure
    filter = True, # removes duplicates, non-regular characters and low AUROC
    min_AUROC=0.8,
)

Note: Sequences with bases different than A, C, G, T, U, N, a, c, g, t, u, n are not supported. The data will be filtered out.

Rouskinhf structure format

# rouskinhf_output_file.json
{
    "reference_name": {
        "sequence": "CACGCUAUG",
        "structure": [(0,8), (1,7)], # base pair representation
        # whatever other info you need
    }
}

Metadata

Release files for rouskinhf 0.4.8

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for rouskinhf 0.4.8
File	Size	Uploaded
rouskinhf-0.4.8.tar.gz	17.3 kB	May 14, 2024	Details

Built distribution (wheel)

Table of built distributions (wheels) for rouskinhf 0.4.8
File	Interpreter	ABI	Platform	Reset
rouskinhf-0.4.8-py3-none-any.whl 19.3 kB May 14, 2024	Python 3	none	any	Details

Total release size: 36.6 kB

Release files / rouskinhf-0.4.8.tar.gz

Download URL	rouskinhf-0.4.8.tar.gz
Size	17.3 kB
Tags	Source
SHA-256 checksum How to use checksums	`61eaf0316e28fa4e8ba82f94d6bbd14a63e174b604f5980f6a27bdab2fd5e436`
BLAKE2b-256 checksum How to use checksums	`ed44cadd00eb40814ee959875deda43a36c11cbe91f5b76e4e83bd2fa6733d4d`
Upload date	May 14, 2024
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/5.0.0 CPython/3.12.2`

Release files / rouskinhf-0.4.8-py3-none-any.whl

Download URL	rouskinhf-0.4.8-py3-none-any.whl
Size	19.3 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`04576cb878ca6c049c22258083381d34a46eb7a583aeaefe0454cd3460a4c3ad`
BLAKE2b-256 checksum How to use checksums	`2e7f68789fba2f5fea1ef590f004f48be92ec856758b73241c92735eaaf2ddb9`
Upload date	May 14, 2024
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/5.0.0 CPython/3.12.2`