DNA analyser IBP

Tool for creating R-loop tracker, P53predictor, G4Killer and G4Hunter analysis. Work as API wrapper for IBP DNA analyzer API bioinformatics.ibp. Currently working with an instance of DNA analyser server running on http://bioinformatics.ibp.cz computational core but can be switched to the local instance of the server.

Getting Started

Prerequisites

python >= 3.10

Installing

To install test version from Pypi.

pipenv install dna-analyser-ibp

pip install dna-analyser-ibp

Quick start

DNA analyser uses pandas.Dataframe or pandas.Series. Firstly the user has to create Api object and login to API.

from DNA_analyser_IBP.api import Api

API = Api()

Enter your email        example@example.cz
Enter your password     ········

2020-09-16 18:51:17.943398 [INFO]: User host is trying to login ...
2020-09-16 18:51:17.990580 [INFO]: User host is successfully loged in ...

If DNA analyser API server is not running on http://bioinformatics.ibp.cz then you have to set server paramether to create Api object.

from DNA_analyser_IBP.api import Api

API = Api(
    server='http://hostname:port/api'
)

Sequence uploading

Sequences can be uploaded from NCBI, plain text or text file. Example bellow illustrates NCBI sequence uploading Homo sapiens chromosome 12.

API.sequence.ncbi_creator(
    circular= True,
    tags=['Homo','sapiens', 'chromosome'],
    name='Homo sapiens chromosome 12',
    ncbi_id='NC_000012.12'
)

API.sequence.load_all(
    tags=['Homo']
)

G4Hunter

G4Hunter is a tool for prediction of G-quadruplex propensity in nucleic acids, this algorithm considers G-richness and G-skewness of a tested sequence and shows a quadruplex propensity score.

sapiens = API.g4hunter.load_all(
    tags=['Homo']
)

API.g4hunter.analyse_creator(
    sequence=sapiens,
    tags=['analyse','Homo', 'sapiens'],
    threshold=1.4,
    window_size=30
)

To load results of G4Hunter analysis.

API.g4hunter.load_all(
    tags=['analyse', 'Homo', 'sapiens']
) 

R-loop tracker

R-loop tracker is a toll for prediction of R-loops in nucleic acids. The algorithms search for R-loop initiation zone based on presence of G-clusters and R-loop elongation zone containing at least 40% of Guanine density.

sapiens = API.g4hunter.load_all(
    tags=['Homo']
)
API.rloopr.analyse_creator(
    sequence=sapiens,
    tags=['analyse', 'Homo', 'sapiens'],
    riz_2g_cluster=True,
    riz_3g_cluster=False
)

To load results of R-loop tracker analysis.

API.rloopr.load_all(
    tags=['analyse', 'Homo', 'sapiens']
) 

G4Killer

G4Killer algorithm allows to mutate DNA sequences with desired G4Hunter score with minimal mutation steps.

API.g4killer.run(
    sequence='AATTATTTGGAAAGGGGGGGTTTTCCGA',
    threshold=0.5
) 

API.g4killer.run_multiple(
    sequences=[
        'AATTATTTGGAAAGGGGGGGTTTTCCGA',
        'AATTATTTGGAAAGGGGGGGTTTTCCGA'
    ],
    threshold=0.5
)

P53 predictor

P53 binding predictor for 20 base pairs sequences.

API.p53.run(
    sequence='GGACATGCCCGGGCATGTCC'
)

API.p53.run_multiple(
    sequences=[
        'GGACATGCCCGGGCATGTCC',
        'GGACATGCCCGGGCATGTCC'
    ]
) 

Development

Dependencies

• requests = "2.31.0"
• pandas = "2.0.0"
• tqdm = "4.66.0"
• pyjwt = "2.8.0"
• matplotlib = "3.7.2"
• requests-toolbelt = "1.0.0"
• tenacity = "8.2.3"

DEV dependencies

• pytest = "7.4.2"

Tests

To run tests only when downloaded directly from this repository.

pytest -v tests/

Authors

• Patrik Kaura - Main developer - patrikkaura

License

This project is licensed under the GPL-3.0 License - see the LICENSE.md file for details.