fasta-one-hot-encoder
Simple python to lazily one-hot encode fasta files using multiple processes, either single bases or considering arbitrary kmers.
Readme
|travis| |sonar_quality| |sonar_maintainability| |codacy| |code_climate_maintainability| |pip| |downloads|
Simple python to lazily one-hot encode fasta files using multiple processes, either single bases or considering arbitrary kmers.
As usual, just download it using pip:
.. code:: shell
pip install fasta_one_hot_encoder
Since some software handling coverages sometime get slightly different results, here's three of them:
|coveralls| |sonar_coverage| |code_climate_coverage|
Bases
|bases|
One-hot encode to bases.
.. code:: python
from fasta_one_hot_encoder import FastaOneHotEncoder
encoder = FastaOneHotEncoder(
nucleotides = "acgt",
lower = True,
sparse = False,
handle_unknown="ignore"
)
path = "test_data/my_test_fasta.fa"
encoder.transform_to_df(path, verbose=True).to_csv(
"my_result.csv"
)
Obtained results should look like:
+---+---+---+---+---+
| | a | c | g | t |
+===+===+===+===+===+
| 0 | 0 | 0 | 1 | 0 |
+---+---+---+---+---+
| 1 | 0 | 1 | 0 | 0 |
+---+---+---+---+---+
| 2 | 0 | 1 | 0 | 0 |
+---+---+---+---+---+
Kmers
|kmers|
One-hot encode to kmers of given length.
.. code:: python
from fasta_one_hot_encoder import FastaOneHotEncoder
encoder = FastaOneHotEncoder(
nucleotides = "acgt",
kmers_length=2,
lower = True,
sparse = False,
handle_unknown="ignore"
)
path = "test_data/my_test_fasta.fa"
encoder.transform_to_df(path, verbose=True).to_csv(
"my_result.csv"
)
Obtained results should look like:
+---+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+ | | aa | ac | ag | at | ca | cc | cg | ct | ga | gc | gg | gt | ta | tc | tg | tt | +===+====+====+====+====+====+====+====+====+====+====+====+====+====+====+====+====+ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | +---+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+ | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | +---+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+----+
.. |bases| image:: https://github.com/LucaCappelletti94/fasta_one_hot_encoder/blob/master/bases.png?raw=true :alt: Bases
.. |kmers| image:: https://github.com/LucaCappelletti94/fasta_one_hot_encoder/raw/master/kmers.png :alt: Kmers
.. |travis| image:: https://travis-ci.org/LucaCappelletti94/fasta_one_hot_encoder.png :target: https://travis-ci.org/LucaCappelletti94/fasta_one_hot_encoder :alt: Travis CI build
.. |sonar_quality| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_fasta_one_hot_encoder&metric=alert_status :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_fasta_one_hot_encoder :alt: SonarCloud Quality
.. |sonar_maintainability| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_fasta_one_hot_encoder&metric=sqale_rating :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_fasta_one_hot_encoder :alt: SonarCloud Maintainability
.. |sonar_coverage| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_fasta_one_hot_encoder&metric=coverage :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_fasta_one_hot_encoder :alt: SonarCloud Coverage
.. |coveralls| image:: https://coveralls.io/repos/github/LucaCappelletti94/fasta_one_hot_encoder/badge.svg?branch=master :target: https://coveralls.io/github/LucaCappelletti94/fasta_one_hot_encoder?branch=master :alt: Coveralls Coverage
.. |pip| image:: https://badge.fury.io/py/fasta_one_hot_encoder.svg :target: https://badge.fury.io/py/fasta_one_hot_encoder :alt: Pypi project
.. |downloads| image:: https://pepy.tech/badge/fasta_one_hot_encoder :target: https://pepy.tech/badge/fasta_one_hot_encoder :alt: Pypi total project downloads
.. |codacy| image:: https://api.codacy.com/project/badge/Grade/b95f6c430646485c82a1f674253f4d42 :target: https://www.codacy.com/app/LucaCappelletti94/fasta_one_hot_encoder?utm_source=github.com&utm_medium=referral&utm_content=LucaCappelletti94/fasta_one_hot_encoder&utm_campaign=Badge_Grade :alt: Codacy Maintainability
.. |code_climate_maintainability| image:: https://api.codeclimate.com/v1/badges/7c5ae881132b6622be2b/maintainability :target: https://codeclimate.com/github/LucaCappelletti94/fasta_one_hot_encoder/maintainability :alt: Maintainability
.. |code_climate_coverage| image:: https://api.codeclimate.com/v1/badges/7c5ae881132b6622be2b/test_coverage :target: https://codeclimate.com/github/LucaCappelletti94/fasta_one_hot_encoder/test_coverage :alt: Code Climate Coverate
FAQs
Simple python to lazily one-hot encode fasta files using multiple processes, either single bases or considering arbitrary kmers.
We found that fasta-one-hot-encoder demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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