https://github.com/vaibhavvikas/fasta-sequence-retrieval
Python Project to extract the amino acid sequences using the nucleotides accession numbers retrieved from the NCBI.
https://github.com/vaibhavvikas/fasta-sequence-retrieval
fasta ncbi
Last synced: over 1 year ago
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Python Project to extract the amino acid sequences using the nucleotides accession numbers retrieved from the NCBI.
- Host: GitHub
- URL: https://github.com/vaibhavvikas/fasta-sequence-retrieval
- Owner: vaibhavvikas
- License: bsd-3-clause
- Created: 2022-10-14T16:41:40.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2022-10-20T17:39:50.000Z (over 3 years ago)
- Last Synced: 2025-01-09T01:06:06.901Z (over 1 year ago)
- Topics: fasta, ncbi
- Language: Python
- Homepage: https://vaibhavvikas.github.io/fasta-sequence-retrieval/
- Size: 7.37 MB
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Authors: AUTHORS.md
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README
## fasta_sequence_retrieval
Python Project to extract the amino acid sequences using the nucleotide accession numbers retrieved from the NCBI. Sample results in `output` directory.
## Features
* Retrieval of the amino acids sequences, along with various details such as locus, definition, organism, host, country, collection_date, protein_id from the NCBI.
* Put the files inside `data` directory.
- If only accession numbers are there in your files, put it inside data directly.
- If your files contain the accession numbers with their sequences similar to the one in `sequence` directory, put that files inside the `sequence` directory.
Note: File names do not matter.
## Project Setup
1. Install python version >= 3.9
2. Clone the repository.
3. Open cmd/terminal and run the following command to install dependencies `pip install -e .`
4. Your output will be generated inside the output directory. Please test with small numbers of seq first to make sure you're getting what is expected.
## Credits
This package was created with Cookiecutter_ and the `vaibhavvikas/cookiecutter-pypackage` project template.
* [Cookiecutter](https://github.com/audreyr/cookiecutter)
* [vaibhavvikas/cookiecutter-pypackage](https://github.com/vaibhavvikas/cookiecutter-pypackage)