vervet
Generates a fasta file from an image containing genbank accession numbers (e.g. phylogenetic trees)
Science Score: 57.0%
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○Scientific vocabulary similarity
Low similarity (8.8%) to scientific vocabulary
Repository
Generates a fasta file from an image containing genbank accession numbers (e.g. phylogenetic trees)
Basic Info
- Host: GitHub
- Owner: GmoreiraVet
- Language: Python
- Default Branch: main
- Size: 102 KB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
Image to GenBank FASTA Downloader
Vervet extracts accession numbers from an image using Optical Character Recognition (OCR) with EasyOCR, validates them, and then fetches the corresponding sequences from GenBank. It saves the sequences to a FASTA file.
Features:
- Extracts text from an image (e.g.,
.jpg,.png) containing accession numbers. - Uses EasyOCR to perform OCR and extract accession numbers.
- Validates accession numbers to check if they exist in GenBank.
- Substitutes commonly misinterpreted characters when a candidate accession number doesn´t exist in genbank
- Fetches the corresponding sequences from GenBank using the Biopython library.
- Saves the fetched sequences in a FASTA format file.
Dependencies
- Python 3.x: Ensure you have Python 3 installed on your machine.
- EasyOCR: For extracting text (accession numbers) from images using OCR.
- Biopython: For interacting with GenBank and fetching sequences.
- Requests: For handling HTTP requests to GenBank.
- Pillow: For image processing.
You can install these dependencies by running the following command:
bash
pip install easyocr biopython requests pillow
Citation
If you use this code in your work, please cite it using the following information:
cff-version: 1.2.0
message: "If you use this code in your work, please cite it using the following information."
authors:
- name: "Guilherme Moreira"
orcid: "https://orcid.org/0009-0002-2828-7202"
affiliation: "ICBAS - Instituto de Ciências Biomédicas Abel Salazar"
title: "Lumberjack"
version: "1.0.0"
doi: "https://doi.org/10.5281/zenodo.14850245"
date-released: 2025-02-11
repository: "https://github.com/GmoreiraVet/Lumberjack"
The DOI for citing this work is: 10.5281/zenodo.14850245.
Owner
- Login: GmoreiraVet
- Kind: user
- Repositories: 1
- Profile: https://github.com/GmoreiraVet
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this code in your work, please cite it using the following information."
authors:
- name: "Guilherme Moreira"
orcid: "https://orcid.org/0009-0002-2828-7202"
affiliation: "ICBAS - Instituto de Ciências Biomédicas Abel Salazar"
title: "Lumberjack"
version: "1.0.0"
doi: "https://doi.org/10.5281/zenodo.14850245"
date-released: 2025-02-11
repository: "https://github.com/GmoreiraVet/Lumberjack"
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