fetch that

A tool to fetch protein and nucleotide sequences using Entrez from Biopython

Image created using DALL-E

Requirements

• Python 3.12.1
• tqdm

Installation

1. Clone the repository to your local machine:

   git clone https://github.com/DEHourigan/fetch-that.git

2. Navigate to the cloned directory:

   cd fetch-that

3. Install the required dependencies:

   conda env create -f fetchthat.yml
   conda activate fetchthat

Usage

python fetchthat.py --infile test_data/protein_acc.txt --db prot --email   [email here] --outfile test_data/out.faa

1. Prepare your data:
   • input is a text file with 1 accession per line

Output

fasta file containing desired sequences

Contributing

DEHourigan

Contact

For any queries, please reach out via GitHub issues or directly to [email protected].

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