aandradebio / getTax

A simple way to retrieve taxonomic information for protein sequences using NCBI's Entrez Utilities.

Taxonomic Information Retrieval Scripts

These scripts are designed to retrieve taxonomic information for protein sequences using NCBI's Entrez Utilities.

Prerequisites

Before running the scripts, ensure that you have the following dependencies installed:

• esearch
• efetch
• xtract

Usage

getTax.sh

Description

The getTax.sh script retrieves taxonomic information for a given protein sequence accession number.

Usage

./getTax.sh [ACCESSION_NUMBER]

Replace [ACCESSION_NUMBER] with the desired protein sequence accession number.

Example:

./getTax.sh AAA46477.1

An easy way to get taxonomy info for multiple accession numbers would be creating a run.sh file.

Usage Example

To process multiple accession numbers, you can use the run.sh script:

run.sh

Description

The run.sh script processes a list of protein sequence accession numbers using the getTax.sh script.

Usage

1. Update run.sh with the desired accession numbers.
2. Execute run.sh.

Example

#!/usr/bin/bash

./getTax.sh AAA46477.1 &
./getTax.sh AAC55975.1 &
./getTax.sh AAD02414.1 &
./getTax.sh AAD47817.1 &
./getTax.sh AAF29594.1 &
./getTax.sh AAF29595.1 &
./getTax.sh AAF80604.1 &
./getTax.sh AAH69831.1 &
wait

The run.sh script can be created based on a file containing multiple accession numbers or you could use:

while read acc; do ./getTax.sh ${acc}; done < accession_numbers.txt

Author

Amanda Araújo Serrão de Andrade [e-mail]

Feel free to contact me, open an issue, or a pull request.