Taxonomy_Fasta_Headers

Overview:

The Taxonomy_Fasta_Headers script is designed to reformat FASTA file headers according to the source database and taxonomy information. FASTA files can originate from various databases such as NCBI, UniRef, ENSEMBL, and Gencode, each with its own header format. This script automates the process of standardizing these headers by:

• NCBI:

  Extracting the organism’s taxonomy from the last square-bracketed segment (e.g., [Homo sapiens]), converting spaces to underscores (resulting in Homo_sapiens), and prefixing it to the header.

• UniRef:

  Locating the TaxID value within the header and prefixing the header with TaxID_<number>: where <number> is the extracted TaxID.

• ENSEMBL and Gencode:

  Requiring the user to provide taxonomy information via a flag. The provided taxonomy is then prepended to the header.

The script carefully processes only the header lines (lines starting with >), leaving the sequence data completely untouched. Additionally, it performs essential validations such as ensuring the input file exists, confirming the file is in FASTA format, and enforcing proper flag usage based on the selected database.

Motivation:

Computational genomics encompasses the searching, clustering, comparison, and evaluation of vast numbers of sequences from a diverse array of organisms.

Although individual transcriptome and proteome sequences are typically assigned unique identifiers, prepending each identifier with its corresponding taxonomy information significantly enhances the clarity and interpretability of computational outputs. By incorporating taxonomy data directly into sequence headers, researchers can more easily trace the organismal origin of each sequence, thereby streamlining downstream analyses and improving overall data integration.

Authorship:

• Author: Rodolfo Aramayo
• Work_Email: raramayo@tamu.edu
• Personal_Email: rodolfo@aramayo.org

Copyright:

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.

Version:

• v1.0.2

Code_Overview:

Code_Overview.md

Usage:

Mini_Tutorial.md

Flags:

--------------------------------------------------------------------------------
FLAG:           "--fasta"
REQUIRED:       Yes
FORMAT:         Alphanumeric String
DEFAULT:        No default
HELP:           Path to the FASTA file to process
--------------------------------------------------------------------------------
FLAG:           "--database"
REQUIRED:       Yes
FORMAT:         Alphanumeric String
CHOICES:        'NCBI', 'UNIREF', 'ENSEMBL', 'GENCODE'
DEFAULT:        No default
HELP:           The database from which the FASTA file originates
--------------------------------------------------------------------------------
FLAG:           "--taxonomy"
REQUIRED:       Yes
FORMAT:         Alphanumeric String
DEFAULT:        No default
HELP:           Genus_Species information (e.g., 'Homo_sapiens')
                Required for ENSEMBL and Gencode files
                Must not be provided for NCBI or UniRef files
--------------------------------------------------------------------------------
FLAG:           "--output"
REQUIRED:       No
FORMAT:         Alphanumeric
DEFAULT:        No default
HELP:           Output file path or directory
                If a directory is provided, the output file will be named
                based on the input file with '_Tax_Headers.fa' appended
--------------------------------------------------------------------------------
FLAG:           "-v", "--version"
REQUIRED:       No
ACTION:         version
FORMAT:         Alphanumeric
HELP:           Show program version's number and exit
--------------------------------------------------------------------------------
FLAG:           "-h", "--help"
REQUIRED:       No
ACTION:         help
FORMAT:         Alphanumeric String
HELP:           show this help message and exit
--------------------------------------------------------------------------------

Dependencies:

Name	URL
Python3	https://www.python.org/downloads/

Development/Testing Environment:

Distributor ID	Description	Release	Codename
Apple, Inc.	Apple M1 Max	15.3.1	Sequoia

• Script was tested with:

Python Version	matplotlib	pandas	seaborn
3.8.20	3.7.5	2.0.3	0.13.2
3.9.21	3.9.4	2.2.3	0.13.2
3.10.16	3.10.1	2.2.3	0.13.2
3.11.11	3.10.1	2.2.3	0.13.2
3.12.9	3.10.1	2.2.3	0.13.2
3.13.2	3.10.1	2.2.3	0.13.2

Repository:

Taxonomy_Fasta_Headers_Python

Issues:

Taxonomy_Fasta_Headers_Python_Issues

Citation:

@misc{RN166,
   author = {Aramayo, Rodolfo},
   title = {Taxonomy_Fasta_Headers_Python},
   publisher = {CERN Data Centre & InvenioRDM},
   month = {2025-04-14},
   keywords = {Bioinformatics
comparative genomics
ensembl
gene annotation
genome annotation
genome browsers},
   DOI = {10.5281/zenodo.15216319},
   url = {https://doi.org/10.5281/zenodo.15216319},
   year = {2025},
   type = {Dataset}
}