Taxonomy_Fasta_Headers

Overview:

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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.
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Motivation

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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.
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Authorship:

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

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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/>.
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Script_Version:

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v1.0.1
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Script_Logic:

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Code_Overview
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Script_Usage:

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Mini_Tutorial
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Script_Flags:

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FLAG:           "-f", "--fasta"
REQUIRED:       "Yes"
FORMAT:         "Alphanumeric String"
DEFAULT:        "No default"
HELP:           "Path to the FASTA file to process."
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FLAG:           "-d", "--database"
REQUIRED:       "Yes"
FORMAT:         "Alphanumeric String"
CHOICES:        "NCBI", "UNIREF", "ENSEMBL", "GENCODE"
DEFAULT:        "No default"
HELP:           "The database from which the FASTA file originates."
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FLAG:           "-t", "--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."
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FLAG:           "-o", "--output"
REQUIRED:       "No"
FORMAT:         "Alphanumeric"
DEFAULT:        "Transcripts_Plots_dir_Run01"
HELP:           "Output directory name."
                "If provided and exists, a numeric suffix is added (e.g., Test01)"
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FLAG:           "-v", "--version"
REQUIRED:       "No"
ACTION:         "version"
FORMAT:         "Alphanumeric"
HELP:           "Show program version's number and exit"
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Dependencies:

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Python3:        Required:
                    https://www.python.org/downloads/
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Development/Testing Environment:

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Distributor ID: Apple, Inc.
Description:    Apple M1 Max
Release:        15.3.1
Codename:       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  |
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Repository:

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https://github.com/raramayo/Taxonomy_Fasta_Headers_Python
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Issues:

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https://github.com/raramayo/Taxonomy_Fasta_Headers_Python/issues
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