This script is a Python program that extracts sequences from a FASTA file that belong to a specific taxon and writes them to a new file. It also generates a summary file containing the count and names of the sequences that were extracted. The script accepts command-line arguments for the input file, output file, summary file, and target taxon. The script also includes error handling to provide helpful messages in case of incorrect arguments or other errors.

The primary aim of this script is to extract sequences belonging to a specific taxon from large FASTA databases, which is a crucial step in preparing data for phylogenetic placement. High-quality and accurate phylogenetic analyses require well-curated reference sequence databases. Manually curating these databases ensures the selection of relevant and known sequences, yielding higher-quality results for specific projects. In many cases, the process of selecting sequences for phylogenetic placement is labor-intensive, as it involves manually hand-picking sequences from reference databases such as SILVA, NCBI, Greengenes, or RDP. Despite the manual effort required, this approach often results in the highest-quality curated datasets, which are critical for building reliable reference sets (RSs) tailored to the needs of a given project. This script is designed to automate part of the curation process by efficiently filtering sequences based on taxonomic assignments, thereby reducing the manual burden while maintaining the integrity of the reference data for accurate downstream phylogenetic analyses. For further information, refer to #Czech et al. 2022.

python extract_specific_taxa_sequences.py -f <input_fasta_file> -o <output_fasta_file> -s <summary_file> -t <target_taxon>

To extract sequences for the genus Pseudomonas from "fasta_db.fasta", and write them to output_Pseudomonas.fasta with a summary in summary.txt, run:

python extract_specific_taxa_sequences.py -f fasta_db.fasta -o output_Pseudomonas.fasta -s summary.txt -t Pseudomonas

Note: The fasta_db.fasta file could be a FASTA database containing 16S rRNA full-length sequences from widely used resources such as SILVA or Greengenes.

optional arguments:
 -h, --help show this help message and exit
 -f INPUT_FILE, --input_file INPUT_FILE
 Path to the input FASTA file containing sequences with taxonomic information in headers.
 -o OUTPUT_FILE, --output_file OUTPUT_FILE
 Path to the output file where sequences of the specified taxon will be written.
 -s SUMMARY_FILE, --summary_file SUMMARY_FILE
 Path to the summary file where the count and names of the sequences will be written.
 -t TARGET_TAXON, --target_taxon TARGET_TAXON
 The taxon to search for in the headers of the input sequences.

Czech, L., Stamatakis, A., Dunthorn, M., & Barbera, P. (2022). Metagenomic analysis using phylogenetic placement—a review of the first decade. Frontiers in Bioinformatics, 2, 871393.

Script created by Georgios Leventis

DOI