flusort

Description

Influenza segment annotation and cleaning script for Pekosz Lab Influenza Surveillance. The current release is targed towards maintainers of influenza genome sequences received from Dr. Heba Mostafa's team. flusort is comprised of 2 python scripts designed to perform BLAST searches on FASTA sequences and append subtype information to their headers based on the BLAST results. It also groups sequences based on their subtype and completeness, providing a summary of the input sequences.

flusort accepts multifasta files containing H1, H3 and IBV (tested on B/Victoria) segment sequences with a strict header following >XXXXXXX_Segment# example: JH11111_1 which would be Sample JH11111 segment 1 (PB2).

The resulting files included a fasta file with appended headers to identify the flu type and subtype with additional information which can be piped directly into augur parse and augur filter.

Dependencies

1. flusort is written in python v3.X.X and requires biopython (validated on v1.83) and numpy (validated on v1.23.4).

2. ⚠️ The current build of flusort requires BLAST 2.13.0+ CLI to be accesible via your global $PATH. Please download and test your local blast installation with blastn -h prior to running. By default, pyflute.py will search for the blastn databse in the "scripts" directory unless specified by the -df flag.

Dependency installation using pip

pip install biopython numpy

Arguments

flusort.py

• -i, --input_file: Path to the input FASTA file. (Required)
• -db, --blast_db: Path to the custom BLAST database file. (Optional)
• -o, --output_directory: Path to the output directory. Defaults to 'flusort_out' in the script's directory. (Optional)

Output

• output.fasta: Filtered sequences written to a single file if not split.
• segment_{segment_number}_sorted.fasta: Filtered sequences for each segment written to separate files if the split flag is used (-s, --split).

Example Usage

first running flusort.py

python flusort.py -i ./example_input/flusort_example.fasta

All outputfiles will be directory named flusort_output will be created unless specified.

Changelog

2024-06-26

• Depreciated flusory_split.py.
• Specification of header metadata delimiters.
• Appended headers now compatible with augur parse:
  • sequence_id_segment_number
  • sequence_id
  • segment_number
  • virus_type_suffix
  • subtype
  • completeness

Feature Roadmap

Reassortment Data Cleaning

A balance.py script which leverages not only the presence of complete genomes, but coverage and fasta quality to clean datasets appropriate for concatenated genome and reassortment analysis.