ganflu

Genome ANnotator for inFLUenza viruses

Usage

ganflu
usage: ganflu [-h] -i INPUT [-o OUTPUT] -t {IAV,IBV,ICV,IDV,auto} [-d DB_DIR]
              [--isolate ISOLATE] [--preserve_original_id] [--log-file LOG_FILE]
              [--verbose] [-v]

ganflu v0.1.0: Influenza virus genome annotation

options:
  -h, --help            show this help message and exit
  -i, --input INPUT     Input FASTA file
  -o, --output OUTPUT   basename for Output GenBank file name (default: <input>)
  -t, --target {IAV,IBV,ICV,IDV,auto}
                        Target virus
  -d, --db_dir DB_DIR   Data path (optional; default: ganflu/db)
  --isolate ISOLATE     isolate name (default: output stem prefix; e.g. "A/Narita/1/2009", "A/goose/Guangdong/1/1996", "B/Lee/1940", "C/Ann_Arbor/1/1950", "D/swine/Oklahoma/1334/2011")
  --preserve_original_id, --preserve-original-id
                        Preserve original FASTA record IDs in GenBank output
  --log-file LOG_FILE   Log file path (default: <output>.log; auto mode: <output>.auto.log)
  --verbose             Show debug logs in the terminal
  -v, --version         show program's version number and exit

Subcommands:
  ganflu gui              Launch the browser-based ganflu Web app
  ganflu gui --help       Show ganflu Web app options

Outputs are written using the output stem:

• <output>.gbk: GenBank annotation
• <output>.gff3: miniprot GFF3
• <output>.cds.fna: CDS nucleotide FASTA
• <output>.faa: amino acid FASTA

Auto mode

Use -t auto to scan each input contig against the packaged IAV, IBV, ICV, and IDV references, classify the best target/segment, and annotate accepted contigs by target.

ganflu -i contigs.fa -o sample -t auto

Auto mode writes target-suffixed annotation outputs plus reports:

• <output>.<target>.gbk
• <output>.<target>.gff3
• <output>.<target>.cds.fna
• <output>.<target>.faa
• <output>.auto.tsv
• <output>.auto.summary.json

Web app

The static browser app is in ganflu/web/ and runs Miniprot WebAssembly plus Pyodide without a backend server.

Launch it from the CLI:

ganflu gui

Then open the URL printed in the terminal. By default ganflu asks the OS for a free local port. Use --open-browser to ask ganflu to open the URL with the system browser.

ganflu gui # or, 
ganflu gui --port 8888 --open-browser

For source checkouts, the same static app can also be served manually:

python tools/prepare_browser_wheel.py
cd ganflu/web
python -m http.server 8765 --bind 127.0.0.1

Then open http://127.0.0.1:8765/.

For a distributable package that includes the web app assets, build in this order:

python tools/prepare_browser_wheel.py
python -m build