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Use FragGeneScanRs as gene predictor instead of FragGeneScan++ #13

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fdf03ce
Use FragGeneScanRs as gene predictor instead of FragGeneScan++
bmesuere Aug 18, 2026
9b69b99
Tell users coming from FragGeneScan++ what changed
bmesuere Aug 18, 2026
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7 changes: 4 additions & 3 deletions README.md
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Expand Up @@ -44,8 +44,9 @@ Statistics at [Ghent University].
umgap -V
```

4. (optional) Install [FragGeneScanPlusPlus] to use as gene predictor in the
pipeline.
4. (optional) Install [FragGeneScanRs] to use as gene predictor in the
pipeline, for example with `cargo install frag_gene_scan_rs`. The setup
script picks it up from your `PATH`, or you can point at it with `-f`.

5. Run [`scripts/umgap-setup.sh`](scripts/umgap-setup.sh) to interactively
configure the UMGAP and download the data files required for some steps of
Expand Down Expand Up @@ -135,6 +136,6 @@ for more info.
[Rust]: https://www.rust-lang.org/
[metagenomics casestudy]: https://unipept.ugent.be/clidocs/casestudies/metagenomics
[rust-install]: https://www.rust-lang.org/tools/install
[FragGeneScanPlusPlus]: https://github.com/unipept/FragGeneScanPlusPlus
[FragGeneScanRs]: https://github.com/unipept/FragGeneScanRs
[EditorConfig]: https://editorconfig.org/
[RustFMT]: https://github.com/rust-lang/rustfmt
36 changes: 20 additions & 16 deletions scripts/umgap-analyse.sh
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Expand Up @@ -115,7 +115,7 @@ fi
debug "parsing the arguments"

count=0
fgspp_used="false"
fgs_used="false"
tryptic_used="false"
ninemer_used="false"
samples=""
Expand All @@ -142,10 +142,10 @@ while getopts c:1:2:t:zo: f; do
case "$type" in
"max-sensitivity") ninemer_used="true" ;;
"high-sensitivity") ninemer_used="true" ;;
"tryptic-sensitivity") fgspp_used="true" ; tryptic_used="true" ;;
"tryptic-precision") fgspp_used="true" ; tryptic_used="true" ;;
"high-precision") fgspp_used="true" ; ninemer_used="true" ;;
"max-precision") fgspp_used="true" ; ninemer_used="true" ;;
"tryptic-sensitivity") fgs_used="true" ; tryptic_used="true" ;;
"tryptic-precision") fgs_used="true" ; tryptic_used="true" ;;
"high-precision") fgs_used="true" ; ninemer_used="true" ;;
"max-precision") fgs_used="true" ; ninemer_used="true" ;;
*) crash "Unrecognized type: '$type'."
esac
log "- Using '$type'."
Expand Down Expand Up @@ -223,10 +223,15 @@ fi
# Environmental checks.
# =========================================================================== #

if [ "$fgspp_used" = "true" ]; then
debug "checking if FGSpp is installed"
if ! [ -h "$(getconfigdir)/FGSpp" ]; then
crash "FragGeneScan++ not found. Please run umgap-setup."
if [ "$fgs_used" = "true" ]; then
debug "checking if FragGeneScanRs is installed"
if ! [ -h "$(getconfigdir)/FragGeneScanRs" ]; then
if [ -h "$(getconfigdir)/FGSpp" ]; then
crash "This configuration still points at FragGeneScan++, which UMGAP no longer
uses. Install FragGeneScanRs (https://github.com/unipept/FragGeneScanRs) and run
umgap-setup again."
fi
crash "FragGeneScanRs not found. Please run umgap-setup."
fi
fi

Expand All @@ -245,9 +250,8 @@ debug "using version '$version'"
# The actual pipeline
# =========================================================================== #

fgspp() {
"$(getconfigdir)/FGSpp/FGSpp" -s stdin -o stdout -w 0 \
-r "$(getconfigdir)/FGSpp/train" -t "illumina_10" -p 4 -c 2
fgs() {
"$(getconfigdir)/FragGeneScanRs" -s stdin -o stdout -w 0 -t "illumina_10" -p 4
}

taxons="$(getconfigdir)/$version/taxons.tsv"
Expand Down Expand Up @@ -287,23 +291,23 @@ while [ -n "${samples}" ]; do
umgap uniq -d / | # join paired ends
umgap taxa2agg -l1 -a hybrid -f 0.25 "$taxons";; # aggregate
"tryptic-sensitivity")
fgspp | # gene prediction
fgs | # gene prediction
umgap prot2tryp2lca -l9 -L45 "$tryptics" | # map to taxa
umgap uniq -d / | # join paired ends
umgap taxa2agg -l1 -m rmq -a mrtl "$taxons" ;; # aggregate
"tryptic-precision")
fgspp | # gene prediction
fgs | # gene prediction
umgap prot2tryp2lca -l9 -L45 "$tryptics" | # map to taxa
umgap uniq -d / | # join paired ends
umgap taxa2agg -l5 -m rmq -a mrtl "$taxons" ;; # aggregate
"high-precision")
fgspp | # gene prediction
fgs | # gene prediction
nc -NU "$socket" | # map to taxa
umgap seedextend -g1 -s3 | # seedextend filter
umgap uniq -d / | # join paired ends
umgap taxa2agg -l2 -a lca\* "$taxons" ;; # aggregate
"max-precision")
fgspp | # gene prediction
fgs | # gene prediction
nc -NU "$socket" | # map to taxa
umgap seedextend -g1 -s4 | # seedextend filter
umgap uniq -d / | # join paired ends
Expand Down
55 changes: 40 additions & 15 deletions scripts/umgap-setup.sh
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Expand Up @@ -57,8 +57,8 @@ Usage: $0 [options]

Options:
-c dir The configuration directory. Defaults to '$config_default'.
-f dir Directory containing the FragGeneScan++ binary (FGSpp) and
training data.
-f path The FragGeneScanRs binary, or a directory containing it. Defaults
to the FragGeneScanRs on your PATH.
-d dir The data directory. The database files will be downloaded here.
Defaults to '$data_default'.
-y Download all files of the latest version without asking.
Expand All @@ -67,7 +67,7 @@ Options:
while getopts c:f:d:y f; do
case "$f" in
c) configdir="$OPTARG" ;;
f) fgsppdir="$OPTARG" ;;
f) fgsrsbin="$OPTARG" ;;
d) datadir="$OPTARG" ;;
y) download_all="true" ;;
\?) crash "$USAGE" ;;
Expand All @@ -93,22 +93,47 @@ if [ ! -d "$configdir" ]; then
fi
fi

# If FGSpp is found and works, link it in the config directory.
if [ -z "$fgsppdir" ]; then
if ! yesno 'FragGeneScan++ (-f) was not provided, only pipelines not using it will be available.'; then
crash 'Pass the location of FragGeneScan++ with -f.'
# Point people coming from the old FragGeneScan++ setup at the change, rather
# than letting them fail the check below with a confusing message.
case "$fgsrsbin" in
*/FGSpp|FGSpp) oldfgs="$fgsrsbin" ;;
esac
if [ -d "$fgsrsbin" ] && [ -x "$fgsrsbin/FGSpp" ] && [ ! -x "$fgsrsbin/FragGeneScanRs" ]; then
oldfgs="$fgsrsbin/FGSpp"
fi
if [ -n "$oldfgs" ]; then
crash "'$oldfgs' is a FragGeneScan++ installation. UMGAP now uses FragGeneScanRs
instead, which is a single binary and carries its own training data. Install it, for
example with 'cargo install frag_gene_scan_rs', then either put it on your PATH or
pass it with -f. See https://github.com/unipept/FragGeneScanRs."
fi

# If FragGeneScanRs is found and works, link it in the config directory.
if [ -d "$fgsrsbin" ]; then
fgsrsbin="$fgsrsbin/FragGeneScanRs"
fi
if [ -z "$fgsrsbin" ]; then
fgsrsbin="$(command -v FragGeneScanRs || true)"
fi
if [ -z "$fgsrsbin" ]; then
if ! yesno 'FragGeneScanRs was not found, only pipelines not using it will be available.'; then
crash 'Install FragGeneScanRs, or pass its location with -f.'
fi
else
cd "$fgsppdir"
if ! printf '>a\nA' | ./FGSpp -s stdin -o stdout -w 0 -t illumina_10 -c 240 > /dev/null; then
crash 'Invoking FGSpp failed, follow installation instructions at https://github.com/unipept/FragGeneScanPlusPlus.'
# A real read, so this checks that a prediction actually comes out, not just
# that the binary starts. FragGeneScanRs also panics on input too short to
# hold a codon, so a placeholder sequence is not usable here.
testread='ATCGCGCACGCGGCCGATGCCCCAGAAGAGATTGACAGCGGTGGGGCGGGCGGCGGCGAGGTGGTCGCAGATCTCGGCGACCTCTGCGTTGAGGGTCGGG'
if ! printf '>a\n%s\n' "$testread" \
| "$fgsrsbin" -s stdin -o stdout -w 0 -t illumina_10 \
| grep -q '^[A-Z]'; then
crash 'Invoking FragGeneScanRs failed, follow installation instructions at https://github.com/unipept/FragGeneScanRs.'
fi
fgsppdir="$(pwd -P)" # make path absolute
cd - > /dev/null
if ln -f -s "$fgsppdir" "$configdir/FGSpp"; then
echo 'Found, tested and remembered the FragGeneScan++ location.'
fgsrsbin="$(cd "$(dirname "$fgsrsbin")" && pwd -P)/$(basename "$fgsrsbin")" # absolute
if ln -f -s "$fgsrsbin" "$configdir/FragGeneScanRs"; then
echo 'Found, tested and remembered the FragGeneScanRs location.'
else
crash 'Could not link the FragGeneScan++ location.'
crash 'Could not link the FragGeneScanRs location.'
fi
fi

Expand Down
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