prform 0.2.0__tar.gz

prform-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Khoa Hoang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

prform-0.2.0/MANIFEST.in

@@ -0,0 +1,6 @@
+include README.md
+include LICENSE
+include pyproject.toml
+recursive-include prform/_data *
+# Superseded artifacts kept in-repo for reproducibility, not shipped.
+prune prform/_data/legacy

prform-0.2.0/PKG-INFO

@@ -0,0 +1,222 @@
+Metadata-Version: 2.4
+Name: prform
+Version: 0.2.0
+Summary: Predict programmed ribosomal frameshift (PRF) sites in RNA sequences.
+Author-email: Khoa Hoang <khoang99@stanford.edu>
+License: MIT
+Project-URL: Homepage, https://github.com/khoa-yelo/PRForm
+Project-URL: Issues, https://github.com/khoa-yelo/PRForm/issues
+Keywords: bioinformatics,rna,ribosomal-frameshift,deep-learning
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch>=2.0
+Requires-Dist: numpy>=1.22
+Requires-Dist: scipy>=1.9
+Requires-Dist: scikit-learn>=1.1
+Requires-Dist: joblib>=1.2
+Requires-Dist: h5py>=3.7
+Provides-Extra: dev
+Requires-Dist: pytest>=7; extra == "dev"
+Dynamic: license-file
+
+# PRForm
+
+Predict programmed ribosomal frameshift (PRF) sites in Viral genomes.
+
+`prform` is a deep-learning tool that scores every nucleotide in viral genome
+sequence for the probability that a -1 or +1 frameshift event occurs there.
+Predictions come from a 1D residual network with a 10 kb receptive
+field.
+
+The model was trained on NCBI ~50,000 deduplicated viral genomes (as of Feb 2026). Trained model checkpoint and calibrator are bundled with the package and ready to run.
+
+## Install
+
+From PyPI:
+
+```bash
+pip install prform
+```
+
+From bioconda:
+
+```bash
+conda install -c bioconda prform
+```
+
+From source (development):
+
+```bash
+git clone https://github.com/khoa-yelo/PRForm.git
+cd PRForm/prform_pkg
+pip install -e .[dev]
+```
+
+## Usage
+
+```bash
+prform predict input.fasta --outdir results/
+```
+
+(equivalent: `python -m prform predict ...` — useful when `~/.local/bin`
+isn't on your `PATH`.)
+
+Writes two files into `results/`:
+
+- `predictions.csv` — one row per FASTA record: the top-k predicted peak
+  positions with their calibrated PRF probability and frameshift type
+  (-1 PRF, +1 PRF, or no frameshift detected).
+- `predictions.h5` — full per-nucleotide calibrated probability tracks.
+
+`predictions.h5` layout:
+
+```
+records/
+    accession_id     (R,) str
+    length           (R,) int
+    top{k}_pos       (R,) int      # k = 1..top_k, 1-based; -1 if no peak
+    top{k}_prob      (R,) float32
+    top{k}_type      (R,) int8     # -1 PRF, +1 PRF, or 0 = no frameshift detected
+per_nucleotide/
+    {accession_id}/                # one group per FASTA record
+        no_PRF_prob      (L,) float32
+        minus1_PRF_prob  (L,) float32
+        plus1_PRF_prob   (L,) float32
+```
+
+With `--both-strands` each orientation gets its own block — `fwd_`/`rev_`
+column and dataset prefixes, and `fwd`/`rev` per-nucleotide subgroups — see
+[Scoring both strands](#scoring-both-strands).
+
+Read a record's per-nucleotide tracks in Python:
+
+```python
+import h5py
+with h5py.File("results/predictions.h5") as f:
+    for acc in f["records/accession_id"].asstr()[:]:
+        g = f[f"per_nucleotide/{acc}"]
+        minus1 = g["minus1_PRF_prob"][:]
+        plus1  = g["plus1_PRF_prob"][:]
+        prf_track = minus1 + plus1
+```
+
+## Scoring both strands
+
+PRForm is a **directional** detector: it only sees a frameshift in the
+orientation it is given. A PRF encoded on the minus strand of your input is
+invisible on a forward-only pass. Pass `--both-strands` to score each record in
+both orientations:
+
+```bash
+prform predict genomes.fasta --outdir results/ --both-strands
+```
+
+**Both orientations are reported.** The peaks and tracks are duplicated into a
+forward block and a reverse block:
+
+```
+predictions.csv
+    accession_id, length,
+    fwd_top{k}_pos, fwd_top{k}_prob, fwd_top{k}_type,
+    rev_top{k}_pos, rev_top{k}_prob, rev_top{k}_type
+
+predictions.h5
+    records/                       # same fwd_/rev_ prefixes as the CSV
+        accession_id, length,
+        fwd_top{k}_{pos,prob,type}, rev_top{k}_{pos,prob,type}
+    per_nucleotide/
+        {accession_id}/
+            fwd/  no_PRF_prob, minus1_PRF_prob, plus1_PRF_prob   (L,) each
+            rev/  no_PRF_prob, minus1_PRF_prob, plus1_PRF_prob   (L,) each
+```
+
+The reverse block is mirrored back into **forward-genome coordinates**, so both
+blocks index the same nucleotide: `fwd_top1_pos`, `rev_top1_pos` and index `i`
+of either track all refer to position `i+1` of the sequence as you supplied it.
+Class channels are *not* swapped — a -1 PRF read on the reverse complement
+stays in `minus1_PRF_prob`, because the shift direction is defined relative to
+the strand being read.
+
+## Test the install
+
+`prform` ships with small FASTA fixtures (one folder per labeled
+frameshift class) so you can verify the install end-to-end without any
+external data. Copy them into your working directory:
+
+```bash
+prform download-examples ./prform_examples
+```
+
+Layout after download:
+
+```
+prform_examples/
+    plus1_PRF/    influenza_pax.fasta
+    minus1_PRF/   coronavirus_khosta2.fasta, phage_tyson.fasta
+    no_PRF/       monkeypox, ledantevirus, nanovirus, ourmiavirus, orbivirus
+```
+
+Run `predict` on each class:
+
+```bash
+# +1 PRF: peak should land near the labeled site
+prform predict prform_examples/plus1_PRF/influenza_pax.fasta \
+    --outdir prform_test/plus1
+
+# -1 PRF: peak should land near the labeled site
+prform predict prform_examples/minus1_PRF/coronavirus_khosta2.fasta \
+    --outdir prform_test/minus1
+
+# no PRF: no frameshift should be called
+prform predict prform_examples/no_PRF/nanovirus.fasta \
+    --outdir prform_test/no_prf
+
+cat prform_test/plus1/predictions.csv
+cat prform_test/minus1/predictions.csv
+cat prform_test/no_prf/predictions.csv
+```
+
+Expected behavior:
+
+| fixture | labeled site | what to look for |
+| --- | --- | --- |
+| `plus1_PRF/influenza_pax.fasta`        | +1 PRF @ pos 582   | `top1_pos` within a few nt of 582,  `top1_type == 1` |
+| `minus1_PRF/coronavirus_khosta2.fasta` | -1 PRF @ pos 13248 | `top1_pos` near 13248,              `top1_type == -1` |
+| `minus1_PRF/phage_tyson.fasta`         | -1 PRF @ pos 10279 | `top1_pos` near 10279,              `top1_type == -1` |
+| `no_PRF/*.fasta`                       | none               | `top1_type == 0` (no frameshift called) |
+
+Each labeled-positive FASTA header carries the labeled site for easy comparison.
+
+## Python API
+
+```python
+from prform import PRFormPredictor
+
+predictor = PRFormPredictor()                      # loads bundled weights
+results = predictor.predict_fasta("input.fasta")   # list of dicts
+# or
+results = predictor.predict_sequences([("rec1", "ACGT" * 1000)])
+# score both orientations, keep the better strand per record
+results = predictor.predict_fasta("input.fasta", both_strands=True)
+```
+
+Each result entry has `accession_id`, `length`, `strand`, `cal_probs_3`
+(3, L) and a `top` list of peak summaries (`pos`, `prob`, `type`) — all from
+the winning strand. With `both_strands=True`, `rec["fwd"]` and `rec["rev"]`
+each hold that orientation's own `cal_probs_3` and `top`, both in
+forward-genome coordinates; otherwise they are `None`.
+
+## Hardware
+
+CPU works. GPU is faster — `prform` automatically uses CUDA when available.
+For long sequences (>1 Mb total input) a GPU is recommended.
+
+## License
+
+MIT

prform-0.2.0/README.md

@@ -0,0 +1,195 @@
+# PRForm
+
+Predict programmed ribosomal frameshift (PRF) sites in Viral genomes.
+
+`prform` is a deep-learning tool that scores every nucleotide in viral genome
+sequence for the probability that a -1 or +1 frameshift event occurs there.
+Predictions come from a 1D residual network with a 10 kb receptive
+field.
+
+The model was trained on NCBI ~50,000 deduplicated viral genomes (as of Feb 2026). Trained model checkpoint and calibrator are bundled with the package and ready to run.
+
+## Install
+
+From PyPI:
+
+```bash
+pip install prform
+```
+
+From bioconda:
+
+```bash
+conda install -c bioconda prform
+```
+
+From source (development):
+
+```bash
+git clone https://github.com/khoa-yelo/PRForm.git
+cd PRForm/prform_pkg
+pip install -e .[dev]
+```
+
+## Usage
+
+```bash
+prform predict input.fasta --outdir results/
+```
+
+(equivalent: `python -m prform predict ...` — useful when `~/.local/bin`
+isn't on your `PATH`.)
+
+Writes two files into `results/`:
+
+- `predictions.csv` — one row per FASTA record: the top-k predicted peak
+  positions with their calibrated PRF probability and frameshift type
+  (-1 PRF, +1 PRF, or no frameshift detected).
+- `predictions.h5` — full per-nucleotide calibrated probability tracks.
+
+`predictions.h5` layout:
+
+```
+records/
+    accession_id     (R,) str
+    length           (R,) int
+    top{k}_pos       (R,) int      # k = 1..top_k, 1-based; -1 if no peak
+    top{k}_prob      (R,) float32
+    top{k}_type      (R,) int8     # -1 PRF, +1 PRF, or 0 = no frameshift detected
+per_nucleotide/
+    {accession_id}/                # one group per FASTA record
+        no_PRF_prob      (L,) float32
+        minus1_PRF_prob  (L,) float32
+        plus1_PRF_prob   (L,) float32
+```
+
+With `--both-strands` each orientation gets its own block — `fwd_`/`rev_`
+column and dataset prefixes, and `fwd`/`rev` per-nucleotide subgroups — see
+[Scoring both strands](#scoring-both-strands).
+
+Read a record's per-nucleotide tracks in Python:
+
+```python
+import h5py
+with h5py.File("results/predictions.h5") as f:
+    for acc in f["records/accession_id"].asstr()[:]:
+        g = f[f"per_nucleotide/{acc}"]
+        minus1 = g["minus1_PRF_prob"][:]
+        plus1  = g["plus1_PRF_prob"][:]
+        prf_track = minus1 + plus1
+```
+
+## Scoring both strands
+
+PRForm is a **directional** detector: it only sees a frameshift in the
+orientation it is given. A PRF encoded on the minus strand of your input is
+invisible on a forward-only pass. Pass `--both-strands` to score each record in
+both orientations:
+
+```bash
+prform predict genomes.fasta --outdir results/ --both-strands
+```
+
+**Both orientations are reported.** The peaks and tracks are duplicated into a
+forward block and a reverse block:
+
+```
+predictions.csv
+    accession_id, length,
+    fwd_top{k}_pos, fwd_top{k}_prob, fwd_top{k}_type,
+    rev_top{k}_pos, rev_top{k}_prob, rev_top{k}_type
+
+predictions.h5
+    records/                       # same fwd_/rev_ prefixes as the CSV
+        accession_id, length,
+        fwd_top{k}_{pos,prob,type}, rev_top{k}_{pos,prob,type}
+    per_nucleotide/
+        {accession_id}/
+            fwd/  no_PRF_prob, minus1_PRF_prob, plus1_PRF_prob   (L,) each
+            rev/  no_PRF_prob, minus1_PRF_prob, plus1_PRF_prob   (L,) each
+```
+
+The reverse block is mirrored back into **forward-genome coordinates**, so both
+blocks index the same nucleotide: `fwd_top1_pos`, `rev_top1_pos` and index `i`
+of either track all refer to position `i+1` of the sequence as you supplied it.
+Class channels are *not* swapped — a -1 PRF read on the reverse complement
+stays in `minus1_PRF_prob`, because the shift direction is defined relative to
+the strand being read.
+
+## Test the install
+
+`prform` ships with small FASTA fixtures (one folder per labeled
+frameshift class) so you can verify the install end-to-end without any
+external data. Copy them into your working directory:
+
+```bash
+prform download-examples ./prform_examples
+```
+
+Layout after download:
+
+```
+prform_examples/
+    plus1_PRF/    influenza_pax.fasta
+    minus1_PRF/   coronavirus_khosta2.fasta, phage_tyson.fasta
+    no_PRF/       monkeypox, ledantevirus, nanovirus, ourmiavirus, orbivirus
+```
+
+Run `predict` on each class:
+
+```bash
+# +1 PRF: peak should land near the labeled site
+prform predict prform_examples/plus1_PRF/influenza_pax.fasta \
+    --outdir prform_test/plus1
+
+# -1 PRF: peak should land near the labeled site
+prform predict prform_examples/minus1_PRF/coronavirus_khosta2.fasta \
+    --outdir prform_test/minus1
+
+# no PRF: no frameshift should be called
+prform predict prform_examples/no_PRF/nanovirus.fasta \
+    --outdir prform_test/no_prf
+
+cat prform_test/plus1/predictions.csv
+cat prform_test/minus1/predictions.csv
+cat prform_test/no_prf/predictions.csv
+```
+
+Expected behavior:
+
+| fixture | labeled site | what to look for |
+| --- | --- | --- |
+| `plus1_PRF/influenza_pax.fasta`        | +1 PRF @ pos 582   | `top1_pos` within a few nt of 582,  `top1_type == 1` |
+| `minus1_PRF/coronavirus_khosta2.fasta` | -1 PRF @ pos 13248 | `top1_pos` near 13248,              `top1_type == -1` |
+| `minus1_PRF/phage_tyson.fasta`         | -1 PRF @ pos 10279 | `top1_pos` near 10279,              `top1_type == -1` |
+| `no_PRF/*.fasta`                       | none               | `top1_type == 0` (no frameshift called) |
+
+Each labeled-positive FASTA header carries the labeled site for easy comparison.
+
+## Python API
+
+```python
+from prform import PRFormPredictor
+
+predictor = PRFormPredictor()                      # loads bundled weights
+results = predictor.predict_fasta("input.fasta")   # list of dicts
+# or
+results = predictor.predict_sequences([("rec1", "ACGT" * 1000)])
+# score both orientations, keep the better strand per record
+results = predictor.predict_fasta("input.fasta", both_strands=True)
+```
+
+Each result entry has `accession_id`, `length`, `strand`, `cal_probs_3`
+(3, L) and a `top` list of peak summaries (`pos`, `prob`, `type`) — all from
+the winning strand. With `both_strands=True`, `rec["fwd"]` and `rec["rev"]`
+each hold that orientation's own `cal_probs_3` and `top`, both in
+forward-genome coordinates; otherwise they are `None`.
+
+## Hardware
+
+CPU works. GPU is faster — `prform` automatically uses CUDA when available.
+For long sequences (>1 Mb total input) a GPU is recommended.
+
+## License
+
+MIT

prform-0.2.0/prform/__init__.py

@@ -0,0 +1,14 @@
+"""prform — predict programmed ribosomal frameshift (PRF) sites."""
+
+from importlib.resources import files
+
+from prform.predictor import PRFormPredictor
+
+
+def examples_dir():
+    """Path to the bundled example FASTA fixtures (positive/ and negative/)."""
+    return files("prform") / "_data" / "examples"
+
+
+__version__ = "0.2.0"
+__all__ = ["PRFormPredictor", "examples_dir", "__version__"]

prform-0.2.0/prform/__main__.py

@@ -0,0 +1,6 @@
+"""Allow `python -m prform ...` regardless of PATH."""
+
+from prform.cli import main
+
+if __name__ == "__main__":
+    main()

prform-0.2.0/prform/_calibrator.py

@@ -0,0 +1,75 @@
+"""
+PRFormCalibrator — five isotonic regressors mapping raw 3-class softmax to
+calibrated per-nucleotide probabilities, plus a record-level isotonic.
+
+Loaded from a dict-of-components joblib file, so the saved data is
+independent of any specific module path.
+"""
+
+from importlib.resources import files
+
+import joblib
+import numpy as np
+from scipy.ndimage import maximum_filter1d
+
+
+class PRFormCalibrator:
+    def __init__(self, iso_class0, iso_class1, iso_class2,
+                 iso_minus1_flank, iso_plus1_flank, iso_seq, flank_k=3):
+        self.iso_class0 = iso_class0
+        self.iso_class1 = iso_class1
+        self.iso_class2 = iso_class2
+        self.iso_minus1_flank = iso_minus1_flank
+        self.iso_plus1_flank = iso_plus1_flank
+        self.iso_seq = iso_seq
+        self.flank_k = int(flank_k)
+
+    def predict(self, probs_3):
+        """
+        probs_3 : (3, L) raw softmax — rows = [no_PRF, dir-1, dir+1].
+
+        Returns
+        -------
+        dict with
+          probs_3            : (3, L) float32, sharp per-class calibrated, renormalized
+          probs_minus1_flank : (L,)   float32, P(any true -1 site within +/- k)
+          probs_plus1_flank  : (L,)   float32, P(any true +1 site within +/- k)
+          sequence           : float, P(record contains any PRF site)
+        """
+        probs_3 = np.asarray(probs_3, dtype=np.float32)
+        if probs_3.ndim != 2 or probs_3.shape[0] != 3:
+            raise ValueError(f"probs_3 must be (3, L); got {probs_3.shape}")
+
+        c0 = self.iso_class0.transform(probs_3[0])
+        c1 = self.iso_class1.transform(probs_3[1])
+        c2 = self.iso_class2.transform(probs_3[2])
+        s = c0 + c1 + c2
+        s = np.where(s == 0, 1.0, s)
+        sharp = np.stack([c0 / s, c1 / s, c2 / s], axis=0).astype(np.float32)
+
+        win = 2 * self.flank_k + 1
+        w1 = maximum_filter1d(probs_3[1], size=win, mode="nearest")
+        w2 = maximum_filter1d(probs_3[2], size=win, mode="nearest")
+        flank_minus1 = self.iso_minus1_flank.transform(w1).astype(np.float32)
+        flank_plus1 = self.iso_plus1_flank.transform(w2).astype(np.float32)
+
+        prf_max = float((probs_3[1] + probs_3[2]).max())
+        seq = float(self.iso_seq.transform([prf_max])[0])
+
+        return {
+            "probs_3": sharp,
+            "probs_minus1_flank": flank_minus1,
+            "probs_plus1_flank": flank_plus1,
+            "sequence": seq,
+        }
+
+    def transform_sequence(self, prf_max):
+        return float(self.iso_seq.transform([float(prf_max)])[0])
+
+
+def load_bundled_calibrator():
+    """Load the calibrator shipped inside the package."""
+    path = files("prform._data").joinpath("calibrator_components.joblib")
+    with path.open("rb") as fh:
+        components = joblib.load(fh)
+    return PRFormCalibrator(**components)

prform-0.2.0/prform/_data/examples/minus1_PRF/GCA_031253115.1_ASM3125311v1_genomic.gff

@@ -0,0 +1,24 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+#!genome-build ASM3125311v1
+#!genome-build-accession NCBI_Assembly:GCA_031253115.1
+##sequence-region MZ190138.1 1 29220
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2836124
+MZ190138.1	Genbank	region	1	29220	.	+	.	ID=MZ190138.1:1..29220;Dbxref=taxon:2836124;collected-by=S. Lenshin%2C A. Romashin;collection-date=2020;country=Russia: Sochi;gbkey=Src;genome=genomic;isolation-source=feces pool;mol_type=genomic RNA;nat-host=Rhinolophus hipposideros (bat);strain=BtCoV/Khosta-2/Rh/Russia/2020
+MZ190138.1	Genbank	CDS	208	13248	.	+	0	ID=cds-QVN46577.1;Dbxref=NCBI_GP:QVN46577.1;Name=QVN46577.1;exception=ribosomal slippage;gbkey=CDS;product=ORF1ab protein;protein_id=QVN46577.1
+MZ190138.1	Genbank	CDS	13248	21386	.	+	0	ID=cds-QVN46577.1;Dbxref=NCBI_GP:QVN46577.1;Name=QVN46577.1;exception=ribosomal slippage;gbkey=CDS;product=ORF1ab protein;protein_id=QVN46577.1
+MZ190138.1	Genbank	CDS	208	13314	.	+	0	ID=cds-QVN46568.1;Dbxref=NCBI_GP:QVN46568.1;Name=QVN46568.1;gbkey=CDS;product=ORF1a protein;protein_id=QVN46568.1
+MZ190138.1	Genbank	gene	21393	25154	.	+	.	ID=gene-S;Name=S;gbkey=Gene;gene=S;gene_biotype=protein_coding
+MZ190138.1	Genbank	CDS	21393	25154	.	+	0	ID=cds-QVN46569.1;Parent=gene-S;Dbxref=NCBI_GP:QVN46569.1;Name=QVN46569.1;gbkey=CDS;gene=S;product=spike glycoprotein;protein_id=QVN46569.1
+MZ190138.1	Genbank	CDS	25163	25975	.	+	0	ID=cds-QVN46570.1;Dbxref=NCBI_GP:QVN46570.1;Name=QVN46570.1;gbkey=CDS;product=ORF3 protein;protein_id=QVN46570.1
+MZ190138.1	Genbank	gene	25999	26229	.	+	.	ID=gene-E;Name=E;gbkey=Gene;gene=E;gene_biotype=protein_coding
+MZ190138.1	Genbank	CDS	25999	26229	.	+	0	ID=cds-QVN46571.1;Parent=gene-E;Dbxref=NCBI_GP:QVN46571.1;Name=QVN46571.1;gbkey=CDS;gene=E;product=envelope protein;protein_id=QVN46571.1
+MZ190138.1	Genbank	gene	26277	26942	.	+	.	ID=gene-M;Name=M;gbkey=Gene;gene=M;gene_biotype=protein_coding
+MZ190138.1	Genbank	CDS	26277	26942	.	+	0	ID=cds-QVN46572.1;Parent=gene-M;Dbxref=NCBI_GP:QVN46572.1;Name=QVN46572.1;gbkey=CDS;gene=M;product=membrane protein;protein_id=QVN46572.1
+MZ190138.1	Genbank	CDS	26953	27141	.	+	0	ID=cds-QVN46573.1;Dbxref=NCBI_GP:QVN46573.1;Name=QVN46573.1;gbkey=CDS;product=ORF6 protein;protein_id=QVN46573.1
+MZ190138.1	Genbank	CDS	27148	27504	.	+	0	ID=cds-QVN46574.1;Dbxref=NCBI_GP:QVN46574.1;Name=QVN46574.1;gbkey=CDS;product=ORF7a protein;protein_id=QVN46574.1
+MZ190138.1	Genbank	CDS	27498	27626	.	+	0	ID=cds-QVN46575.1;Dbxref=NCBI_GP:QVN46575.1;Name=QVN46575.1;gbkey=CDS;product=ORF7b protein;protein_id=QVN46575.1
+MZ190138.1	Genbank	gene	27623	28876	.	+	.	ID=gene-N;Name=N;gbkey=Gene;gene=N;gene_biotype=protein_coding
+MZ190138.1	Genbank	CDS	27623	28876	.	+	0	ID=cds-QVN46576.1;Parent=gene-N;Dbxref=NCBI_GP:QVN46576.1;Name=QVN46576.1;gbkey=CDS;gene=N;product=nucleocapsid protein;protein_id=QVN46576.1
+###