jsrc 0.2.0__tar.gz → 0.2.2__tar.gz

{jsrc-0.2.0/src/jsrc.egg-info → jsrc-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: jsrc
-Version: 0.2.0
+Version: 0.2.2
 Summary: Python library for bioinformatics and scientific computing
 Author-email: Jiaoyuan <imjiaoyuan@gmail.com>
 License-Expression: MIT
@@ -38,27 +38,36 @@ Python library for bioinformatics and scientific computing.
 
 ## Installation
 
-PyPI:
+Recommended (global CLI via `uv tool`):
 ```bash
-pip install jsrc
+uv tool install jsrc
 ```
 
-uv:
+Using `uv` virtual environment:
 ```bash
+uv venv
+source .venv/bin/activate
 uv pip install jsrc
 ```
 
-From source:
+Using Conda virtual environment + pip:
+```bash
+conda create -n jsrc python=3.11 -y
+conda activate jsrc
+pip install jsrc
+```
+
+From source (development):
 ```bash
 git clone https://github.com/imjiaoyuan/jsrc.git
 cd jsrc
 uv venv
-uv sync --extra dev
+uv sync --extra dev --extra all
 ```
 
 Run `jsrc --help` to get started.
 
-For detailed usage, see the [Documentation](docs/en/index.md).中文文档请参阅 [文档](docs/zh/index.md)。
+For detailed usage, see the [Documentation](docs/en/index.md). 中文文档请参阅 [文档](docs/zh/index.md)。
 
 ## Quick Start
 
@@ -84,7 +93,7 @@ jsrc vision extract --help
 | `plot` | Gene/exon/chromosome/domain and other plots | `jsrc plot gene ...` |
 | `analyze` | Phylogeny, motif, consensus, SNP/INDEL, QC | `jsrc analyze phylo ...` |
 | `gs` | Genomic selection dataset build/split/train | `jsrc gs train ...` |
-| `grn` | GRN conversion, centrality, local viewer | `jsrc grn net2json ...` |
+| `grn` | GRN conversion, centrality, build packaging, local serve | `jsrc grn build ...` |
 | `vision` | Object extraction, morphology traits, EFD | `jsrc vision extract ...` |
 | `job` | Background job submit/list/log/kill/history | `jsrc job submit "cmd"` |
 
@@ -136,10 +145,13 @@ jsrc vision traits -i test/leaf1.jpg --channel a --invert
 
 **grn module**
 
-Generate 1000-gene random network viewer with full-view mode (top 200 nodes):
+Generate and launch a 1000-gene random network viewer:
 
 ```bash
-jsrc grn net2json -i test/grn/network.tsv -o test/grn/json/grn.json -n test/grn/annotation.tsv -z test/grn/grn-viewer.zip -s
+jsrc grn net2json -i test/grn/network.tsv -o test/grn/grn.json
+jsrc grn anno2json -i test/grn/annotation.tsv -o test/grn/annotation.json
+jsrc grn build -d test/grn/public -g test/grn/grn.json -n test/grn/annotation.json -z test/grn/grn-viewer.zip -a -t 200
+jsrc grn serve -d test/grn/public -g test/grn/public/json/grn.json -n test/grn/public/json/annotation.json -p 8000 -a -t 200
 ```
 
 ![](assets/grn.jpg)

{jsrc-0.2.0 → jsrc-0.2.2}/README.md

@@ -4,27 +4,36 @@ Python library for bioinformatics and scientific computing.
 
 ## Installation
 
-PyPI:
+Recommended (global CLI via `uv tool`):
 ```bash
-pip install jsrc
+uv tool install jsrc
 ```
 
-uv:
+Using `uv` virtual environment:
 ```bash
+uv venv
+source .venv/bin/activate
 uv pip install jsrc
 ```
 
-From source:
+Using Conda virtual environment + pip:
+```bash
+conda create -n jsrc python=3.11 -y
+conda activate jsrc
+pip install jsrc
+```
+
+From source (development):
 ```bash
 git clone https://github.com/imjiaoyuan/jsrc.git
 cd jsrc
 uv venv
-uv sync --extra dev
+uv sync --extra dev --extra all
 ```
 
 Run `jsrc --help` to get started.
 
-For detailed usage, see the [Documentation](docs/en/index.md).中文文档请参阅 [文档](docs/zh/index.md)。
+For detailed usage, see the [Documentation](docs/en/index.md). 中文文档请参阅 [文档](docs/zh/index.md)。
 
 ## Quick Start
 
@@ -50,7 +59,7 @@ jsrc vision extract --help
 | `plot` | Gene/exon/chromosome/domain and other plots | `jsrc plot gene ...` |
 | `analyze` | Phylogeny, motif, consensus, SNP/INDEL, QC | `jsrc analyze phylo ...` |
 | `gs` | Genomic selection dataset build/split/train | `jsrc gs train ...` |
-| `grn` | GRN conversion, centrality, local viewer | `jsrc grn net2json ...` |
+| `grn` | GRN conversion, centrality, build packaging, local serve | `jsrc grn build ...` |
 | `vision` | Object extraction, morphology traits, EFD | `jsrc vision extract ...` |
 | `job` | Background job submit/list/log/kill/history | `jsrc job submit "cmd"` |
 
@@ -102,10 +111,13 @@ jsrc vision traits -i test/leaf1.jpg --channel a --invert
 
 **grn module**
 
-Generate 1000-gene random network viewer with full-view mode (top 200 nodes):
+Generate and launch a 1000-gene random network viewer:
 
 ```bash
-jsrc grn net2json -i test/grn/network.tsv -o test/grn/json/grn.json -n test/grn/annotation.tsv -z test/grn/grn-viewer.zip -s
+jsrc grn net2json -i test/grn/network.tsv -o test/grn/grn.json
+jsrc grn anno2json -i test/grn/annotation.tsv -o test/grn/annotation.json
+jsrc grn build -d test/grn/public -g test/grn/grn.json -n test/grn/annotation.json -z test/grn/grn-viewer.zip -a -t 200
+jsrc grn serve -d test/grn/public -g test/grn/public/json/grn.json -n test/grn/public/json/annotation.json -p 8000 -a -t 200
 ```
 
 ![](assets/grn.jpg)

{jsrc-0.2.0 → jsrc-0.2.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "jsrc"
-version = "0.2.0"
+version = "0.2.2"
 description = "Python library for bioinformatics and scientific computing"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -39,5 +39,8 @@ build-backend = "setuptools.build_meta"
 where = ["src"]
 include = ["jsrc*"]
 
+[tool.setuptools.package-data]
+"jsrc.grn" = ["sources/*"]
+
 [tool.black]
 target-version = ["py310"]

{jsrc-0.2.0 → jsrc-0.2.2}/src/jsrc/analyze/bootstrap_phylo.py

@@ -14,6 +14,7 @@ from jsrc.analyze.core import pad_alignment
 
 logger = logging.getLogger(__name__)
 
+
 def _tree_from_alignment(aln: MultipleSeqAlignment):
     calculator = DistanceCalculator("identity")
     dm = calculator.get_distance(aln)

{jsrc-0.2.0 → jsrc-0.2.2}/src/jsrc/analyze/msa_consensus.py

@@ -7,6 +7,7 @@ from typing import Any
 from Bio import SeqIO
 
 from jsrc.analyze.core import pad_alignment
+from jsrc.core import progressbar
 
 logger = logging.getLogger(__name__)
 
@@ -25,9 +26,11 @@ def cmd(args: Namespace) -> None:
             max_len,
         )
     seqs = [str(r.seq) for r in pad_alignment(records)]
+    seq_len = len(seqs[0])
     consensus_chars = []
     conservation = []
-    for i in range(len(seqs[0])):
+    bar = progressbar(total=seq_len, desc="Consensus")
+    for i in range(seq_len):
         col = [s[i] for s in seqs if s[i] != "-"]
         if not col:
             consensus_chars.append("N")
@@ -37,7 +40,9 @@ def cmd(args: Namespace) -> None:
         base, c = cnt.most_common(1)[0]
         consensus_chars.append(base)
         conservation.append(c / len(col))
+        bar.update()
     consensus = "".join(consensus_chars)
+    bar.finish()
     avg_cons = sum(conservation) / len(conservation) if conservation else 0.0
     payload = {
         "sequence_count": len(records),

{jsrc-0.2.0 → jsrc-0.2.2}/src/jsrc/cli.py

@@ -9,15 +9,9 @@ from jsrc import __version__
 
 def setup_logging(verbose: bool = False) -> None:
     level = logging.DEBUG if verbose else logging.INFO
-    logging.basicConfig(level=level, format="%(message)s", stream=sys.stderr, force=True)
-
-
-def _dispatch(module_name: str, func_name: str = "cmd") -> argparse.Action:
-    def _runner(args: argparse.Namespace) -> None:
-        module = importlib.import_module(module_name)
-        getattr(module, func_name)(args)
-
-    return _runner
+    logging.basicConfig(
+        level=level, format="%(message)s", stream=sys.stderr, force=True
+    )
 
 
 MODULES = {
@@ -40,7 +34,9 @@ def _iter_enabled_modules() -> list[str]:
     return [n for n in names if n in MODULES and n not in disabled]
 
 
-def _register_modules(subparsers: argparse.Action, *, debug: bool = False) -> tuple[list[str], list[str]]:
+def _register_modules(
+    subparsers: argparse.Action, *, debug: bool = False
+) -> tuple[list[str], list[str]]:
     loaded: list[str] = []
     errors: list[str] = []
     for name in _iter_enabled_modules():

jsrc-0.2.2/src/jsrc/core.py

@@ -0,0 +1,107 @@
+import sys
+import time
+from typing import Any, Generator, Iterable
+
+
+def _fmt_duration(seconds: float) -> str:
+    t = int(seconds)
+    h, m, s = t // 3600, (t % 3600) // 60, t % 60
+    if h:
+        return f"{h}:{m:02d}:{s:02d}"
+    return f"{m:02d}:{s:02d}"
+
+
+class progressbar:
+    def __init__(
+        self,
+        total: int = 0,
+        desc: str = "",
+        width: int = 40,
+        min_interval: float = 0.1,
+        tty_only: bool = True,
+    ):
+        self.total = total
+        self.desc = desc
+        self.width = width
+        self.min_interval = min_interval
+        self.n = 0
+        self.start_time = time.time()
+        self._last_update = 0.0
+        self._finished = False
+        self._enabled = not tty_only or sys.stderr.isatty()
+
+    def update(self, n: int = 1) -> None:
+        if not self._enabled or self._finished:
+            self.n += n
+            return
+        self.n += n
+        self._try_render()
+
+    def set(self, n: int) -> None:
+        if not self._enabled or self._finished:
+            self.n = n
+            return
+        self.n = n
+        self._try_render()
+
+    def finish(self) -> None:
+        if not self._enabled or self._finished:
+            return
+        self.n = self.total if self.total > 0 else self.n
+        self._render(time.time())
+        self._finished = True
+
+    def _try_render(self) -> None:
+        now = time.time()
+        if self.n < self.total and now - self._last_update < self.min_interval:
+            return
+        self._render(now)
+
+    def _render(self, now: float) -> None:
+        elapsed = now - self.start_time
+
+        if self.total > 0:
+            pct = self.n / self.total
+            filled = int(self.width * pct)
+            bar = "#" * filled + " " * (self.width - filled)
+
+            rate = self.n / elapsed if self.n > 0 and elapsed > 0 else 0
+            remaining = (self.total - self.n) / rate if rate > 0 else 0
+
+            sys.stderr.write(
+                f"\r{self.desc} [{bar}] {self.n}/{self.total}"
+                f" ({pct * 100:5.1f}%)"
+                f" [{_fmt_duration(elapsed)}<{_fmt_duration(remaining)}]"
+            )
+        else:
+            rate = self.n / elapsed if elapsed > 0 else 0
+            sys.stderr.write(
+                f"\r{self.desc} {self.n} [{_fmt_duration(elapsed)}"
+                f" ({rate:.0f} items/s)]"
+            )
+
+        if 0 < self.total <= self.n:
+            sys.stderr.write("\n")
+        else:
+            sys.stderr.flush()
+
+    def __enter__(self) -> "progressbar":
+        return self
+
+    def __exit__(self, *args: object) -> None:
+        self.finish()
+
+    def iter(
+        self, items: Iterable[Any], total: int | None = None
+    ) -> Generator[Any, None, None]:
+        if total is not None:
+            self.total = total
+        elif hasattr(items, "__len__"):
+            self.total = len(items)
+        else:
+            self.total = 0
+        self.n = 0
+        for item in items:
+            yield item
+            self.update()
+        self.finish()

{jsrc-0.2.0 → jsrc-0.2.2}/src/jsrc/grn/__init__.py

@@ -1,6 +1,6 @@
 from typing import Any
 
-from jsrc.grn import anno2json, centrality, net2json, serve
+from jsrc.grn import anno2json, build, centrality, net2json, serve
 
 
 def register_subparser(subparsers: Any) -> None:
@@ -8,6 +8,7 @@ def register_subparser(subparsers: Any) -> None:
     grn_sub = grn_parser.add_subparsers(dest="grn_cmd")
     grn_parser.set_defaults(_group_parser=grn_parser)
 
+    build.register(grn_sub)
     net2json.register(grn_sub)
     anno2json.register(grn_sub)
     serve.register(grn_sub)

jsrc-0.2.2/src/jsrc/grn/build.py

@@ -0,0 +1,88 @@
+import os
+import pathlib
+import shutil
+import zipfile
+from argparse import Namespace
+from pathlib import Path
+from typing import Any
+
+from jsrc.grn.core import ensure_dir, write_text
+
+_SCRIPT_TEMPLATE = (pathlib.Path(__file__).parent / "sources" / "script.js").read_text(
+    encoding="utf-8"
+)
+_INDEX_HTML = (pathlib.Path(__file__).parent / "sources" / "index.html").read_text(
+    encoding="utf-8"
+)
+_STYLE_CSS = (pathlib.Path(__file__).parent / "sources" / "style.css").read_text(
+    encoding="utf-8"
+)
+
+
+def _sync_assets(
+    base: str,
+    view_mode: str,
+    threshold: int,
+    max_nodes: int,
+) -> None:
+    ensure_dir(base)
+    ensure_dir(os.path.join(base, "css"))
+    ensure_dir(os.path.join(base, "js"))
+    ensure_dir(os.path.join(base, "json"))
+    write_text(os.path.join(base, "index.html"), _INDEX_HTML)
+    write_text(os.path.join(base, "css/style.css"), _STYLE_CSS)
+    script = (
+        _SCRIPT_TEMPLATE.replace("__JSRC_VIEW_MODE__", view_mode)
+        .replace("__JSRC_FULL_THRESHOLD__", str(threshold))
+        .replace("__JSRC_MAX_DISPLAY_NODES__", str(max_nodes))
+    )
+    write_text(os.path.join(base, "js/script.js"), script)
+
+
+def _zip_viewer(viewer_dir: Path, zip_output: str) -> None:
+    zip_path = Path(zip_output).expanduser().resolve()
+    zip_path.parent.mkdir(parents=True, exist_ok=True)
+    wanted = [
+        viewer_dir / "index.html",
+        viewer_dir / "css" / "style.css",
+        viewer_dir / "js" / "script.js",
+        viewer_dir / "json" / "grn.json",
+        viewer_dir / "json" / "annotation.json",
+    ]
+    with zipfile.ZipFile(zip_path, "w", compression=zipfile.ZIP_DEFLATED) as zf:
+        for f in wanted:
+            if f.exists():
+                zf.write(f, arcname=str(f.relative_to(viewer_dir)))
+
+
+def cmd(args: Namespace) -> None:
+    root = Path(args.dir).expanduser().resolve()
+    view_mode = "expand" if args.expand else "auto"
+    _sync_assets(str(root), view_mode, args.threshold, args.max_nodes)
+    if args.grn_json:
+        shutil.copy(args.grn_json, root / "json" / "grn.json")
+    if args.annotation_json:
+        shutil.copy(args.annotation_json, root / "json" / "annotation.json")
+    if args.zip_output:
+        _zip_viewer(root, args.zip_output)
+
+
+def register(subparsers: Any) -> None:
+    p = subparsers.add_parser("build", help="Build GRN viewer package")
+    p.add_argument("-d", "--dir", default=".", help="Output directory (default: .)")
+    p.add_argument("-g", "--grn-json", help="grn.json to copy into package")
+    p.add_argument(
+        "-n", "--annotation-json", help="annotation.json to copy into package"
+    )
+    p.add_argument("-z", "--zip-output", help="ZIP output path")
+    mode = p.add_mutually_exclusive_group()
+    mode.add_argument("-a", "--all", action="store_true", help="Full view mode")
+    mode.add_argument(
+        "-e", "--expand", action="store_true", help="Click-to-expand mode"
+    )
+    p.set_defaults(all=True)
+    p.add_argument(
+        "-t", "--threshold", type=int, default=300, help="Auto full-view threshold"
+    )
+    p.add_argument("--max-nodes", type=int, default=0, help="Max nodes (0 = all)")
+    p.set_defaults(func=cmd)

jsrc-0.2.2/src/jsrc/grn/net2json.py

@@ -0,0 +1,45 @@
+import csv
+import logging
+from argparse import Namespace
+from typing import Any
+
+from jsrc.grn.core import write_json
+
+logger = logging.getLogger(__name__)
+
+
+def network_to_json(
+    input_path: str, output_path: str
+) -> tuple[list[dict[str, Any]], int]:
+    links = []
+    with open(input_path, "r", encoding="utf-8") as f:
+        reader = csv.reader(f, delimiter="\t")
+        for row in reader:
+            if len(row) < 3:
+                continue
+            source_id = str(row[0]).replace("_", "-")
+            target_id = str(row[1]).replace("_", "-")
+            try:
+                weight = float(row[2])
+            except ValueError:
+                continue
+            links.append({"source": source_id, "target": target_id, "val": weight})
+    write_json(output_path, links)
+    nodes = set()
+    for item in links:
+        nodes.add(item["source"])
+        nodes.add(item["target"])
+    logger.info("Network JSON written: %s", output_path)
+    logger.info("Genes: %d | Edges: %d", len(nodes), len(links))
+    return links, len(nodes)
+
+
+def cmd(args: Namespace) -> None:
+    network_to_json(args.input, args.output)
+
+
+def register(subparsers: Any) -> None:
+    p = subparsers.add_parser("net2json", help="Convert GRN edge table to grn.json")
+    p.add_argument("-i", "--input", required=True, help="Input edge table (TSV)")
+    p.add_argument("-o", dest="output", required=True, help="Output JSON path")
+    p.set_defaults(func=cmd)

{jsrc-0.2.0 → jsrc-0.2.2}/src/jsrc/grn/serve.py

@@ -6,17 +6,12 @@ from argparse import Namespace
 from typing import Any
 
 from jsrc.grn.core import ensure_dir, write_json
-from jsrc.grn.viewer import sync_viewer_assets
+from jsrc.grn.build import _sync_assets
 
 
 def cmd(args: Namespace) -> None:
-    view_mode = "expand" if args.some else "auto"
-    sync_viewer_assets(
-        args.dir,
-        init_empty_json=False,
-        view_mode=view_mode,
-        full_view_threshold=args.threshold,
-    )
+    view_mode = "expand" if args.expand else "auto"
+    _sync_assets(args.dir, view_mode, args.threshold, 0)
     ensure_dir(f"{args.dir}/json")
     src_grn = os.path.abspath(args.grn_json)
     dst_grn = os.path.abspath(f"{args.dir}/json/grn.json")
@@ -58,12 +53,12 @@ def register(subparsers: Any) -> None:
         help="Mode all: auto full-view when gene count <= threshold",
     )
     mode.add_argument(
-        "-s",
-        "--some",
+        "-e",
+        "--expand",
         action="store_true",
-        help="Mode some: manual click-to-expand only",
+        help="Click-to-expand mode",
     )
-    p.set_defaults(all=True, some=False)
+    p.set_defaults(all=True, expand=False)
     p.add_argument(
         "-t",
         "--threshold",

jsrc-0.2.2/src/jsrc/grn/sources/index.html

@@ -0,0 +1,37 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>GRN</title>
+    <link rel="stylesheet" href="css/style.css">
+    <script src="//unpkg.com/d3"></script>
+    <script src="//unpkg.com/force-graph"></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/html2canvas/1.4.1/html2canvas.min.js"></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/jspdf/2.5.1/jspdf.umd.min.js"></script>
+</head>
+<body>
+    <div id="controls">
+        <div class="row">
+            <button onclick="goBack()" id="btnBack" disabled>&lt;</button>
+            <button onclick="goForward()" id="btnFwd" disabled>&gt;</button>
+            <button onclick="exportImage('pdf')" class="btn-export">PDF</button>
+            <button onclick="resetView()" class="btn-reset">Reset</button>
+        </div>
+
+        <div class="row search-row">
+            <input type="text" id="geneInput" placeholder="Enter Gene ID">
+            <button onclick="startNewSearch()" class="btn-search">Search</button>
+        </div>
+
+        <div id="legend">Line thickness indicates weight</div>
+        <div id="nodeCount">Nodes: 0</div>
+        <div id="neighborList"></div>
+    </div>
+
+    <div id="watermark">GRN</div>
+    <div id="emptyState">No Nodes</div>
+    <div id="graph"></div>
+
+    <script src="js/script.js"></script>
+</body>
+</html>