biopipen 0.21.0__py3-none-any.whl → 0.34.26__py3-none-any.whl

biopipen/utils/reference.py

@@ -1,5 +1,10 @@
+"""Utilities for indexing reference files"""
+from __future__ import annotations
+
 import tempfile
+from os import PathLike
 from pathlib import Path
+from typing import Literal
 
 from ..core.config import config
 from biopipen.utils.misc import run_command
@@ -18,7 +23,12 @@ def gztype(gzfile):
     return "flat"
 
 
-def tabix_index(infile, preset, tmpdir=None, tabix=config.exe.tabix):
+def tabix_index(
+    infile: str | PathLike,
+    preset: Literal["gff", "bed", "sam", "vcf", "gaf"],
+    tmpdir: Literal[False] | str | PathLike | None = None,
+    tabix: str = config.exe.tabix,
+) -> str | PathLike:
     """Index input file using tabix
 
     1. Try to check if there is an index file in the same directory where infile
@@ -28,22 +38,47 @@ def tabix_index(infile, preset, tmpdir=None, tabix=config.exe.tabix):
        it in tmpdir
     4. Index the bgzipped file and return the bgzipped file
 
+    Args:
+        infile: The input file to be indexed
+        preset: The preset used to index the file
+        tmpdir: The directory to link the infile there and index it
+            If False, try to index the infile directly. The directory where
+            the infile is should be writable.
+        tabix: The path to tabix
+
     Returns:
         The infile itself or re-bgzipped infile. This file comes with the
         index file in the same directory
     """
-    if tmpdir is None:
-        tmpdir = Path(tempfile.mkdtemp(prefix="biopipen_tabix_index_"))
-    else:
-        tmpdir = Path(tmpdir)
 
     infile = Path(infile)
     gt = gztype(infile)
-
-    if gt == "bgzip" and infile.with_suffix(infile.suffix + ".tbi").is_file():
+    index_file = infile.with_suffix(infile.suffix + ".tbi")
+    # if index file exists, and it's newer than the infile, return infile
+    if (
+        gt == "bgzip"
+        and index_file.is_file()
+        and index_file.stat().st_mtime > infile.resolve().stat().st_mtime
+    ):
         # only bgzipped file is possible to have index file
         return infile
 
+    if tmpdir is False:
+        # index the infile directly
+        run_command([tabix, "-p", preset, infile], fg=True)
+        return infile
+
+    if tmpdir is None:
+        from hashlib import md5
+        # use a hash of infile to create the tempdir
+        tmpdir = Path(tempfile.gettempdir()).joinpath(
+            f"biopipen_tabix_index_{md5(str(infile).encode()).hexdigest()}"
+        )
+    else:
+        tmpdir = Path(tmpdir)
+
+    tmpdir.mkdir(exist_ok=True, parents=True)
+
     # /path/to/some.vcf -> some.vcf
     # /path/to/some.vcf.gz -> some.vcf
     basename = infile.stem if infile.name.endswith(".gz") else infile.name
@@ -53,15 +88,24 @@ def tabix_index(infile, preset, tmpdir=None, tabix=config.exe.tabix):
     if gt == "gzip":
         # re-bgzip
         run_command(
-            ["gunzip", "-c", infile], stdout=new_infile.with_suffix(""),
+            ["gunzip", "-f", "-c", infile], stdout=new_infile.with_suffix(""),
         )
-        run_command(["bgzip", new_infile.with_suffix("")], fg=True)
+        run_command(["bgzip", "-f", new_infile.with_suffix("")], fg=True)
     elif gt == "flat":
-        run_command(["bgzip", "-c", infile], stdout=new_infile)
+        run_command(["bgzip", "-f", "-c", infile], stdout=new_infile)
     else:
+        if new_infile.is_symlink():
+            new_infile.unlink()
         # directory of infile may not have write permission
         new_infile.symlink_to(infile)
 
+    new_index_file = new_infile.with_suffix(new_infile.suffix + ".tbi")
+    if (
+        new_index_file.is_file()
+        and new_index_file.stat().st_mtime > infile.resolve().stat().st_mtime
+    ):
+        return new_infile
+
     run_command([tabix, "-p", preset, new_infile], fg=True)
     return new_infile
 
@@ -82,15 +126,15 @@ def _run_bam_index(
 
 
 def bam_index(
-    bam,
-    bamdir=tempfile.gettempdir(),
-    tool="samtools",
-    samtools=config.exe.samtools,
-    sambamba=config.exe.sambamba,
-    ncores=1,
-    ext=".bam.bai",
-    force=False,
-):
+    bam: str | Path,
+    bamdir: Path | str = tempfile.gettempdir(),
+    tool: str = "samtools",
+    samtools: str = config.exe.samtools,
+    sambamba: str = config.exe.sambamba,
+    ncores: int = 1,
+    ext: str = ".bam.bai",
+    force: bool = False,
+) -> Path:
     """Index a bam file
 
     First look for the index file in the same directory as the bam file,
@@ -131,7 +175,7 @@ def bam_index(
         return bam
 
     if indexfile.is_file():
-        return str(bam)
+        return bam
 
     linkfile = Path(bamdir).joinpath(bam.name)
     indexfile = linkfile.with_suffix(ext)

biopipen/utils/reporter.py

@@ -0,0 +1,177 @@
+from __future__ import annotations
+from typing import Sequence
+from os import PathLike
+from pathlib import Path
+
+"""An implementation of reporter in python
+"https://pwwang.github.io/biopipen.utils.R/reference/Reporter.html
+
+to generate a json file for pipen-report to build a report for a process.
+"""
+
+import json
+
+
+class Reporter:
+
+    def __init__(self):
+        self.report = {}
+
+    def add(
+        self,
+        *args,
+        h1: str,
+        h2: str = "#",
+        h3: str = "#",
+        ui: str = "flat",
+    ) -> None:
+        """Add a content to the report
+
+        Args:
+            *args: The content of the report
+            h1 (str): The first level header
+            h2 (str): The second level header
+            h3 (str): The third level header
+            ui (str): The user interface of the report
+        """
+
+        self.report.setdefault(h1, {})
+        self.report[h1].setdefault(h2, {})
+        self.report[h1][h2].setdefault(h3, {})
+        self.report[h1][h2][h3][ui] = []
+
+        for arg in args:
+            self.report[h1][h2][h3][ui].append(arg)
+
+    def add2(
+        self,
+        *args,
+        hs: Sequence[str],
+        hs2: Sequence[str] = (),
+        ui: str = "flat",
+        collapse: str = ": ",
+    ) -> None:
+        """Add a content to the report
+
+        Args:
+            *args: The content of the report
+            hs: The headings of the case
+            hs2: The headings that must be shown.
+                When there are more items in `hs`, they will be concatenated.
+                For example, if `hs = c("Section1", "Case1")`, and `hs2 = c("A", "B")`,
+                then headings will be `h1 = "Section1: Case1"` and `h2 = "A"` and
+                `h3 = "B"`.
+            ui: The user interface of the report
+            collapse: The separator to concatenate the headings
+        """
+        if len(hs2) > 2:
+            raise ValueError("hs2 must have 2 or less items")
+
+        if len(hs2) == 2:
+            h1 = collapse.join(hs)
+            h2 = hs2[0]
+            h3 = hs2[1]
+        elif len(hs2) == 1:
+            h1 = hs[0]
+            hs = hs[1:]
+            if hs:
+                h2 = collapse.join(hs)
+                h3 = hs2[0]
+            else:
+                h2 = hs2[0]
+                h3 = "#"
+        else:
+            h1 = hs[0]
+            hs = hs[1:]
+            if hs:
+                h2 = hs[0]
+                hs = hs[1:]
+            else:
+                h2 = "#"
+
+            if hs:
+                h3 = collapse.join(hs)
+            else:
+                h3 = "#"
+
+        self.add(*args, h1=h1, h2=h2, h3=h3, ui=ui)
+
+    def image(
+        self,
+        prefix: str,
+        more_formats: str | Sequence[str],
+        save_code: bool,
+        kind: str = "image",
+        **kwargs,
+    ) -> dict:
+        """Generate a report for an image to be added.
+
+        Args:
+            prefix: The prefix of the image.
+            more_formats: More formats of the image available.
+            save_code: Whether to save the code to reproduce the plot.
+            kind: The kind of the report, default is "image".
+            **kwargs: Other arguments to add to the report.
+
+        Returns:
+            dict: The structured report for the image
+
+        Examples:
+            >>> reporter = Reporter()
+            >>> reporter.add(
+            >>>   {
+            >>>     "name": "Image 1",
+            >>>     "contents": [
+            >>>       reporter.image("/path/to/image1", "pdf", save_code=True)
+            >>>     ]
+            >>>   },
+            >>>   h1="Images",
+            >>>   h2="Image 1",
+            >>> )
+        """
+        out = {
+            "kind": kind,
+            "src": f"{prefix}.png",
+            **kwargs,
+        }
+
+        if more_formats or save_code:
+            out["download"] = []
+
+        if more_formats:
+            for mf in more_formats:
+                out["download"].append(f"{prefix}.{mf}")
+
+        if save_code:
+            out["download"].append(
+                {
+                    "src": f"{prefix}.code.zip",
+                    "tip": "Download the code to reproduce the plot",
+                    "icon": "Code",
+                }
+            )
+
+        return out
+
+    def clear(self):
+        """Clear the report"""
+        self.report = {}
+
+    def save(self, path: str | PathLike, clear: bool = True) -> None:
+        """Save the report to a file
+
+        Args:
+            path: The path to save the report
+                If the path is a directory, the report will be saved as `report.json`
+                in the directory. Otherwise, the report will be saved to the file.
+            clear: Whether to clear the report after saving.
+        """
+        path = Path(path)
+        if path.is_dir():
+            path = path / "report.json"
+
+        with open(path, "w") as f:
+            json.dump(self.report, f, indent=2)
+
+        if clear:
+            self.clear()

biopipen/utils/vcf.py

@@ -326,7 +326,7 @@ class Variant:
         if isinstance(samples, str):
             samples = Samples.from_str(samples, format)
         elif isinstance(samples[0], str):
-            samples = Samples.from_strs(samples, format)
+            samples = Samples.from_strs(samples, format)  # type: ignore
         else:
             samples = Samples.from_strss(samples, format)
 

biopipen-0.34.26.dist-info/METADATA

@@ -0,0 +1,27 @@
+Metadata-Version: 2.4
+Name: biopipen
+Version: 0.34.26
+Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
+License: MIT
+Author: pwwang
+Author-email: pwwang@pwwang.com
+Requires-Python: >=3.9,<4.0
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Provides-Extra: log2file
+Provides-Extra: runinfo
+Requires-Dist: datar[pandas] (>=0.15.8,<0.16.0)
+Requires-Dist: pipen-board[report] (>=0.17,<0.18)
+Requires-Dist: pipen-cli-run (>=0.15,<0.16)
+Requires-Dist: pipen-deprecated (>=0.0,<0.1)
+Requires-Dist: pipen-filters (>=0.15,<0.16)
+Requires-Dist: pipen-log2file (>=0.10.2,<0.11.0) ; extra == "log2file"
+Requires-Dist: pipen-poplog (>=0.3,<0.4)
+Requires-Dist: pipen-runinfo (>=0.9,<0.10) ; extra == "runinfo"
+Requires-Dist: pipen-verbose (>=0.14,<0.15)

biopipen-0.34.26.dist-info/RECORD

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