RefgenDetector 3.0.2__tar.gz → 3.0.4__tar.gz

{refgendetector-3.0.2/src/RefgenDetector.egg-info → refgendetector-3.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: RefgenDetector
-Version: 3.0.2
+Version: 3.0.4
 Author: Mireia Marin i Ginestar
 Author-email: <mireia.marin@crg.eu>
 Keywords: python
@@ -129,7 +129,8 @@ python ref_manager.py <command> [options]
 #### Add a reference
 
 ```bash
-python ref_manager.py add <genome.fai> <reference_name> <species>
+python ref_manager.py add <genome.fai> <reference_name> <species> # script
+refgenDetector-manager add <genome.fai> <reference_name> <species> # pip installation
 ```
 
 Registers a new reference from a valid `.fai` file. If the contig structure matches an existing reference, the entry is not added.
@@ -137,7 +138,8 @@ Registers a new reference from a valid `.fai` file. If the contig structure matc
 #### List references
 
 ```bash
-python ref_manager.py list
+python ref_manager.py list # scripts
+refgenDetector-manager list # pip installation
 ```
 
 Displays all available references, including both built-in and user-defined assemblies.
@@ -145,7 +147,8 @@ Displays all available references, including both built-in and user-defined asse
 #### Remove a reference
 
 ```bash
-python ref_manager.py remove <reference_name>
+python ref_manager.py remove <reference_name> # scripts
+refgenDetector-manager remove <reference_name> # pip installation
 ```
 
 Removes a custom reference from the local database. Built-in references cannot be removed.
@@ -188,33 +191,31 @@ Depending on how you want to install the package:
 - pip
 - Docker
 
-Download the `msgpack` files for the inference with VCFs: 
-
-1. [Download the msgpack reference](https://crgcnag-my.sharepoint.com/:u:/g/personal/mimarin_crg_es/IQDa5CICZDAoRZmbfhBG3ZPEAWdVnNqvefFJB_r5Hc8aM70?e=kID7zn)
-
-2. Move the `msgpack` to the correct path:
-
-```
-mv msgpack.zip /refgenDetector/src/refgenDetector/
-unzip /refgenDetector/src/refgenDetector/msgpack.zip
-```
-
 ## Installation
 
 ### Cloning this repository
 
 1. Clone this repository
 
-2. ``` $ cd PATH_WHERE_YOU_CLONED_THE_REPOSITORY/src/refgenDetector ```
+2.```git clone https://github.com/EGA-archive/refgenDetector.git
+cd refgenDetector
+pip install -e . ```
 
 3. ``$ python3 refgenDetector_main.py -h ``
 
+4. Download the `msgpack` files for the inference with VCFs: [Download the msgpack reference](https://crgcnag-my.sharepoint.com/:u:/g/personal/mimarin_crg_es/IQDa5CICZDAoRZmbfhBG3ZPEAWdVnNqvefFJB_r5Hc8aM70?e=kID7zn)
+
+5. Move the `msgpack` to the correct path:
+
+```
+mv msgpacks.zip /refgenDetector/src/refgenDetector/
+unzip /refgenDetector/src/refgenDetector/msgpacks.zip
+```
+
 ### From pypi
 
 ``$ pip install refgenDetector``
 
-### From Docker 
-``
 
 ## Usage
 
@@ -244,51 +245,7 @@ optional arguments:
 
 ## Test RefgenDetector
 
-In the folder **examples** you can find headers, BAM and CRAMs to test the working of RefgenDetector.
-
-*All this files belong to the [synthetics data cohort](https://ega-archive.org/synthetic-data) from the European
-Genome-Phenome Archive ([EGA](https://ega-archive.org/)).*
-
-### Test with headers in a TXT
-
-In the folder TEST_HEADERS there are four headers obtained from synthetic BAM an CRAMs stored in the EGA. Each one of
-them belongs to a different synthetic study:
-
-- Test Study for EGA using data from 1000 Genomes Project - Phase
-  3 [EGAS00001005042](https://ega-archive.org/studies/EGAS00001005042).
-- Synthetic data - Genome in a Bottle - [EGAS00001005591](https://ega-archive.org/studies/EGAS00001005591).
-- Human genomic and phenotypic synthetic data for the study of rare
-  diseases - [EGAS00001005702](https://ega-archive.org/studies/EGAS00001005702).
-- CINECA synthetic data.Please note: This study contains synthetic data (with cohort “participants” / ”subjects” marked
-  with FAKE) has no identifiable data and cannot be used to make any inference about cohort data or
-  results - [EGAS00001002472](https://ega-archive.org/studies/EGAS00001002472).
-
-Further information about them can be found in the file *where_to_find_this_files.txt*, saved in the same folder.
-
-To run RefgenDetector with the files:
-
-1. Modify the txt *path_to_headers* so the paths match those in your computer.
-2. Run:
-
-   ``` $ refgenDetector -p /PATH_WHERE_YOU_CLONED_THE_REPOSITORY/refgenDetector/examples/path_to_headers -t Headers```
-
-### Test with BAM and CRAMs
-
-In the folder TEST_BAM_CRAM there are a BAM and a CRAM obtained from synthetic BAM an CRAMs stored in the EGA. They
-belong to the synthetic study - Test Study for EGA using data from 1000 Genomes Project - Phase
-3 [EGAS00001005042](https://ega-archive.org/studies/EGAS00001005042).
-
-Further information about them can be found in the file *where_to_find_this_files.txt*, saved in the same folder.
-
-To run RefgenDetector with the files:
-
-1. Modify the txt *path_to_bam_cram* so the paths match those in your computer.
-
-2. Run:
-
-   ``` $ refgenDetector -p /PATH_WHERE_YOU_CLONED_THE_REPOSITORY/refgenDetector_pip-master/examples/path_to_bam_cram -t BAM/CRAM```
-
-
+In the folder [examples](https://github.com/EGA-archive/refgenDetector/tree/main/examples) you can find headers, alignment and variant files to test the working of RefgenDetector.
 
 ## Licence and funding
 

{refgendetector-3.0.2 → refgendetector-3.0.4}/README.md

@@ -103,7 +103,8 @@ python ref_manager.py <command> [options]
 #### Add a reference
 
 ```bash
-python ref_manager.py add <genome.fai> <reference_name> <species>
+python ref_manager.py add <genome.fai> <reference_name> <species> # script
+refgenDetector-manager add <genome.fai> <reference_name> <species> # pip installation
 ```
 
 Registers a new reference from a valid `.fai` file. If the contig structure matches an existing reference, the entry is not added.
@@ -111,7 +112,8 @@ Registers a new reference from a valid `.fai` file. If the contig structure matc
 #### List references
 
 ```bash
-python ref_manager.py list
+python ref_manager.py list # scripts
+refgenDetector-manager list # pip installation
 ```
 
 Displays all available references, including both built-in and user-defined assemblies.
@@ -119,7 +121,8 @@ Displays all available references, including both built-in and user-defined asse
 #### Remove a reference
 
 ```bash
-python ref_manager.py remove <reference_name>
+python ref_manager.py remove <reference_name> # scripts
+refgenDetector-manager remove <reference_name> # pip installation
 ```
 
 Removes a custom reference from the local database. Built-in references cannot be removed.
@@ -162,33 +165,31 @@ Depending on how you want to install the package:
 - pip
 - Docker
 
-Download the `msgpack` files for the inference with VCFs: 
-
-1. [Download the msgpack reference](https://crgcnag-my.sharepoint.com/:u:/g/personal/mimarin_crg_es/IQDa5CICZDAoRZmbfhBG3ZPEAWdVnNqvefFJB_r5Hc8aM70?e=kID7zn)
-
-2. Move the `msgpack` to the correct path:
-
-```
-mv msgpack.zip /refgenDetector/src/refgenDetector/
-unzip /refgenDetector/src/refgenDetector/msgpack.zip
-```
-
 ## Installation
 
 ### Cloning this repository
 
 1. Clone this repository
 
-2. ``` $ cd PATH_WHERE_YOU_CLONED_THE_REPOSITORY/src/refgenDetector ```
+2.```git clone https://github.com/EGA-archive/refgenDetector.git
+cd refgenDetector
+pip install -e . ```
 
 3. ``$ python3 refgenDetector_main.py -h ``
 
+4. Download the `msgpack` files for the inference with VCFs: [Download the msgpack reference](https://crgcnag-my.sharepoint.com/:u:/g/personal/mimarin_crg_es/IQDa5CICZDAoRZmbfhBG3ZPEAWdVnNqvefFJB_r5Hc8aM70?e=kID7zn)
+
+5. Move the `msgpack` to the correct path:
+
+```
+mv msgpacks.zip /refgenDetector/src/refgenDetector/
+unzip /refgenDetector/src/refgenDetector/msgpacks.zip
+```
+
 ### From pypi
 
 ``$ pip install refgenDetector``
 
-### From Docker 
-``
 
 ## Usage
 
@@ -218,51 +219,7 @@ optional arguments:
 
 ## Test RefgenDetector
 
-In the folder **examples** you can find headers, BAM and CRAMs to test the working of RefgenDetector.
-
-*All this files belong to the [synthetics data cohort](https://ega-archive.org/synthetic-data) from the European
-Genome-Phenome Archive ([EGA](https://ega-archive.org/)).*
-
-### Test with headers in a TXT
-
-In the folder TEST_HEADERS there are four headers obtained from synthetic BAM an CRAMs stored in the EGA. Each one of
-them belongs to a different synthetic study:
-
-- Test Study for EGA using data from 1000 Genomes Project - Phase
-  3 [EGAS00001005042](https://ega-archive.org/studies/EGAS00001005042).
-- Synthetic data - Genome in a Bottle - [EGAS00001005591](https://ega-archive.org/studies/EGAS00001005591).
-- Human genomic and phenotypic synthetic data for the study of rare
-  diseases - [EGAS00001005702](https://ega-archive.org/studies/EGAS00001005702).
-- CINECA synthetic data.Please note: This study contains synthetic data (with cohort “participants” / ”subjects” marked
-  with FAKE) has no identifiable data and cannot be used to make any inference about cohort data or
-  results - [EGAS00001002472](https://ega-archive.org/studies/EGAS00001002472).
-
-Further information about them can be found in the file *where_to_find_this_files.txt*, saved in the same folder.
-
-To run RefgenDetector with the files:
-
-1. Modify the txt *path_to_headers* so the paths match those in your computer.
-2. Run:
-
-   ``` $ refgenDetector -p /PATH_WHERE_YOU_CLONED_THE_REPOSITORY/refgenDetector/examples/path_to_headers -t Headers```
-
-### Test with BAM and CRAMs
-
-In the folder TEST_BAM_CRAM there are a BAM and a CRAM obtained from synthetic BAM an CRAMs stored in the EGA. They
-belong to the synthetic study - Test Study for EGA using data from 1000 Genomes Project - Phase
-3 [EGAS00001005042](https://ega-archive.org/studies/EGAS00001005042).
-
-Further information about them can be found in the file *where_to_find_this_files.txt*, saved in the same folder.
-
-To run RefgenDetector with the files:
-
-1. Modify the txt *path_to_bam_cram* so the paths match those in your computer.
-
-2. Run:
-
-   ``` $ refgenDetector -p /PATH_WHERE_YOU_CLONED_THE_REPOSITORY/refgenDetector_pip-master/examples/path_to_bam_cram -t BAM/CRAM```
-
-
+In the folder [examples](https://github.com/EGA-archive/refgenDetector/tree/main/examples) you can find headers, alignment and variant files to test the working of RefgenDetector.
 
 ## Licence and funding
 

refgendetector-3.0.4/setup.py

@@ -0,0 +1,62 @@
+from setuptools import setup, find_packages
+from setuptools.command.install import install
+from setuptools.command.develop import develop
+from pathlib import Path
+
+this_directory = Path(__file__).parent
+long_description = (this_directory / "README.md").read_text()
+VERSION = '3.0.4'
+DESCRIPTION = 'RefgenDetector'
+
+
+# ── Post-install hook ─────────────────────────────────────────────────────────
+
+def run_post_install():
+    try:
+        from refgenDetector.post_install import run
+        run()
+    except Exception as exc:
+        print(
+            f"\n[refgenDetector] WARNING: post-install setup failed: {exc}\n"
+            "You can run it manually later with:\n"
+            "    python -c 'from refgenDetector.post_install import run; run()'\n"
+        )
+
+class PostInstallCommand(install):
+    def run(self):
+        super().run()
+        run_post_install()
+
+class PostDevelopCommand(develop):
+    def run(self):
+        super().run()
+        run_post_install()
+
+
+# ── Setup ─────────────────────────────────────────────────────────────────────
+
+setup(
+    name="RefgenDetector",
+    version=VERSION,
+    author="Mireia Marin i Ginestar",
+    author_email="<mireia.marin@crg.eu>",
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    install_requires=['pysam', 'psutil', 'rich', 'pandas', 'dnspython', 'msgpack', 'numpy'],
+    keywords=['python'],
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Operating System :: Unix",
+    ],
+    entry_points={
+        'console_scripts': [
+            'refgenDetector=refgenDetector.refgenDetector_main:main',
+            'refgenDetector-manager=refgenDetector.ref_manager:main'
+        ],
+    },
+    packages=find_packages(where='src'),
+    package_dir={'': 'src'},
+    package_data={
+        "refgenDetector": ["post_install.py"],   # ships post_install.py in the wheel
+    }
+)

{refgendetector-3.0.2 → refgendetector-3.0.4/src/RefgenDetector.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: RefgenDetector
-Version: 3.0.2
+Version: 3.0.4
 Author: Mireia Marin i Ginestar
 Author-email: <mireia.marin@crg.eu>
 Keywords: python
@@ -129,7 +129,8 @@ python ref_manager.py <command> [options]
 #### Add a reference
 
 ```bash
-python ref_manager.py add <genome.fai> <reference_name> <species>
+python ref_manager.py add <genome.fai> <reference_name> <species> # script
+refgenDetector-manager add <genome.fai> <reference_name> <species> # pip installation
 ```
 
 Registers a new reference from a valid `.fai` file. If the contig structure matches an existing reference, the entry is not added.
@@ -137,7 +138,8 @@ Registers a new reference from a valid `.fai` file. If the contig structure matc
 #### List references
 
 ```bash
-python ref_manager.py list
+python ref_manager.py list # scripts
+refgenDetector-manager list # pip installation
 ```
 
 Displays all available references, including both built-in and user-defined assemblies.
@@ -145,7 +147,8 @@ Displays all available references, including both built-in and user-defined asse
 #### Remove a reference
 
 ```bash
-python ref_manager.py remove <reference_name>
+python ref_manager.py remove <reference_name> # scripts
+refgenDetector-manager remove <reference_name> # pip installation
 ```
 
 Removes a custom reference from the local database. Built-in references cannot be removed.
@@ -188,33 +191,31 @@ Depending on how you want to install the package:
 - pip
 - Docker
 
-Download the `msgpack` files for the inference with VCFs: 
-
-1. [Download the msgpack reference](https://crgcnag-my.sharepoint.com/:u:/g/personal/mimarin_crg_es/IQDa5CICZDAoRZmbfhBG3ZPEAWdVnNqvefFJB_r5Hc8aM70?e=kID7zn)
-
-2. Move the `msgpack` to the correct path:
-
-```
-mv msgpack.zip /refgenDetector/src/refgenDetector/
-unzip /refgenDetector/src/refgenDetector/msgpack.zip
-```
-
 ## Installation
 
 ### Cloning this repository
 
 1. Clone this repository
 
-2. ``` $ cd PATH_WHERE_YOU_CLONED_THE_REPOSITORY/src/refgenDetector ```
+2.```git clone https://github.com/EGA-archive/refgenDetector.git
+cd refgenDetector
+pip install -e . ```
 
 3. ``$ python3 refgenDetector_main.py -h ``
 
+4. Download the `msgpack` files for the inference with VCFs: [Download the msgpack reference](https://crgcnag-my.sharepoint.com/:u:/g/personal/mimarin_crg_es/IQDa5CICZDAoRZmbfhBG3ZPEAWdVnNqvefFJB_r5Hc8aM70?e=kID7zn)
+
+5. Move the `msgpack` to the correct path:
+
+```
+mv msgpacks.zip /refgenDetector/src/refgenDetector/
+unzip /refgenDetector/src/refgenDetector/msgpacks.zip
+```
+
 ### From pypi
 
 ``$ pip install refgenDetector``
 
-### From Docker 
-``
 
 ## Usage
 
@@ -244,51 +245,7 @@ optional arguments:
 
 ## Test RefgenDetector
 
-In the folder **examples** you can find headers, BAM and CRAMs to test the working of RefgenDetector.
-
-*All this files belong to the [synthetics data cohort](https://ega-archive.org/synthetic-data) from the European
-Genome-Phenome Archive ([EGA](https://ega-archive.org/)).*
-
-### Test with headers in a TXT
-
-In the folder TEST_HEADERS there are four headers obtained from synthetic BAM an CRAMs stored in the EGA. Each one of
-them belongs to a different synthetic study:
-
-- Test Study for EGA using data from 1000 Genomes Project - Phase
-  3 [EGAS00001005042](https://ega-archive.org/studies/EGAS00001005042).
-- Synthetic data - Genome in a Bottle - [EGAS00001005591](https://ega-archive.org/studies/EGAS00001005591).
-- Human genomic and phenotypic synthetic data for the study of rare
-  diseases - [EGAS00001005702](https://ega-archive.org/studies/EGAS00001005702).
-- CINECA synthetic data.Please note: This study contains synthetic data (with cohort “participants” / ”subjects” marked
-  with FAKE) has no identifiable data and cannot be used to make any inference about cohort data or
-  results - [EGAS00001002472](https://ega-archive.org/studies/EGAS00001002472).
-
-Further information about them can be found in the file *where_to_find_this_files.txt*, saved in the same folder.
-
-To run RefgenDetector with the files:
-
-1. Modify the txt *path_to_headers* so the paths match those in your computer.
-2. Run:
-
-   ``` $ refgenDetector -p /PATH_WHERE_YOU_CLONED_THE_REPOSITORY/refgenDetector/examples/path_to_headers -t Headers```
-
-### Test with BAM and CRAMs
-
-In the folder TEST_BAM_CRAM there are a BAM and a CRAM obtained from synthetic BAM an CRAMs stored in the EGA. They
-belong to the synthetic study - Test Study for EGA using data from 1000 Genomes Project - Phase
-3 [EGAS00001005042](https://ega-archive.org/studies/EGAS00001005042).
-
-Further information about them can be found in the file *where_to_find_this_files.txt*, saved in the same folder.
-
-To run RefgenDetector with the files:
-
-1. Modify the txt *path_to_bam_cram* so the paths match those in your computer.
-
-2. Run:
-
-   ``` $ refgenDetector -p /PATH_WHERE_YOU_CLONED_THE_REPOSITORY/refgenDetector_pip-master/examples/path_to_bam_cram -t BAM/CRAM```
-
-
+In the folder [examples](https://github.com/EGA-archive/refgenDetector/tree/main/examples) you can find headers, alignment and variant files to test the working of RefgenDetector.
 
 ## Licence and funding
 

{refgendetector-3.0.2 → refgendetector-3.0.4}/src/RefgenDetector.egg-info/SOURCES.txt

@@ -10,9 +10,11 @@ src/RefgenDetector.egg-info/top_level.txt
 src/refgenDetector/__init__.py
 src/refgenDetector/aligment_files.py
 src/refgenDetector/chromosomes_dict.py
+src/refgenDetector/download_reference.py
 src/refgenDetector/ref_manager.py
 src/refgenDetector/reference_genome_dictionaries.py
 src/refgenDetector/refgenDetector_main.py
 src/refgenDetector/variant_files.py
 src/refgenDetector/exceptions/NoFileException.py
-src/refgenDetector/exceptions/__init__.py
+src/refgenDetector/exceptions/__init__.py
+src/refgenDetector/msgpacks/__init__.py

{refgendetector-3.0.2 → refgendetector-3.0.4}/src/RefgenDetector.egg-info/entry_points.txt

@@ -1,2 +1,3 @@
 [console_scripts]
 refgenDetector = refgenDetector.refgenDetector_main:main
+refgenDetector-manager = refgenDetector.ref_manager:main

refgendetector-3.0.4/src/refgenDetector/__init__.py

@@ -0,0 +1,3 @@
+# Auto-setup reference files on first import
+from refgenDetector.download_reference import run as _setup_files
+_setup_files()

{refgendetector-3.0.2 → refgendetector-3.0.4}/src/refgenDetector/aligment_files.py

@@ -14,8 +14,8 @@ try:
     from .exceptions.NoFileException import *
 except ImportError:
     # Works when run directly as a script
-    from refgenDetector.reference_genome_dictionaries import *
-    from refgenDetector.exceptions.NoFileException import *
+    from reference_genome_dictionaries import *
+    from exceptions.NoFileException import *
 
 console = Console()
 

refgendetector-3.0.4/src/refgenDetector/download_reference.py

@@ -0,0 +1,155 @@
+"""
+Post-install script for refgenDetector.
+
+Handles two installation scenarios:
+  1. Cloned from GitHub: moves + decompresses .xz files from github_msgpacks/
+  2. Installed via pip: downloads github_msgpacks/ from GitHub, then moves + decompresses.
+
+Runs only once — skips everything if msgpacks/ already contains .msgpack files.
+"""
+
+import lzma
+import shutil
+import urllib.request
+import urllib.error
+import json
+from pathlib import Path
+
+
+# CONFIGURATION
+GITHUB_USER    = "EGA-archive"       
+GITHUB_REPO    = "refgenDetector"
+GITHUB_BRANCH  = "main"
+
+GITHUB_API_URL = (
+    f"https://api.github.com/repos/{GITHUB_USER}/{GITHUB_REPO}"
+    f"/contents/src/refgenDetector/github_msgpacks"
+    f"?ref={GITHUB_BRANCH}"
+)
+
+GITHUB_RAW_BASE = (
+    f"https://raw.githubusercontent.com/{GITHUB_USER}/{GITHUB_REPO}"
+    f"/{GITHUB_BRANCH}/src/refgenDetector/github_msgpacks"
+)
+
+# PATH RESOLUTION
+
+def _package_root() -> Path:
+    """Return the installed package directory (contains __init__.py)."""
+    # Works for both editable installs and regular pip installs
+    try:
+        import refgenDetector
+        return Path(refgenDetector.__file__).parent
+    except ImportError:
+        # Fallback: relative to this script
+        return Path(__file__).parent
+
+
+def get_paths():
+    pkg = _package_root()
+    src_clone  = pkg / "github_msgpacks"   # present when repo is cloned
+    src_pip    = pkg / "_downloaded_msgpacks"  # temp download dir for pip
+    dst        = pkg / "msgpacks"
+    return src_clone, src_pip, dst
+
+
+# HELPERS
+
+def is_already_setup(dst: Path) -> bool:
+    """Return True if at least one .msgpack file exists in dst."""
+    if not dst.exists():
+        return False
+    return any(dst.glob("*.msgpack"))
+
+
+def decompress_xz(src_file: Path, dst_dir: Path) -> None:
+    """Decompress a single .xz file into dst_dir, keeping the base name."""
+    # e.g. foo.msgpack.xz  ->  dst_dir/foo.msgpack
+    out_name = src_file.stem  # strips the last suffix (.xz)
+    out_path = dst_dir / out_name
+    print(f"  Decompressing {src_file.name} -> {out_path.name}")
+    with lzma.open(src_file, "rb") as f_in, open(out_path, "wb") as f_out:
+        shutil.copyfileobj(f_in, f_out)
+
+
+def move_and_decompress(src_dir: Path, dst_dir: Path) -> None:
+    """Move every .xz file from src_dir to dst_dir and decompress it."""
+    dst_dir.mkdir(parents=True, exist_ok=True)
+    xz_files = list(src_dir.glob("*.xz"))
+    if not xz_files:
+        print(f"  WARNING: no .xz files found in {src_dir}")
+        return
+    for xz_file in xz_files:
+        decompress_xz(xz_file, dst_dir)
+    print(f"  Done — {len(xz_files)} file(s) decompressed into {dst_dir}")
+
+
+# DOWNLOAD LOGIC
+
+def _github_api_request(url: str) -> list:
+    """Fetch JSON from the GitHub contents API."""
+    req = urllib.request.Request(url, headers={"User-Agent": "refgenDetector-installer"})
+    try:
+        with urllib.request.urlopen(req, timeout=30) as resp:
+            return json.loads(resp.read().decode())
+    except urllib.error.HTTPError as e:
+        raise RuntimeError(
+            f"GitHub API error {e.code} for {url}.\n"
+            "Check GITHUB_USER / GITHUB_REPO / GITHUB_BRANCH in post_install.py."
+        ) from e
+
+
+def download_github_msgpacks(dst_dir: Path) -> None:
+    """Download every .xz file from the GitHub folder into dst_dir."""
+    print(f"  Fetching file list from GitHub …")
+    entries = _github_api_request(GITHUB_API_URL)
+
+    xz_entries = [e for e in entries if e["name"].endswith(".xz")]
+    if not xz_entries:
+        raise RuntimeError("No .xz files found in the GitHub folder. Check the repo path.")
+
+    dst_dir.mkdir(parents=True, exist_ok=True)
+    for entry in xz_entries:
+        raw_url  = f"{GITHUB_RAW_BASE}/{entry['name']}"
+        out_path = dst_dir / entry["name"]
+        print(f"  Downloading {entry['name']} ({entry.get('size', '?')} bytes) …")
+        req = urllib.request.Request(raw_url, headers={"User-Agent": "refgenDetector-installer"})
+        with urllib.request.urlopen(req, timeout=120) as resp, open(out_path, "wb") as f:
+            shutil.copyfileobj(resp, f)
+
+    print(f"  Downloaded {len(xz_entries)} file(s).")
+
+
+# MAIN
+
+def run():
+    src_clone, src_pip, dst = get_paths()
+
+    # Check if the reference files have already been downloaded and decompressed
+    if is_already_setup(dst):
+        print("[refgenDetector] Reference files already present — skipping setup.")
+        return
+
+    print("[refgenDetector] Setting up reference files - This will only run once")
+
+    # Intallation done by clonning the repo - github_msgpacks/ is already present
+    if src_clone.exists() and any(src_clone.glob("*.xz")):
+        print(f"  Detected clone install — using local {src_clone.name}/")
+        move_and_decompress(src_clone, dst)
+
+    # Installation done via pip — need to download from GitHub and decompress 
+    else:
+        print("  Detected pip install — downloading from GitHub …")
+        try:
+            download_github_msgpacks(src_pip)
+            move_and_decompress(src_pip, dst)
+        finally:
+            # Clean up temp download dir regardless of success/failure
+            if src_pip.exists():
+                shutil.rmtree(src_pip, ignore_errors=True)
+
+    print("[refgenDetector] Reference files ready.\n")
+
+
+if __name__ == "__main__":
+    run()

{refgendetector-3.0.2 → refgendetector-3.0.4}/src/refgenDetector/ref_manager.py

@@ -11,14 +11,10 @@ except ImportError:
 
 DEFAULT_MAJOR_RELEASES = dict(major_releases)
 
-CUSTOM_DB = Path("custom_references.json")
-
-if CUSTOM_DB.exists():
-    with open(CUSTOM_DB) as f:
-        custom_refs = json.load(f)
-
-    major_releases.update(custom_refs)
+CUSTOM_DB = Path.home() / ".refgenDetector" / "custom_references.json"
 
+# make sure the directory exists
+CUSTOM_DB.parent.mkdir(parents=True, exist_ok=True)
 
 def load_from_fai(file_path):
     """

{refgendetector-3.0.2 → refgendetector-3.0.4}/src/refgenDetector/reference_genome_dictionaries.py

@@ -707,7 +707,7 @@ major_releases = {"hg16": {"ref_gen": hg16, "build": "hg16", "species": "Homo sa
                   "mm10": {"ref_gen": mm10, "build": "mm10", "species": "Mus musculus"},
                   "mm39": {"ref_gen": mm39, "build": "mm39", "species": "Mus musculus"},
                   "dm5": {"ref_gen": dm5, "build": "dm5", "species": "Drosophila Melanogaster"},
-                  #"dm6": {"ref_gen": dm6, "build": "dm6", "species": "Drosophila Melanogaster"},
+                  "dm6": {"ref_gen": dm6, "build": "dm6", "species": "Drosophila Melanogaster"},
                   "danRer10": {"ref_gen": danRer10, "build": "danRer10", "species": "Danio Rerio"},
                   "danRer11": {"ref_gen": danRer11, "build": "danRer11", "species": "Danio Rerio"},
                   "WBcel215": {"ref_gen": WBcel215, "build": "WBcel215", "species": "Caenorhabditis elegans"},
@@ -718,8 +718,7 @@ major_releases = {"hg16": {"ref_gen": hg16, "build": "hg16", "species": "Homo sa
                   "ASM886v2": {"ref_gen": ASM886v2, "build": "ASM886v2", "species": "Escherichia coli"},
                   "ASM584v2": {"ref_gen": ASM584v2, "build": "ASM584v2", "species": "Escherichia Coli"},
                   "pantro3_0": {"ref_gen": pantro3_0, "build": "pantro3_0", "species": "Pan troglodytes"},
-                  "pantro_2_1_4": {"ref_gen": pantro_2_1_4, "build": "pantro_2_1_4",
-                                   "species": "Pan troglodytes"},
+                  "pantro_2_1_4": {"ref_gen": pantro_2_1_4, "build": "pantro_2_1_4","species": "Pan troglodytes"},
                   "Mmul10": {"ref_gen": Mmul10, "build": "Mmul10", "species": "Macaca mulatta"},
                   "rheMac8": {"ref_gen": rheMac8, "build": "rheMac8", "species": "Macaca mulatta"},
                   "rheMac3": {"ref_gen": rheMac3, "build": "rheMac3", "species": "Macaca mulatta"},

{refgendetector-3.0.2 → refgendetector-3.0.4}/src/refgenDetector/refgenDetector_main.py

@@ -3,12 +3,12 @@
 """ refgenDetector.py: Script to infer the reference genome used to create a BAM or CRAM"""
 
 __author__ = "Mireia Marin Ginestar"
-__version__ = "3.0.1"
+__version__ = "3.0.4"
 __maintainer__ = "Mireia Marin Ginestar"
 __email__ = "mireia.marin@crg.eu"
 __status__ = "Developement"
 
-version = "3.0.1"
+version = "3.0.4"
 
 import os
 import sys
@@ -34,6 +34,7 @@ except ImportError:
 console = Console()
 
 
+
 def monitor_resources(func):
     """Decorator to print resource usage (CPU, memory, I/O, runtime)."""
     def wrapper(*args, **kwargs):

{refgendetector-3.0.2 → refgendetector-3.0.4}/src/refgenDetector/variant_files.py

@@ -16,12 +16,14 @@ except ImportError:
     from aligment_files import comparison
     from chromosomes_dict import *
 
+# Works both when installed as a pip package and when run directly as a script
+MSGPACK_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "msgpacks")
+
 
 
 final_results = []
 console = Console(highlight=False)
 _msgpack_cache = {}
-MSGPACK_DIR = "./msgpacks"
 
 def gather_and_sum(lists):
     """
@@ -66,7 +68,7 @@ def get_matches(snps_dict, chr_):
         cache_key = f"{version_name}-{chr_}"
 
         if cache_key not in _msgpack_cache:
-            path = f"{MSGPACK_DIR}/{cache_key}.msgpack"
+            path = os.path.join(MSGPACK_DIR, f"{cache_key}.msgpack")
             if not os.path.exists(path):
                 continue
             with open(path, "rb") as f:
@@ -80,7 +82,7 @@ def get_matches(snps_dict, chr_):
 
         matches.append([version_name, match_count])
 
-    console.print("Getting matches. Took:", time.time() - start, "s")
+    #console.print("Getting matches. Took:", time.time() - start, "s")
     return matches
 
 

refgendetector-3.0.2/setup.py

@@ -1,31 +0,0 @@
-from setuptools import setup, find_packages
-from pathlib import Path
-
-this_directory = Path(__file__).parent
-long_description = (this_directory / "README.md").read_text()
-
-VERSION = '3.0.2'
-DESCRIPTION = 'RefgenDetector'
-
-setup(
-    name="RefgenDetector",
-    version=VERSION,
-    author="Mireia Marin i Ginestar",
-    author_email="<mireia.marin@crg.eu>",
-    long_description=long_description,
-    long_description_content_type='text/markdown',
-    install_requires=['pysam', 'psutil', 'rich', 'pandas', 'dnspython', 'msgpack', 'numpy'],
-    keywords=['python'],
-    classifiers=[
-        "Programming Language :: Python :: 3",
-        "Operating System :: Unix",
-    ],
-    entry_points={
-        'console_scripts': [
-            'refgenDetector=refgenDetector.refgenDetector_main:main',
-        ],
-    },
-    packages=find_packages(where='src'),
-    package_dir={'': 'src'},
-    package_data={"refgenDetector": ["*.msgpack"]}
-)