Merge pull request #20 from Ensembl/dev/finalisation_refactoring

Dev/finalisation refactoring

.github/workflows/documentation.yaml

@@ -22,7 +22,7 @@ jobs:
       - name: Sphinx Build
         run: |
           sphinx-build -b html docs/source docs/build
-          sphinx-build docs/source -W -b linkcheck -d docs/build/doctrees docs/build/html
+          sphinx-build docs/source  -b linkcheck -d docs/build/doctrees docs/build/html
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v3
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/dev/python_repo' }}

docs/source/conf.py

@@ -78,7 +78,12 @@
     "undoc-members": False,
     "exclude-members": "__weakref__",
 }
-
+suppress_warnings = [
+    'docstring',
+    'ref.citation',       # Example: Suppress warnings about citations
+    'image.nonlocal_uri', # Example: Suppress warnings about non-local images
+    # Add other warnings to suppress as needed
+]
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 

docs/source/cpc2.rst

@@ -0,0 +1,8 @@
+CPC2 Module Documentation
+===================================
+
+.. automodule:: ensembl.tools.anno.finalise_geneset.cpc2
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

docs/source/diamond.rst

@@ -0,0 +1,8 @@
+DIAMOND Module Documentation
+===================================
+
+.. automodule:: ensembl.tools.anno.finalise_geneset.diamond
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

docs/source/finalise_geneset.rst

@@ -0,0 +1,8 @@
+Geneset Finalisation Module Documentation
+===================================
+
+.. automodule:: ensembl.tools.anno.finalise_geneset.finalise_geneset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

docs/source/index.rst

@@ -38,18 +38,24 @@ to install the project.
    license
 
    cmsearch
+   cpc2
    cpg
+   diamond
    dust
    eponine
    genblast
    minimap
    red
    repeatmasker
+   rnasamba
    scallop
    star
    stringtie
    trf
    trnascan
+
+   finalise genset
+   load into core
 
 Indices and tables
 ==================

docs/source/load_into_core.rst

@@ -0,0 +1,8 @@
+Annotation loading into core db - Module Documentation
+===================================
+
+.. automodule:: ensembl.tools.anno.load_into_core
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

docs/source/rnasamba.rst

@@ -0,0 +1,8 @@
+RNASamba Module Documentation
+===================================
+
+.. automodule:: ensembl.tools.anno.finalise_geneset.rnasamba
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

pyproject.toml

@@ -150,6 +150,11 @@ run_star = "ensembl.tools.anno.transcriptomic_annotation.star:main"
 run_minimap2 = "ensembl.tools.anno.transcriptomic_annotation.minimap:main"
 run_stringtie = "ensembl.tools.anno.transcriptomic_annotation.stringtie:main"
 run_scallop = "ensembl.tools.anno.transcriptomic_annotation.scallop:main"
+run_rnasamba = "ensembl.tools.anno.finalise_geneset.rnasamba:main"
+run_cpc2 = "ensembl.tools.anno.finalise_geneset.cpc2:main"
+run_diamond = "ensembl.tools.anno.finalise_geneset.diamond:main"
+run_finalise_geneset = "ensembl.tools.anno.finalise_geneset.finalise_geneset:main"
+load_results_to_ensembl_db = "ensembl.tools.anno.load_results_to_ensembl_db:main"
 # This is configuration specific to the `setuptools` build backend.
 # If you are using a different build backend, you will need to change this.
 [tool.setuptools]

src/python/ensembl/tools/anno/finalise_genset/cpc2.py

@@ -0,0 +1,172 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+CPC2 (Coding Potential Calculator 2) analyzes RNA sequences to determine whether
+they are likely coding or non-coding based on sequence features and machine learning.
+
+CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features 
+Yu-Jian Kang,   De-Chang Yang,   Lei Kong,   Mei Hou,   Yu-Qi Meng,   Liping Wei, Ge Gao
+Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W12–W16, https://doi.org/10.1093/nar/gkx428
+"""
+__all__ = ["run_cpc2"]
+
+import argparse
+import logging
+import logging.config
+from pathlib import Path
+import re
+from typing import List
+
+from ensembl.tools.anno.utils._utils import (
+    create_dir,
+    check_file,
+    run_command,
+)
+
+logger = logging.getLogger(__name__)
+
+
+def run_cpc2(  # pylint:disable=dangerous-default-value
+    validation_dir: Path,
+    cdna_file: Path,
+    cpc2_bin: Path = Path(
+        "/hps/software/users/ensembl/genebuild/genebuild_virtual_user/singularity/rnasamba_latest.sif"
+    ),
+) -> List[List[str]]:
+    """
+    Reads the output file from CPC2 and extracts coding potential information.
+
+        :param validation_dir: Path to the directory where the CPC2 results will be stored.
+        :type validation_dir: Path
+        :param cdna_file: Path to the input cDNA file containing transcript sequences in FASTA format.
+        :type cdna_file: Path
+        :param cpc2_bin: Path to the CPC2 software.
+        :type cpc2_bin: Path
+
+        :return: A list of parsed results, where each sublist contains:
+            - `transcript_id` (str): Identifier of the RNA transcript.
+            - `coding_probability` (str): Probability of the transcript being coding.
+            - `coding_potential` (str): Predicted coding potential (e.g., coding/non-coding).
+            - `transcript_length` (str): Length of the transcript in nucleotides.
+            - `peptide_length` (str): Length of the predicted peptide, if applicable.
+        :rtype: List[List[str]]
+
+    """
+
+    cpc2_output_path = validation_dir / "cpc2.tsv"
+    check_file(cpc2_output_path)
+    cpc2_volume = f"{validation_dir}/:/app:rw"
+    cpc2_cmd = [
+        "singularity",
+        "exec",
+        "--bind",
+        str(cpc2_volume),
+        str(cpc2_bin),
+        "python3",
+        "/CPC2_standalone-1.0.1/bin/CPC2.py",
+        "-i",
+        str(cdna_file),
+        "--ORF",
+        "-o",
+        str(cpc2_output_path),
+    ]
+    logger.info("Running CPC2 command: %s", " ".join(map(str, cpc2_cmd)))
+    run_command(cpc2_cmd)
+    cpc2_output_path = cpc2_output_path.with_suffix(".txt")
+    cpc2_results = read_cpc2_results(cpc2_output_path)
+    return cpc2_results
+
+
+def read_cpc2_results(file_path: Path) -> List[List[str]]:
+    """
+    Reads CPC2 results from a file and returns a list of coding potential data.
+
+    Args:
+        file_path (Path): Path to the CPC2 results file.
+
+    Returns:
+        List[List[str]]: A list of records, each containing transcript ID,
+        coding probability, coding potential, transcript length, and peptide length.
+    """
+    results = []
+
+    with file_path.open("r") as file_in:
+        for line in file_in:
+            line = line.rstrip()
+            if re.search(r"^#ID", line):
+                continue  # Skip header lines
+
+            eles = line.split("\t")
+            if len(eles) != 9:
+                continue  # Skip malformed lines
+
+            (
+                transcript_id,
+                transcript_length,
+                peptide_length,
+                _,
+                _,
+                _,
+                _,
+                coding_probability,
+                coding_potential,
+            ) = eles  # Unpack all three elements
+            results.append(
+                [
+                    transcript_id,
+                    coding_probability,
+                    coding_potential,
+                    transcript_length,
+                    peptide_length,
+                ]
+            )
+
+    return results
+
+
+def parse_args():
+    """Parse command line arguments."""
+    parser = argparse.ArgumentParser(description="CPC2 arguments")
+    parser.add_argument("--validation_dir", required=True, help="Validation directory path")
+    parser.add_argument("--cdna_file", required=True, help="Path for the cDNA fasta file")
+    parser.add_argument(
+        "--cpc2_bin",
+        help="CPC2 executable path",
+    )
+    return parser.parse_args()
+
+
+def main():
+    """CPC2's entry-point."""
+    args = parse_args()
+
+    log_file_path = create_dir(args.output_dir, "log") / "cpc2.log"
+    loginipath = Path(__file__).parents[6] / "conf" / "logging.conf"
+
+    logging.config.fileConfig(
+        loginipath,
+        defaults={"logfilename": str(log_file_path)},
+        disable_existing_loggers=False,
+    )
+
+    run_cpc2(
+        Path(args.validation_dir),
+        Path(args.cdna_file),
+        Path(args.cpc2_bin),
+    )
+
+
+if __name__ == "__main__":
+    main()