Release V218 #83
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Release V218 #83
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Deleted conda_recipe directory, test scripts, and utility modules from src/. Also updated .gitignore with comprehensive Python ignores and incremented CRISPRme version to 2.1.8 in crisprme.py.
Introduces a Singularity recipe based on the micromamba Docker image. Installs system dependencies and sets up CRISPRitz and CRISPRme in a micromamba-managed environment for containerized execution.
Updated shell script and Python logic to check for directory existence instead of emptiness before moving files. Added a function in crisprme.py to verify if a folder is empty and improved error handling when the output folder is not empty, prompting the user to select another folder or clean up before rerunning.
Reorganized and modularized the code for generating population distribution barplots. Added type annotations, improved error handling, and split logic into functions for data parsing, computation, and plotting. Enhanced documentation and clarified command-line argument usage. The script now produces clearer, more maintainable code and saves barplots as PNG files for each guide.
Renamed remove_contiguous_samples_cfd.py to remove_contiguous_samples.py and updated references in merge_close_targets_cfd.sh. Deleted remove_contiguous_samples_cfd_new.py. Modified process_summaries.py to change argument handling for bulge and output path. Updated submit_job_automated_new_multiple_vcfs.sh to support multiple annotation files, pass annotation column names, and switch to python scripts for annotation and radar chart generation. These changes improve flexibility and maintainability of the post-processing pipeline.
Simplifies annotation file input by using a single realpath variable and removes handling of multiple annotation files and column names. Updates downstream script calls to use the new annotation variable and adjusts arguments for radar chart and post-processing steps for consistency.
Deleted hg38_gnomAD.samplesID.txt as it is no longer needed. Cleaned up merge_close_targets_cfd.sh by removing commented lines and updated the radar_chart_dict_generator.py to skip entries containing 'RNA,DNA' in the annotation processing.
Introduced annotation.py for annotating off-target results using BED files. Updated submit_job_automated_new_multiple_vcfs.sh to use annotation.py instead of annotate_final_results.py for both primary and alternative target annotation steps.
Added a check for existing tabix index before creating one in annotation.py. Updated radar_chart_dict_generator.py to use pysam.TabixFile for annotation file access and handle cases where the annotation file is empty ('vuoto.txt').
Updated annotation.py to check for vuoto.txt using os.path.basename for robustness. Removed redundant vuoto.txt check in radar_chart_dict_generator.py to streamline annotation file reading.
ManuelTgn
added
bug
Added steps to decompress and sort gene annotation BED files before processing. Updated cleanup to remove temporary sorted files, ensuring compatibility with compressed input and improving workflow robustness.
Replaces manual argument parsing in complete-search with modular validation functions, improves error handling, and updates help output for clarity. Removes redundant echo statement in submit_job_automated_new_multiple_vcfs.sh. Enhances maintainability and robustness of CLI input processing.
Adds the '-f' flag to the bgzip command in _compress_file to ensure existing files are overwritten during compression.
Removes intermediate files after processing personal annotations and refines output folder error messages for clarity in CRISPRme runs.
Added a check to ignore annotations containing '_personal' when processing the annotations list in fillDict. This prevents counting or processing these specific annotation types.
Removes redundant tabix index existence check in annotation.py and ensures files are only removed if they exist in crisprme.py. Also updates cleanup logic to avoid removing .tbi files unnecessarily.
Updated post_process.sh and submit_job_automated_new_multiple_vcfs.sh to skip gene annotation processing when the input file is 'vuoto.txt' or '_', preventing unnecessary operations and potential errors when no annotation data is provided.
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