0.5.5.1

This is a patch for version v0.5.5.

An unfinished inversion detection program had mistakenly been included in the production code.

Since the inversion detection program is scheduled for implementation in version v0.5.6 or later, the code in question has been removed.

0.5.5

📝 Documentation

• Add FAQ.md and FAQ_JP.md to address the question: "Why is the read count of the Control sample lower in the output BAM file?". [Commit Detail]

🔧 Maintenance

• Integrating insertion and inversion detection: Issue #31

  • Add sv_handler [Commit Detail]

  • Modify arguments of is_insertion to is_sv [Commit Detail]

  • Remame insertions_to_fasta.generate_insertions_fasta to insertion_detector.detect_insertions because the function is not only for generating fasta files but also for generating csv tag. [Commit Detail]

• Remove unused dependencies

  • networkx: Issue #49 [Commit Detail]

0.5.4

💥 Breaking

• Use simulated annealing to optimize cluster assignments in clustering.constrained_kmenas [Commit Detail]

  • Since ortools is not installable on osx-arm64 in Bioconda, I implemented an alternative method, simulated annealing, to solve min_cost_flow.

• Change the criteria for terminating clustering. [Commit Detail]

  • The following termination criteria have been added:
    • Minimum cluster size is less than or equal to 0.5% of the sample's read number.
    • Decrease in the proportion of samples with a silhouette score of 0.25 or higher.
  • The following termination criterion has been removed:
    • Adjusted Rand Index >= 0.95, as it led to early termination when minor clusters were generated.

• The threshold for clustering.strand bias determination has been loosened. [Commit Detail]

  • This adjustment addresses cases like +:13, -:2 (0.87) observed in example_flox/flox-1nt-deletion.
  • Since the minor allele is particularly susceptible, further adjustments may be necessary in the future.

🌟 New Features

• Support for Apple Silicon (osx-arm64) in Bioconda🍎 Issue: #46

0.5.3

💥 Breaking

• Update clustering.clustering: Use Constrained Kmeans clustering to address the issue of cluster imbalance where extremely minor clusters were preferentially separated. Set min_cluster_size to 0.5% of the sample read count. [Commit Detail]

  • As a result, clustering.label_merger.py is no longer needed and has been removed.

• Update consensus.call_consensus: For mutations determined to be sequence errors, we previously replaced them with unknown (N), but this N had low interpretability. Therefore, mutations that DAJIN2 determines to be sequence errors will now be assigned the same base as the reference genome. [Commit Detail]

🐛 Bug Fixes

• Due to a bias in classifiler.calc_match where alleles with shorter sequences were prioritized, the operation of dividing by sequence length has been removed. [Commit Detail]

• Fix preporcess.mapping.generate_sam to perform alignments with map-ont and splice in addition to sr for sequence lengths of 500 bp or less, and select the optimal prefix from these alignments. Issue: #45 [Commit Detail]

0.5.2

📝 Documentation

• Add FAQ.md and FAQ_JP.md to provide answers to questions. [Commit Detail]

🌟 New Features

• Update mutation_extractor [Commit Detail]
  • Simplified the logic of the is_dissimilar_loci if statement. Additionally, changed the threshold for determining a mutation in Consensus from 75% to 50% (to accommodate the insertion allele in Cas3 Tyr Barcode10).
  • Updated detect_anomalies to use MLPClassifier to detect mutations more flexibly and accurately compared to the previous threshold setting with MiniBatchKMeans.

🔧 Maintenance

• Make DAJIN2 compatible with Python 3.11 and 3.12. Issue: #43 [Commit Detail]

  • pysam and mappy builds with Python 3.11 and 3.12 are now available on Bioconda.

• Update GitHub Actions to test with Python 3.11 and 3.12. Issue: #43 [Commit Detail]

• Resolve the B023 Function definition does not bind loop variable alignment_lengths issue. [Commit Detail]

• Add question.yml in GitHub Issue template. [Commit Detail]

🐛 Bug Fixes

• Update cssplits_handler._get_index_of_large_deletions: Modified to split large deletions when a match of 10 or more bases is found within the identified large deletion. Issue: #42 [Commit Detail]

0.5.1

🚀 New Features

• Enable to accept additional file formats as an input. Issue: #37
  • FASTA [Commit Detail]
  • BAM [Commit Detail]

📝 Documentation

• Add a description of the procedure for accepting files generated by Dorado basecaller as input. Issue: #37 [Commit Detail]

🔧 Maintenance

• Specify the Python version to be between 3.8 and 3.10. [Commit Detail]

• Change mutation_exporter.report_mutations to return list[list[str]]. Update the tests accordingly. [Commit Detail]

• Apply formatting with Ruff [Commit Detail]

🐛 Bug Fixes

• Add reallocate_insertion_within_deletion into report.mutation_exporter and reflected it in the mutation info. [Commit Detail]

0.5.0

📝 Documentation

• Update the issue template from md to yml and modify it to make it easier for users to fill out each item. [Commit Detail]

💥 Breaking

• Extremely low-frequency alleles (less than 0.05%) are considered Nanopore sequence errors and are not clustered #36.

  • Configure clustering.extract_labels so that alleles with a low number of reads (0.05% or fewer or 5 reads or fewer) are not clustered. [Commit Detail]
  • Change clustering.clustering to stop if the minimum value of the elements in the cluster is 0.5% or less. [Commit Detail]
  • Add consensus.remove_minor_alleles to remove minor alleles with fewer than 5 reads or less than 0.5% [Commit Detail]

• Save subsetted fastq of a control sample if the read number is too large (> 10,000 reads). The control will have a maximum of 10,000 reads to avoid excessive computational load. [Commit Detail]

• If the read length is 500 bases or less, change the mappy preset to sr. [Commit Detail]

• Update extract_best_preset to prioritize map-ont and remove splice preset if inversion is observed. [Commit Detail]

• Update the algorithms of cssplits_hander.reallocate_insertion_within_deletion to automate change point detection by incorporating temporal changes. [Commit Detail]

🔧 Maintenance

• Update deploy_pypi.yml to use the latest version of Actions. Refer to the latest official YAML for guidance. [Commit Detail]

• Integrate requirements.txt and MANIFEST.in into pyproject.toml by replacing setup.py [Commit Detail]

• Modify to record the execution command of DAJIN2 in the log file [Commit Detail]

• Add a test to check if the version in test_version.sh matches the version in pyproject.toml and utils.config [Commit Detail]

• Rename consensus.subset_clust to consensus.downsample_by_label to clarify the function's purpose. [Commit Detail]

• Update extract_unique_insertions to merge highly similar extracted insertion sequences. [Commit Detail]

  • Fix extract_unique_insertions: There is a bug where removing the key twice in fasta_insertions_unique caused the index and key to become misaligned in enumerate(distances) if i != key. Therefore, the removal of keys from fasta_insertions_unique is now done all at once at the end. [Commit Detail]

• Add control characters for fastx_handler.sanitize_filename as forbidden chars. [Commit Detail]

• Chang the naming convention for the temporary directory: <sample_name>/<process_content>/<allele_name>/(<label_name>)/file_name. Example: flox/consensus/control/1/mutation_loci.pickle. [Commit Detail]

• Move sanitze_name function from utils.fastx_handlerto utils.io [Commit Detail]

🐛 Bug Fixes

• Remove sam_handler.remove_overlapped_reads to prevent unnecessary trimming of reads. [Commit Detail]

• Fix preprocess.insertions_to_fasta.remove_minor_groups to delete the keys (insertion loci) when insertions are removed and result in an empty dict. This prevents errors when accessing non-existent keys in subset_insertions. [Commit Detail]

• Fix the bug in cssplits_handler.convert_cssplits_to_cstag where the insertion cs tag is not merged with the next cs tag if they have the same operator (e.g., +A|+A|=T, =T: before: +aa=T=T, after: +aa=TT). [Commit Detail]

• Modify the system to separate intermediate files using a directory structure instead of underscores (_), ensuring that no errors occur even if users use allele names containing underscores [Commit Detail]

  • Thank you @geedrn for reporting the issue #39!

0.4.6

💥 Breaking

• Update the log file Commit Detail

  • Add the version of DAJIN2 to the log file to track the version of the analysis.
  • Rename the log file to DAJIN2_log_<current time>.txt from <current time>_DAJIN2.log to enabling open the file in any text editor.

• Update mutation_extractor.is_dissimilar_loci Commit Detail

  • Rename to is_dissimilar_loci from identify_dissimilar_loci to explicitly indicate that a boolean is returned.
  • Changed to use cosine distance instead of cosine similarity to make "difference from control" more intuitive.
  • Added a condition to ensure that the cosine distance is not dependent on the specific index: Calculate the cosine distance for 10 bases starting from the neighbor of the corresponding indel, and add the condition that the cosine distances of these adjacent 10 bases should be similar.

• Update preprocess.insertions_to_fasta.py which detects unintended insertion alleles. Commit Detail

  • clustering_insertions: To accelerate MeanShift clustering, set bin_seeding=True. Additionally, because clustering decoys without variation becomes extremely slow, we have switched to using decoys that include slight variations.
  • extract_unique_insertions: Within unintended insertion alleles, alleles similar to the intended allele provided by the user are now excluded.
    • The similarity is defined as there being differences of more than 10 bases

• Update preprocess.insertions_to_fasta.clustering_insertions to consider the length of each insertion sequence during clustering. This allows two alleles, such as N,(30-base Insertion) and (30-base Insertion),N, to be weighted with different scores as [(1, 30), (30, 1)], enabling correct clustering. Commit Detail

• Update preprocess.homopolymer_handler: Scaling data to [0, 1] for cosine similarity, normalizing to match scales due to significant differences in mutation rates between samples and controls. Commit Detail

📝 Documentation

• Add the descriptions about required Python version supporting from 3.8 to 3.10 due to a Bioconda issue to the README.md. Commit Detail

• Enhance the descriptions in GitHub Issue templates to clarify their purpose. Commit Detail

🔧 Maintenance

• Move DAJIN2_VERSION to utils.config.py from main.py to make it easier to recognize its location. Commit Detail

• Update io.read_csv to return a list[dict[str, str]], not list[str] to align the output format with read_xlsx. Commit Detail

• Update utils.input_validator and preprocess.genome_fetcher to temporarily disable SSL certificate verification, allowing access to UCSC servers. Commit Detail

• Add an example of flox knockin design to the examples Commit Detail

• Update preprocess.insertions_to_fasta.py: The label names for the insertions were not starting from 1, so they have been revised to begin at 1. Commit Detail

• Change installer from pip to conda to install mappy in macos-latest (macos-14-arm64) in Github Action Commit Detail

🚀 Performance

• Update consensus.similarity_searcher to cache onehot encoded controls to avoid redundant computations and increase processing speed. Commit Detail

🐛 Bug Fixes

• Debug clustering.strand_bias_handler Commit Detail

  • For positive_strand_counts_by_labels: dict, there was a bug that caused an error and halted execution when accessing a non-existent key. It has been fixed to output 0 instead.
  • Created a wrapper function annotate_strand_bias_by_labels for outputting strand bias. Fixed a bug where the second and subsequent arguments were not being correctly passed when reallocating clusters with strand bias.

• Fix preprocess.knockin_handler to correctly identify the flox knock-in sites as deletions not present in the control. Commit Detail

• Bug fix of reallocate_insertion_within_deletion Commit Detail

  • In the script that considers the region between two deletions as an insertion sequence, the size of the other deletion was not taken into account. Even if there was a single base deletion, the entire sequence between the deletions was considered as an insertion sequence. Therefore, the region between two deletions is now defined only if the size of both deletions is equal to or greater than the specified threshold (default = 3).

0.4.5

🐛 Bug Fixes

• In version 0.4.4 of strand_bias_handler.remove_biased_clusters, there was an error in the continuation condition for removing biased clusters, which has now been corrected. The correct condition should be 'there are alleles with and without strand bias and the iteration count is less than or equal to 1000'. Instead, it was incorrectly set to 'there are alleles with and without strand bias or the iteration count is less than or equal to 1000'.

0.4.4

💥 Breaking

• Update the threshold from 5 to 0.5 at identify_dissimilar_loci to capture 1% minor alleles. Commit Detail

• Return smaller allele clustering labels (labels_previous) when the adjusted Rand index is sufficiently high to reduce predicted allele numbers.
  Commit Detail

🔧 Maintenance

• Add the detailed discription at identify_dissimilar_loci to clarify the purpose of the function. Commit Detail

• Update a function name of utils.io.check_excel_or_csv to utils.io.determine_file_type for clarity. Commit Detail

• Update examples: In tyr_c230gt_01, the point mutation of Tyr was previously 0.7%, but has been increased to 1.0% by adding point mutation reads from tyr_c230gt_50. Commit Detail

• Rename validate_columns_of_batch_file in test_main.py. Commit Detail

• Add tests of strand_bias_handler Commit Detail

• Add type hints and comments in return_labels Commit Detail