Change log

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Major changes to BioKIT are summarized here.

0.1.0: Functions that remove adapters from FASTQ files (trim_se_adapters_fastq and trim_pe_adapters_fastq) are now part of BioKIT. Note, these identify exact matches of adapters.

Parsimony informative sites, constant sites, and variable sites functions now have a verbose option that allows users to examine the characterization of each site in an alignment.

The name gw-RSCU has been shortened to gRSCU.

0.0.9: Functions that look at codons (e.g., RSCU and gw-RSCU) now can account for ambiguous codons. For example, codons that have ambiguous characters like the codon “CNN.” These codons are skipped during analysis of RSCU and gw-RSCU.

1.0.1: Added “X” as a gap character during alignment recoding

1.1.0: Added Dayhoff-9, -12, -15, and -18 recoding schemes

1.1.3: Fixed bug in RSCU calculations

1.1.4: Added structured output support (tsv/json/yaml) to additional commands and expanded integration coverage with output format consistency and CLI output contract tests.

1.1.5: Updated dependency pinning to fix installation failures and moved supported Python versions to 3.11, 3.12, and 3.13 only.

1.1.18: Added sample_sequences (alias: sample_seqs) command to randomly draw N sequences (-n/--number) or a percentage (-p/--percent, default 10%) from a FASTA file without replacement. Supports reproducible sampling via -s/--seed and optional output file via -o/--output.

1.1.17: Added find_orfs (alias: orfs) command to identify all open reading frames above a minimum length in nucleotide sequences, searching all 6 reading frames (3 forward, 3 reverse). Reports id, frame, start, stop, and length in nucleotides and amino acids. With --extract, outputs the ORF sequences as FASTA; with --protein, outputs protein translations instead of nucleotides. Supports custom genetic codes via -tt/--translation_table.

1.1.16: Added kmer_frequency (alias: kmer_freq) command to count all k-mers of a given size in sequences. Useful for genomic signatures, metagenomics binning prep, and alignment-free sequence comparison. Supports --canonical to collapse each k-mer with its reverse complement and -v/--verbose for per-sequence counts. K-mers containing non-ACGT characters are skipped.

1.1.15: Added homopolymer_runs (alias: homopolymer) command to find the longest homopolymer run per sequence in a FASTA file. Reports length, base, and 1-based start position. Relevant for nanopore/PacBio QC where homopolymer errors are the dominant error mode. Use --per-base to report the longest run for each of A, C, G, T.

1.1.14: Added fastq_to_fasta (alias: fq2fa) command to convert FASTQ files to FASTA by stripping quality scores. Supports stdin input via - and optional output file via -o/--output.

1.1.13: Added genbank_to_fasta (alias: gb2fa) command to extract sequences from GenBank flat files. Optionally filters by feature type (e.g., CDS, rRNA, tRNA, gene) via -t/--feature_type and can output protein translations for CDS features via --translate.

1.1.12: Added assembly_curve (alias: asm_curve) command to output cumulative length vs. contig rank (sorted by descending length). Supports optional plotting via -p/--plot to generate a PNG assembly curve figure.

1.1.11: Added melting_temperature (alias: tm) command to calculate melting temperature of nucleotide sequences using nearest-neighbor thermodynamics. Supports custom Na+ and oligo concentrations.

1.1.10: Added shuffle_sequences (alias: shuffle_seqs) command to randomly shuffle nucleotide or amino acid order within each sequence while preserving composition. Supports reproducible shuffling via -s/--seed.

1.1.9: Added restriction_sites (alias: re_sites) command to find restriction enzyme recognition sites in sequences. Reports cut positions and fragment sizes for one or more enzymes per sequence. Uses BioPython’s Restriction module.

1.1.8: Added gc_content_four_fold_degenerate_sites (alias: gc4) command to calculate GC content at four-fold degenerate sites in coding sequences. Supports custom translation tables via -tt and per-sequence output via -v.

1.1.7: Added protein_charge (alias: prot_charge) command to calculate the net charge of protein sequences at a given pH (default 7.0). Uses BioPython’s ProteinAnalysis for the calculation. Supports tsv, json, and yaml output.

1.1.6: Added fasta_deduplication (alias: dedup) command to remove duplicate sequences from multi-FASTA files. Sequences are compared case-insensitively and the first occurrence of each unique sequence is kept.