SeqForge v0.6.0

SeqForge v0.6.0

SeqForge 0.6.0 expands sequence analysis with motif searching, advanced k-mer analysis, sequence distances, reverse transcription, and sequence alignment, together with corresponding CLI support and FASTQ handling.

✨ New features

Motif analysis

• Motif searching with find_motif()
• Case-insensitive motif matching
• Overlapping motif detection
• User-facing motif positions are reported using 1-based coordinates
• CLI support for literal, FASTA, and FASTQ input

🧬 Reverse transcription

• RNA → complementary DNA reverse transcription
• Supported through the Python API with Sequence.reverse_transcribe()
• Preserves the sequence identifier
• CLI support for literal, FASTA, and FASTQ input

🧪 Advanced k-mer analysis

• Sliding-window k-mer generation
• K-mer counting
• K-mer frequency calculation
• Searching for multiple k-mers with find_kmers()
• 1-based positions for k-mer searches
• CLI support for k-mer counts, frequencies, and searches
• DNA, RNA, and protein molecule-type support

📏 Sequence distances

• Hamming distance calculation with Sequence.distance()
• Pairwise distance analysis for collections of sequences
• Support for DNA, RNA, and protein sequences
• CLI commands for individual and pairwise distance analysis

🧬 Sequence alignment

• Global pairwise sequence alignment
• Configurable match, mismatch, and gap scores
• Progressive multiple sequence alignment
• Support for DNA, RNA, and protein sequences
• CLI alignment command with literal, FASTA, and FASTQ input

💻 CLI improvements

New commands and capabilities include:

• align
• distance
• distances
• kmer advanced modes
• motif
• reverse-transcribe

Existing commands were also extended with broader FASTQ and molecule-type support where applicable.

🧪 Testing and quality

The 0.6.0 release continues SeqForge's test-driven development approach with automated coverage for the new API and CLI functionality, including FASTA and FASTQ multi-record workflows.

📦 Installation

uv sync

SeqForge v0.5.0

SeqForge v0.5.0

SeqForge v0.5.0 introduces sequence filtering and windowed GC analysis, with full CLI integration.

Added

• Sequence filtering by minimum and maximum length
• Sequence filtering by motif
• FASTQ read filtering by minimum mean quality
• New filter CLI command
• Combined filtering criteria using AND semantics
• GC content analysis using sliding windows
• Windowed GC analysis for literal, FASTA, and FASTQ input
• 1-based positions in windowed GC output

CLI examples

seqforge filter sequences.fasta --min-length 100
seqforge filter sequences.fasta --motif ATG
seqforge filter reads.fastq --min-quality 30

seqforge gc sequence.fasta --window-size 100

Quality

• 311 tests passing
• Python 3.12+ supported

SeqForge v0.4.0

🧬 SeqForge v0.4.0

SeqForge v0.4.0 introduces explicit molecule-type support, extending the toolkit beyond DNA-focused analysis.

✨ What's new

• DNA, RNA, and protein molecule types
• Molecule-aware sequence validation
• RNA reverse-complement support
• RNA translation and ORF detection
• Protein amino acid statistics
• Molecule-aware CLI commands
• DNA/RNA/protein support across literal, FASTA, and FASTQ workflows
• Expanded documentation and docstrings

🧪 Testing

• 264 tests passing

🐍 Requirements

• Python 3.12+

SeqForge 0.3.0

SeqForge 0.3.0

SeqForge 0.3.0 expands the toolkit beyond its initial FASTA and CLI foundations, adding biological reading-frame conventions, strand-aware transcription, FASTQ support, read-quality analysis, and k-mer analysis.

Highlights

• Migrated user-facing reading frames from 0/1/2 to biological 1/2/3.
• Added coding and template strand semantics to DNA transcription.
• Added seqforge transcribe with support for:
  • literal sequences
  • FASTA files
  • multi-record FASTA files
  • coding, template, and both-strand transcription
• Added FASTQ parsing with multi-record support.
• Added FastqRead with Phred+33 quality analysis.
• Added per-read quality metrics:
  • mean quality
  • minimum quality
  • maximum quality
• Expanded stats for FASTQ input with:
  • read count
  • mean read length
  • overall mean quality
  • mean GC content
  • minimum read length
  • maximum read length
• Added FASTQ support to GC-content analysis.
• Added k-mer generation and counting to the Python API.
• Added seqforge kmer with:
  • literal sequence input
  • FASTA input
  • FASTQ input
  • multi-record processing
  • --counts
• Improved input resolution with FASTA and FASTQ record handling.
• Expanded automated test coverage to 182 tests.
• Updated documentation for FASTQ, k-mers, reading frames, and strand-aware transcription.

Examples

seqforge transcribe gene.fasta --strand template

seqforge stats reads.fastq

seqforge kmer genome.fasta --k 3

seqforge kmer reads.fastq --k 31 --counts

seqforge orf genome.fasta --strand both --frame 2

Notes

SeqForge 0.3.0 continues to focus on clear APIs, predictable behaviour, automated testing, and an intuitive command-line experience.

This release establishes FASTQ as a supported format for read-oriented analysis while keeping reference-sequence operations such as translation, transcription, and ORF detection focused on literal sequences and FASTA input.

Testing

The release was built and verified with:

uv run pytest
uv build

Test suite: 182 passed.

SeqForge v0.2.0

SeqForge 0.2.0

SeqForge 0.2.0 expands the project from a core DNA sequence analysis library into a more practical command-line toolkit.

Highlights

• Added a functional CLI with:
  • seqforge gc
  • seqforge stats
  • seqforge translate
  • seqforge orf
  • seqforge version
• Added direct FASTA file input from the CLI.
• Added multi-record FASTA processing.
• Added explicit reading-frame selection for translation and ORF detection.
• Added forward, reverse, and both-strand ORF searches.
• Added strand-aware ORF output for the CLI.
• Added consistent CLI input resolution for literal sequences and FASTA files.
• Improved error handling for missing and invalid FASTA files.
• Centralized codon interpretation for translation and ORF detection.
• Expanded the automated test suite to 118 tests.
• Updated the documentation for the new CLI and FASTA workflows.

Examples

seqforge stats sequence.fasta
seqforge translate gene.fasta --frame 1
seqforge orf genome.fasta --strand both

Notes

SeqForge 0.2.0 continues to focus on a clear Python API, predictable behaviour, automated testing, and an intuitive command-line experience.

SeqForge v0.1.0

SeqForge v0.1.0

Initial release of SeqForge, a Python toolkit for biological sequence analysis.

Highlights

• FASTA parsing
• Sequence statistics
• GC content
• Reverse complement
• DNA → RNA transcription
• DNA → protein translation
• IUPAC ambiguity-code support
• Motif searching
• ORF detection
• Python API
• Command-line interface
• Python 3.12+ support

Quality

• 68 automated tests
• GitHub Actions CI
• Source distribution and wheel builds
• Clean installation verified from the built wheel

Installation

Download the wheel or source distribution from the assets below.