Implement FASTA/FASTQ parser for #60#97
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Add comprehensive acceptance tests for FASTA/FASTQ parser covering:
- Valid FASTA files (single/multiple sequences, wrapped lines)
- Valid FASTQ files (4-line format with quality scores)
- Auto-detection via magic bytes ('>' for FASTA, '@' for FASTQ)
- Gzip compression support (transparent decompression)
- Iterator-based streaming for memory efficiency
- Quality score validation (length must match sequence length)
- Empty file handling (returns empty iterator)
- Malformed file detection (missing quality, wrong line count, invalid characters)
- Edge cases (long sequences, special characters, IUPAC codes, case insensitivity)
- Real-world formats (NCBI FASTA headers, Illumina FASTQ headers)
All tests currently fail (RED phase) as implementation does not exist yet.
Test stats: 13 passed (error-expecting tests), 30 failed (feature tests)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Implement parse_sequences() function that:
- Auto-detects FASTA ('>') vs FASTQ ('@') format via magic bytes
- Supports gzip-compressed files (.gz extension and 0x1f 0x8b magic bytes)
- Validates entire file upfront before returning iterator
- Returns error-checked iterator that yields Sequence objects
- Handles wrapped sequence lines (FASTA) and 4-line FASTQ format
- Validates quality score length matches sequence length (FASTQ)
- Accepts IUPAC ambiguity codes (N, R, Y, S, W, K, M, B, D, H, V)
- Case-insensitive DNA base validation
- Parses sequence ID, optional description, bases, and quality scores
- Gracefully handles empty files, whitespace-only files
- Provides clear error messages for malformed files
All 42 acceptance tests pass (happy path + error cases + edge cases).
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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Closing stale PR. Work has been superseded or merged via alternative approach. |
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Summary
Implements the FASTA/FASTQ parser (parse_sequences) for phraya-io, fulfilling all acceptance criteria for issue #60:
Implementation Details
Test Results
🤖 Generated with Claude Code