Source: https://github.com/aipoch/medical-research-skills

biopython-sequence-io

When to Use

• Converting between common sequence formats (e.g., FASTA ↔ GenBank, FASTQ → FASTA) while preserving identifiers and annotations.
• Reading and writing sequence datasets for downstream pipelines (alignment, assembly, annotation) with consistent parsing and output.
• Performing basic sequence operations (reverse complement, translation, slicing) without implementing custom parsers.
• Processing large sequence files efficiently via streaming iteration or indexed access instead of loading everything into memory.
• Computing simple sequence statistics and filtering records (length, GC content, ambiguous bases) during ingestion.

Key Features

• Sequence objects and basic operations using Bio.Seq.Seq (slicing, reverse complement, transcription/translation).
• Robust sequence I/O via Bio.SeqIO for parsing and writing FASTA/GenBank/FASTQ and other supported formats.
• Format conversion by reading records in one format and writing them in another.
• Scalable processing with iterator-based parsing and optional indexed access (SeqIO.index) for large files.
• Common filtering/statistics patterns (length thresholds, GC%, quality-aware handling for FASTQ).