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compressed-files

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Read, write, and index compressed sequence files (gzip, bzip2, xz, BGZF) with Biopython and bgzip/samtools. Use when working with .gz, .bz2, or .bgz sequence files, when random access into a compressed FASTA/FASTQ is needed, or when SeqIO.index/faidx/tabix rejects a plain .gz. Covers the BGZF-vs-gzip seekability asymmetry, the 'rt'-not-'rb' handle trap, virtual offsets, and gzip-to-BGZF conversion.

When to use

• | Use case | Format | Why | |----------|--------|-----| | Sequential read/write, sharing | gzip | Universal, fast, every tool reads it | | Need `faidx`/`tabix`/`SeqIO.index` | **BGZF** | Only seekable compressed format | | BAM, tabix-index…

When not to use

• Random access on plain gzip files
• Indexing bzip2 or xz files
• Reading plain gzip with bgzf.open

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