Version Compatibility

Reference examples tested with: BioPython 1.83+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Compressed Files

Handle gzip, bzip2, and BGZF compressed sequence files with Biopython.

"Read a compressed sequence file" → Open a compressed file handle in text mode, then parse with the standard SeqIO interface.

• gzip: gzip.open(path, 'rt') (Python stdlib)
• bzip2: bz2.open(path, 'rt') (Python stdlib)
• BGZF: bgzf.open(path, 'rt') (BioPython) or direct SeqIO.parse(path, fmt)