Version Compatibility

Reference examples tested with: pandas 2.2+

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

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

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

Methylation Calling

"Extract methylation calls from my Bismark BAM" → Generate per-cytosine methylation reports (CpG, CHG, CHH contexts) from aligned bisulfite sequencing data.

• CLI: bismark_methylation_extractor --bedGraph --cytosine_report sample.bam

Basic Extraction