Version Compatibility

Reference examples tested with: bedtools 2.31+, 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.

GTF/GFF Handling

"Parse gene annotations from GTF/GFF" → Read gene models, extract features by type (gene, exon, CDS), and query attributes from annotation files.

• Python: gffutils.create_db('file.gtf') (gffutils), pyranges.read_gtf() (pyranges)
• CLI: awk on tab-delimited GTF fields

GTF and GFF3 are standard gene annotation formats. Both use 1-based coordinates.