⚡ Optimize calculate_tm to avoid string slicing#101
⚡ Optimize calculate_tm to avoid string slicing#101google-labs-jules[bot] wants to merge 2 commits intostablefrom
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- Added `_NN_THERMO_DATA_TUPLE` to map character tuples to thermodynamic values. - Replaced `range(n-1)` loop with `zip(seq, seq[1:])` to iterate over pairs without slicing new strings. - Measured ~8.5% performance improvement on 10k bp sequences.
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💡 What: Refactored
calculate_tminsrc/amplifyp/melting.pyto usezip(seq, seq[1:])and a pre-computed tuple-keyed dictionary_NN_THERMO_DATA_TUPLEinstead of string slicingseq[i : i+2]inside the loop.🎯 Why: String slicing in a tight loop creates unnecessary temporary string objects.
📊 Measured Improvement:
calculate_tmbenchmark on a 10k bp sequence showed ~8.5% improvement (4.64s vs 5.07s for 1000 iterations).PR created automatically by Jules for task 1120015268960086894 started by @fangfufu