Create script to auto-fill control/condition samples

[sgiannouk]

Create a helper script (pipelines/geo/autoassign_sample_groups.py) that automatically fetches GEO sample metadata and classifies samples as control or condition based on their titles/characteristics.

Goals
[ ] Parse mirna_experiment_info.tsv

[ ] For each GSE, query NCBI Entrez API to get all GSM sample metadata

[ ] Classify samples into Control and Condition using Claude Code skills

[ ] Output a draft TSV with control_samples and condition_samples columns filled

[ ] Flag when done/ambiguous cases for manual review

Final Workflow

1. Run autoassign_sample_groups.py → generates draft with auto-filled columns
2. Manual review and corrections
3. Run RNA-seq pipeline with verified sample assignments