Fix notebook NameErrors and add scan/enrichment examples

[ShinyaYoshida-biomet]

Summary

Since I got these errors when I tried to execute the notebook, I fixed the name and attribute references, respectively.

Fix 1

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[16], line 3
      1 from pyjaspar.analysis import pearson_correlation, best_correlation
----> 3 m1 = jdb.fetch_motif_by_id("MA0001.1")
      4 m2 = jdb.fetch_motif_by_id("MA0002.1")
      6 # Column-wise Pearson correlation

NameError: name 'jdb' is not defined

before:

m1 = jdb.fetch_motif_by_id("MA0001.1")
m2 = jdb.fetch_motif_by_id("MA0002.1")

after:

m1 = jdb_obj.fetch_motif_by_id("MA0001.1")
m2 = jdb_obj.fetch_motif_by_id("MA0002.1")

Fix 2

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[21], line 4
      2 models = jdb.dl.search_models(tf_name="REST", cell_line="K562")
      3 for m in models:
----> 4     print(f"{m.model_id}: {m.tf_name} ({m.cell_line}) ({p.tax_group})")

NameError: name 'p' is not defined

before:

# Search profiles by TF name and combined filters
models = jdb.dl.search_models(tf_name="REST", cell_line="K562")
for m in models:
    print(f"{m.model_id}: {m.tf_name} ({m.cell_line}) ({p.tax_group})")

after:

# Search profiles by TF name and combined filters
models = jdb.dl.search_models(tf_name="REST", cell_line="K562")
for m in models:
    print(f"{m.model_id}: {m.tf_name} ({m.cell_line}) ({m.tax_id})")

Added scan and enrichment examples

The "Analysis module" section only had a similarity/correlation example. I added a scan_sequence example (CTCF motif against a sequence containing its consensus) and a motif_enrichment example (pulling a small set of candidate motifs by tf_family="Homeo" rather than by hardcoded ID, then showing that only the true positive comes out enriched against a matched-length background set).

Both new cells were executed and their outputs saved, same as the rest of the notebook.

Test plan

• Ran the full notebook top to bottom (jupyter execute --inplace) after each fix, confirmed no errors
• Verified the two NameErrors no longer occur
• Verified the new scan/enrichment cells produce correct, sensible output (CTCF hits found in the scan sequence; only the Dbx motif enriched in the enrichment example, as designed)