<jupyter_start><jupyter_text>Load Vogelstein and Park gene info<jupyter_code>vogelstein_genes = '/'.join([
    cfg.vogelstein_base_url,
    cfg.vogelstein_commit,
    'data',
    'vogelstein_cancergenes.tsv'
])
print(vogelstein_genes)
vogelstein_df = (
    pd.read_csv(vogelstein_genes, sep='\t')
      .rename(columns={'Gene Symbol'   : 'gene',
                       'Classification*': 'classification'})
)
vogelstein_df.head()
park_loss_df = pd.read_csv(cfg.data_dir / 'park_loss_df.tsv', sep='\t')
park_loss_df.head()
park_gain_df = pd.read_csv(cfg.data_dir / 'park_gain_df.tsv', sep='\t')
park_gain_df.head()<jupyter_output><empty_output><jupyter_text>Look at overlap between Park and Vogelstein genes<jupyter_code>sns.set_style('white')

park_loss_genes = set(park_loss_df.Gene.unique())
vogelstein_genes = set(vogelstein_df.gene.unique())

venn2_unweighted([park_loss_genes, vogelstein_genes], ['Park (loss)', 'Vogelstein'])
plt.title('Park/Vogelstein gene set overlap')
print(len(park_loss_genes - vogelstein_genes))
print(sorted(park_loss_genes - vogelstein_genes))
sns.set_style('white')

park_gain_genes = set(park_gain_df.Gene.unique())
vogelstein_genes = set(vogelstein_df.gene.unique())

venn2_unweighted([park_gain_genes, vogelstein_genes], ['Park (gain)', 'Vogelstein'])
plt.title('Park/Vogelstein gene set overlap')
print(len(park_gain_genes - vogelstein_genes))
print(sorted(park_gain_genes - vogelstein_genes))<jupyter_output><empty_output>
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{'chain_length': '2', 'dir': 'jupyter-structured-clean-dedup', 'id': '132265', 'license': 'BSD-3-Clause', 'n_tokens_mistral': 610, 'n_tokens_neox': 550, 'n_words': 73, 'path': '0_download_data/1_park_overlap.ipynb', 'repo_name': 'jjc2718/mutation-fn', 'size': '1459'}