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Two minor logger formatting tweaks (#186)
Linebreaks and spacing for canonical mismatch errors
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missense_kinase_toolkit/databases/mkt/databases/cbioportal.py

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -99,7 +99,8 @@ def __post_init__(self):
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super().__post_init__()
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if not self.check_entity_id():
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logger.warning(
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f"Study {self.get_entity_id()} not found in cBioPortal instance {self.instance}"
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f"Study {self.get_entity_id()} not found "
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f"in cBioPortal instance {self.instance}"
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)
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if self.pathfile is not None:
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try:
@@ -588,7 +589,7 @@ def remove_mismatched_uniprot_mutations(
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str_errors = "\n".join(set_kinase_mismatch)
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logger.error(
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"HGNC gene names of kinases with mismatches between "
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f"cBioPortal and canonical Uniprot sequences:\n {str_errors}"
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f"cBioPortal and canonical Uniprot sequences:\n{str_errors}"
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)
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df_filtered = df.loc[
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~df["gene_hugoGeneSymbol"].isin(set_kinase_mismatch), :

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