Mercurial > repos > bimib > cobraxy

comparison COBRAxy/ras_generator.py @ 530:352c51a39e23 draft

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author francesco_lapi
date Wed, 22 Oct 2025 12:18:07 +0000
parents 6acd64232dad
children 1fc5c1edb0ef
comparison
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529:6acd64232dad 530:352c51a39e23
348 # Store genes not mapped for later use 348 # Store genes not mapped for later use
349 self.genes_not_mapped = sorted(genes_not_mapped) 349 self.genes_not_mapped = sorted(genes_not_mapped)
350 350
351 # create the dataframe of ras (rules x samples) 351 # create the dataframe of ras (rules x samples)
352 ras_df = pd.DataFrame(data=ras_df, index=range(len(self.dict_rule_reactions)), columns=self.cell_ids) 352 ras_df = pd.DataFrame(data=ras_df, index=range(len(self.dict_rule_reactions)), columns=self.cell_ids)
353 ras_df['REACTIONS'] = [reaction_ids for rule, reaction_ids in self.dict_rule_reactions.items()] 353 ras_df['Reactions'] = [reaction_ids for rule, reaction_ids in self.dict_rule_reactions.items()]
354 354
355 reactions_common = pd.DataFrame() 355 reactions_common = pd.DataFrame()
356 reactions_common["REACTIONS"] = ras_df['REACTIONS'] 356 reactions_common["Reactions"] = ras_df['Reactions']
357 reactions_common["proof2"] = ras_df['REACTIONS'] 357 reactions_common["proof2"] = ras_df['Reactions']
358 reactions_common = reactions_common.explode('REACTIONS') 358 reactions_common = reactions_common.explode('Reactions')
359 reactions_common = reactions_common.set_index("REACTIONS") 359 reactions_common = reactions_common.set_index("Reactions")
360 360
361 ras_df = ras_df.explode("REACTIONS") 361 ras_df = ras_df.explode("Reactions")
362 ras_df = ras_df.set_index("REACTIONS") 362 ras_df = ras_df.set_index("Reactions")
363 363
364 if drop_na_rows: 364 if drop_na_rows:
365 ras_df = ras_df.dropna(how="all") 365 ras_df = ras_df.dropna(how="all")
366 366
367 if drop_duplicates: 367 if drop_duplicates: