Mercurial > repos > greg > pima_report

comparison pima_report.py @ 6:b13d4c14caaa draft

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author greg
date Thu, 09 Mar 2023 17:54:17 +0000
parents 9cb62054a87a
children 9213359bfda8
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5:7177d81eb7cb 6:b13d4c14caaa
419 def add_contamination(self): 419 def add_contamination(self):
420 self.ofh.write("\nXXXXXX In add_contamination\n\n") 420 self.ofh.write("\nXXXXXX In add_contamination\n\n")
421 if self.kraken2_report_file is None: 421 if self.kraken2_report_file is None:
422 return 422 return
423 # Read in the Kraken fractions and pull out the useful parts 423 # Read in the Kraken fractions and pull out the useful parts
424 self.kraken_fracs = pandas.read_csv(self.kraken_report_file, delimiter='\t', header=None) 424 self.kraken_fracs = pandas.read_csv(self.kraken2_report_file, delimiter='\t', header=None)
425 self.kraken_fracs.index = self.kraken_fracs.iloc[:, 4].values 425 self.kraken_fracs.index = self.kraken_fracs.iloc[:, 4].values
426 self.kraken_fracs = self.kraken_fracs.loc[self.kraken_fracs.iloc[:, 3].str.match('[UG]1?'), :] 426 self.kraken_fracs = self.kraken_fracs.loc[self.kraken_fracs.iloc[:, 3].str.match('[UG]1?'), :]
427 self.kraken_fracs = self.kraken_fracs.loc[(self.kraken_fracs.iloc[:, 0] >= 1) | (self.kraken_fracs.iloc[:, 3] == 'U'), :] 427 self.kraken_fracs = self.kraken_fracs.loc[(self.kraken_fracs.iloc[:, 0] >= 1) | (self.kraken_fracs.iloc[:, 3] == 'U'), :]
428 self.kraken_fracs = self.kraken_fracs.iloc[:, [0, 1, 3, 5]] 428 self.kraken_fracs = self.kraken_fracs.iloc[:, [0, 1, 3, 5]]
429 self.kraken_fracs.columns = ['Fraction', 'Reads', 'Level', 'Taxa'] 429 self.kraken_fracs.columns = ['Fraction', 'Reads', 'Level', 'Taxa']