Mercurial > repos > greg > pima_report
changeset 10:7c4077c9b3ad draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 09 Mar 2023 18:21:26 +0000 |
| parents | 9d608c530bbc |
| children | 4a7c31f28197 |
| files | pima_report.py |
| diffstat | 1 files changed, 9 insertions(+), 10 deletions(-) [+] |
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--- a/pima_report.py Thu Mar 09 18:13:37 2023 +0000 +++ b/pima_report.py Thu Mar 09 18:21:26 2023 +0000 @@ -429,16 +429,15 @@ kraken_fracs['Taxa'] = kraken_fracs['Taxa'].str.lstrip() self.doc.new_line() self.doc.new_header(2, 'Contamination check') - for read_type, kraken_fracs in kraken_fracs.iteritems(): - self.doc.new_line(self.read_type + ' classifications') - self.doc.new_line() - Table_List = ["Percent of Reads", "Reads", "Level", "Label"] - for index, row in kraken_fracs.iteritems(): - Table_List = Table_List + row.tolist() - row_count = int(len(Table_List) / 4) - self.doc.new_table(columns=4, rows=row_count, text=Table_List, text_align='left') - if self.contamination_methods_title not in self.methods: - self.methods[self.contamination_methods_title] = '' + self.doc.new_line(self.read_type + ' classifications') + self.doc.new_line() + Table_List = ["Percent of Reads", "Reads", "Level", "Label"] + for index, row in kraken_fracs.iterrows(): + Table_List = Table_List + row.tolist() + row_count = int(len(Table_List) / 4) + self.doc.new_table(columns=4, rows=row_count, text=Table_List, text_align='left') + if self.contamination_methods_title not in self.methods: + self.methods[self.contamination_methods_title] = '' method = 'Kraken2 version %s was used to assign the raw reads into taxa.' % self.kraken2_version self.methods[self.contamination_methods_title] = self.methods[self.contamination_methods_title].append(pandas.Series(method))