Mercurial > repos > greg > pima_report
changeset 11:4a7c31f28197 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 09 Mar 2023 18:34:01 +0000 |
| parents | 7c4077c9b3ad |
| children | 99613333fd1f |
| files | pima_report.py |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/pima_report.py Thu Mar 09 18:21:26 2023 +0000 +++ b/pima_report.py Thu Mar 09 18:34:01 2023 +0000 @@ -438,7 +438,7 @@ 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 + method = '%s was used to assign the raw reads into taxa.' % self.kraken2_version.rstrip('report') self.methods[self.contamination_methods_title] = self.methods[self.contamination_methods_title].append(pandas.Series(method)) def add_alignment(self): @@ -523,7 +523,7 @@ self.ofh.write("Before new_table, len(Table_List):: %s\n" % str(len(Table_List))) self.doc.new_table(columns=5, rows=row_count, text=Table_List, text_align='left') if self.blastn_version is not None: - blastn_version = 'The genome assembly was queried for features using blastn version %s.' % self.blastn_version + blastn_version = 'The genome assembly was queried for features using %s.' % self.blastn_version bedtools_version = 'Feature hits were clustered using bedtools and the highest scoring hit for each cluster was reported.' method = '%s %s' % (blastn_version, bedtools_version) self.methods[self.feature_methods_title] = self.methods[self.feature_methods_title].append(pandas.Series(method)) @@ -744,7 +744,7 @@ self.evaluate_assembly() self.add_assembly_information() if self.flye_assembly_info_file is not None: - method = 'ONT reads were assembled using %s' % self.flye_version + method = 'ONT reads were assembled using %s' % self.flye_version.rstrip('assembly info') self.methods[self.assembly_methods_title] = self.methods[self.assembly_methods_title].append(pandas.Series(method)) # Pull in the assembly summary and look at the coverage. assembly_info = pandas.read_csv(self.flye_assembly_info_file, header=0, index_col=0, sep='\t')