fixes issue encountered during testing. #96
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qp_klp/Protocol.py
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| with open(files_to_count_path, 'w') as f: | ||
| # for raw_counts_r1r2, count corrected.err_barcode_removed files | ||
| # (TellReadJob final output). | ||
| for root, dirs, files in walk(self.raw_fastq_files_path): | ||
| for _file in files: | ||
| if 'corrected.err_barcode_removed' in _file: | ||
| print(join(root, _file), file=f) |
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I don't really understand this step, it's just used for printing and not nothing gets written in the file, is that what you want to do?
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Actually, this is equivalent to writing f.write("%s\n" % join(root, _file)). There is an additional parameter "file=f" that redirects the print statement from stdout to the file handle 'f'. I've been using this form lately instead of constructing a string just for the sake of appending a newline.
qp_klp/Protocol.py
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| # (TellReadJob final output). | ||
| for root, dirs, files in walk(self.raw_fastq_files_path): | ||
| for _file in files: | ||
| if 'corrected.err_barcode_removed' in _file: |
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Why are these files being examined?
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yup, I have this marked in my notes. there is a patch for this that expects the integrated results directory instead of Full.
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