MycoSNP results to Labware 8 #33
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Adding mycosnp_results_files.py to prepare mycosnp qc results for labware8 import
jwarnn
approved these changes
Jul 27, 2023
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One other thing. The results files have DB ids for SRR and Genebank but those won't be available from the mycosnp results so will there be a companion script or will those have to be added manually? |
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The SRA accessions are a long conversation with an unknown ending. 😅 |
erinyoung
reviewed
Jul 27, 2023
mycosnp_results_files.py
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| # Writing the files for each sample separately | ||
| arln_filename = 'labware8/arln_' + sample + '_results.txt' | ||
| sample_df.to_csv(arln_filename, columns=arln_labware_cols, index=False, sep='\t') |
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The file needs to be a csv file, so please delete the '\t'
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changed the sep='\t' to sep=',' and changed 'results.txt' to 'results.csv'
changed from tab separated to csv
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I have converted this to a draft for now. |
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Adding mycosnp_results_files.py to prepare mycosnp qc results for labware8 import. Some of the changes from Erin's granduer_results_files.py script include functions to gather samplesheet data from either NextSeq 2k or MiSeq due to either being used to sequence C. auris, using 'glob' dependency to find 'qc_report.txt' at any level, parsing of qc_report.txt with qc metrics for passing samples, and only the passing samples with a 'Y' being moved into the 'labware8' directory to use as import.