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Adding mycosnp_results_files.py to prepare mycosnp qc results for labware8 import
jwarnn
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Jul 27, 2023
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I was able to get this script to run and produce an output that looks like what is intended. Has there been any testing as to if the files are picked up by LabWare8?
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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
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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.