Mercurial > repos > sanbi-uwc > summarize_poliovirus_alignment
comparison summarize_alignment.py @ 5:7bcfc97b9284 draft default tip
planemo upload for repository https://github.com/pvanheus/polio_report commit 753aad311378b064f2152c8e99e7c8097c7f4321-dirty
| author | sanbi-uwc |
|---|---|
| date | Fri, 11 Nov 2022 06:19:00 +0000 |
| parents | 5c8dfc4d9d68 |
| children |
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| 4:eae57366bc55 | 5:7bcfc97b9284 |
|---|---|
| 28 alignment_summary["sample_name"], | 28 alignment_summary["sample_name"], |
| 29 alignment_summary["best_reference"], | 29 alignment_summary["best_reference"], |
| 30 alignment_summary["mismatches"], | 30 alignment_summary["mismatches"], |
| 31 alignment_summary["perc_mismatches"], | 31 alignment_summary["perc_mismatches"], |
| 32 round(alignment_summary["quality"], 2), | 32 round(alignment_summary["quality"], 2), |
| 33 alignment_summary["vp1_coverage_perc"], | |
| 33 mismatch_list, | 34 mismatch_list, |
| 34 sep="\t", | 35 sep="\t", |
| 35 file=summary_output, | 36 file=summary_output, |
| 36 ) | 37 ) |
| 37 variant_list_output = open(args.variant_list_outputs[i], "w") | 38 variant_list_output = open(args.variant_list_outputs[i], "w") |