Mercurial > repos > sanbi-uwc > summarize_poliovirus_alignment

annotate summarize_alignment.py @ 5:7bcfc97b9284 draft default tip

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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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7e49c6b19f5e planemo upload commit a99e10fec2fac5aae70974c977eb3b362a1a8429
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1 #!/usr/bin/env python
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3 import argparse
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4 import json
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6 def comma_split(args: str) -> list[str]:
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7 return args.split(",")
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10 if __name__ == "__main__":
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11 parser = argparse.ArgumentParser()
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12 parser.add_argument("--summary_output_filename", help="Path to summary output file")
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13 parser.add_argument("--variant_list_outputs", nargs="+")
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14 parser.add_argument("--datasets", nargs="+")
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15 args = parser.parse_args()
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16
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17 galaxy_metadata = {}
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18 summary_output = open(args.summary_output_filename, "w")
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19 for i, json_filename in enumerate(args.datasets):
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20 alignment_summary = json.load(open(json_filename))
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21 mismatch_list = ";".join(
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22 [
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23 ":".join([str(part) for part in el[1:]])
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24 for el in alignment_summary["mismatch_list"]
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25 ]
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26 )
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27 print(
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28 alignment_summary["sample_name"],
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29 alignment_summary["best_reference"],
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30 alignment_summary["mismatches"],
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31 alignment_summary["perc_mismatches"],
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32 round(alignment_summary["quality"], 2),
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33 alignment_summary["vp1_coverage_perc"],
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34 mismatch_list,
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35 sep="\t",
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36 file=summary_output,
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37 )
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38 variant_list_output = open(args.variant_list_outputs[i], "w")
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39 print('genome pos', 'VP1 pos', 'ref', 'sequence', sep='\t', file=variant_list_output)
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40 for variant in alignment_summary["mismatch_list"]:
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41 print("\t".join([str(el) for el in variant]), file=variant_list_output)
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42 variant_list_output.close()