Mercurial > repos > sanbi-uwc > assess_poliovirus_alignment
comparison assess_alignment.py @ 4:1897677e107c draft
planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty
| author | sanbi-uwc |
|---|---|
| date | Fri, 22 Jul 2022 09:55:46 +0000 |
| parents | 31ca16290d4f |
| children | 0e556a3f85d6 |
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| 3:52c2d2b7da6c | 4:1897677e107c |
|---|---|
| 104 for i, state in enumerate(base_state): | 104 for i, state in enumerate(base_state): |
| 105 # i is in zero-based genome coordinates | 105 # i is in zero-based genome coordinates |
| 106 if state == "M": | 106 if state == "M": |
| 107 # for mismatch store [pos_in_genome, pos_in_vp1, reference_base, sequenced_base] | 107 # for mismatch store [pos_in_genome, pos_in_vp1, reference_base, sequenced_base] |
| 108 mismatch_list.append( | 108 mismatch_list.append( |
| 109 [i, i - offset + 1, reference["align"][i], mismatch_bases[i]] | 109 [i + 1, i - offset + 1, reference["align"][i], mismatch_bases[i]] |
| 110 ) | 110 ) |
| 111 return [conflicts, matches, mismatches, mismatch_list] | 111 return [conflicts, matches, mismatches, mismatch_list] |
| 112 | 112 |
| 113 | 113 |
| 114 def analyse_trace_quality(json_file: TextIO) -> float: | 114 def analyse_trace_quality(json_file: TextIO) -> float: |