ydeng/autoBIGS.engine
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

began adding PubMLST support

Browse Source
This commit is contained in:
Harrison Deng
2025-01-08 16:54:57 +00:00
parent ad28d9bf20
commit d580402523
9 changed files with 23717 additions and 23 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
src/automlst/engine/local/abif.py
View File

@@ -110,6 +110,6 @@ def _biopython_local_pairwise_alignment(reference: NamedString, query: NamedStri
alignment_result = sorted(aligner.align(reference.sequence, query.sequence))[0] # take the best alignment
return NamedString(alignment_result.sequences[0].id, alignment_result.sequences[0].seq), NamedString(alignment_result.sequences[1].id, alignment_result.sequences[1].seq)
async def reference_consensus_assembly(reference: NamedString, sanger_traces: Collection[SangerTraceData]) -> AsyncGenerator[NamedString]:
async def reference_consensus_assembly(reference: NamedString, sanger_traces: Collection[SangerTraceData]) -> AsyncGenerator[NamedString, Any]:
for sanger_trace in sanger_traces:
yield (await asyncio.to_thread(_biopython_local_pairwise_alignment, reference, sanger_trace))[1]