add revcomp_i5 task and bump reports docker #277
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tomkinsc
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Apr 29, 2021
| for row in sheet: | ||
| if row.get('barcode_2') | ||
| and all(s in 'ATGC' for s in row['barcode_2']): | ||
| row['barcode_2'] = str(Bio.Seq.Seq(row['barcode_2']).reverse_complement()) |
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Not that biopython increases the size of the docker image much, but builtins could be used for reverse complementing via bytearray.maketrans() (ex. here; could extend to ambiguity codes.). Probably faster too, though that's not a concern for sample sheets.
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well the general purpose py3-bio docker image already had it, so I figured I'd keep it simple
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This will come in handy! Especially if we automatically re-try demux with a rev-comped sample sheet for failing runs where that's a plausible fix. |
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Yeah then we just have to detect the failure mode reliably and then we can use this to try it… |
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