extend sub matrix alphabets to avoid exceptions during alignment

gamcil / clinker

Gene cluster comparison figure generator

MIT License

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extend sub matrix alphabets to avoid exceptions during alignment #55

Closed gamcil closed 3 years ago

gamcil commented 3 years ago

PairwiseAligner from BioPython.Align throws ValueError when letter in sequence isn't found in the subsitution matrix. BLOSUM62 (default) does not contain some extended IUPAC codes (e.g. U), causing crashes (https://github.com/gamcil/clinker/issues/11). This PR checks for missing codes and alters the matrix before alignments to mitigate this.