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05/06/fea amino acid properties #5
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chrismacklin
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May 7, 2019
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Nice improvement, will merge after tweaks.
src/AmyrisBio/biolib.fs
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| (End, { trigram="End" ; letter = '*' ; hydrophobicity = None }) | ||
| ] |> Map.ofList | ||
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| let aaLetterToSymbolic (aa:char) = |
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Please rename as aaLetterToSymbol for consistency,
src/AmyrisBio/biolib.fs
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| | 'Y' -> Tyr | ||
| | 'W' -> Trp | ||
| | '*' -> End | ||
| | _ -> failwithf "ERROR: unknown amino acid letter '%c' in aaLetterToSymbolic" aa |
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Could we use the Result type here instead of raising an exception?
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If it must be an exception, let's either use a more specific exception class or declare a custom exception type.
src/AmyrisBio/biolib.fs
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| /// Translates amino acid represented with one character to a trigram, eg 'W' -> "Trp" , '*' -> "End" | ||
| let aaTrigramToSymbolic (aa:string) = |
src/AmyrisBio/biolib.fs
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| | "Tyr" -> Tyr | ||
| | "Trp" -> Trp | ||
| | "End" -> End | ||
| | _ -> failwithf "bad aa '%s' in aaLetterToSymbolic" aa |
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Result type here as well would be nice.
…mments MIN: addressed review comments
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@chrismacklin , i have addressed all your comments and updated this PR. I think this PR would be easier to be merged before the migration to .net core. |
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This is a small extension to the amino acid representation / handling, a severely neglected corner of our basic representation, that puts the letter e.g. 'K' , symbolic Lys and trigram "Lys" forms on same footing and allows interconversion. Also pulls in some common properties and references. I keep on rewriting standalone versions of this all the time, so contributing back something more permanent