Port prot2pept to typescript #176
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pverscha
reviewed
Jun 21, 2024
lib/commands/prot2pept.ts
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| pattern = new RegExp(this.program.opts().pattern, "g"); | ||
| } catch (e) { | ||
| this.program.error(`Your pattern was invalid: ${(e as Error).message}`); | ||
| //process.exit(1); |
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I think this should be uncommented again for the final release?
| } | ||
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| static splitProtein(line: string, pattern: RegExp): string { | ||
| return line.replaceAll(pattern, "$1\n$2").replaceAll(pattern, "$1\n$2").replaceAll("\n\n", "\n"); |
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I'm probably overlooking something, but why do we perform replaceAll(pattern, "$1\n$2") twice with the same pattern?
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It's to catch overlapping patterns, like KRKRK
pverscha
reviewed
Jun 21, 2024
Co-authored-by: Pieter Verschaffelt <[email protected]>
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This PR ports prot2pept to typescript.
I ran a benchmark on swissprot. The output is exactly the same between both implementations. Performance improved from 26.5 to 5 seconds.