8000 Add option to use FASTA files with protein sequences using Fred2 by skrakau · Pull Request #42 · nf-core/epitopeprediction · GitHub
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Add option to use FASTA files with protein sequences using Fred2 #42

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Merged
merged 1 commit into from
Apr 14, 2020
Merged

Add option to use FASTA files with protein sequences using Fred2 #42

merged 1 commit into from
Apr 14, 2020

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skrakau
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@skrakau skrakau commented Apr 2, 2020 •
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Alternative to #33 using Fred2.

Many thanks for contributing to nf-core/epitopeprediction!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

PR checklist

  • This comment contains a description of changes (with reason)
  • If you've fixed a bug or added code that should be tested, add tests!
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Learn more about contributing: https://github.com/nf-core/epitopeprediction/tree/master/.github/CONTRIBUTING.md

@skrakau skrakau requested a review from christopher-mohr April 2, 2020 16:23
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skrakau commented Apr 2, 2020

If the FASTA ID of the proteins contains "|"s, this will not be split as within Fred2 normally. Everything until the first whitespace is used.

In general, using the protein IDs in the results file decreases the readability for peptides occurring in many proteins, but I also don't know any better solution for now.

@skrakau skrakau mentioned this pull request Apr 7, 2020
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christopher-mohr
christopher-mohr requested changes Apr 7, 2020
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@skrakau skrakau force-pushed the add_fasta_option_with_fred2 branch from 24ba9f6 to 6ba69d8 Compare April 9, 2020 19:22
@christopher-mohr christopher-mohr merged commit 0511221 into nf-core:dev Apr 14, 2020
@skrakau skrakau mentioned this pull request Aug 25, 2020
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