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fgrep (grep -F) option #1184
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Yes, I think so :) Thanks and sorry for my late reply. |
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fgrep
functionality (available withgrep -F
) allows searching form
multiple fixed strings amongn
sequences in O(n) time rather than O(n*m) by leveraging the Aho-Corasick algorithm. For a concrete example, I have afasta_to_tabular
result (20,000 lines) that I want to search for many accession IDs (8,000); or, I might just as easily wish to search for a large number of arbitrary peptide sequences.So, my issue (or question) is the approach to take:
grep
" might be used with fixed strings, even though they are technically regular expressions matching one sequence.grep -F
.@bgruening Would you suggest that I submit a PR for the "Search in textfiles (grep)" tool?
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