I have a fasta file with a thousand sequences with a distribution of lengths between 100 and 150bp. I would like to add Ns to all sequences whose length is <150. I know it is possible but thus far I have yet to find anything to easily do this. Please help. Thanks!
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Cross-posted:
https://www.biostars.org/p/238635/
Please link other sites when you cross-post, so people don't waste their time answering a question that has already been answered. -
Not fast, but something like:
Code:perl -e 'while(<>) {if (/^>/) {print;next}; chomp; print $_,"N" x (150-length($_)),"\n"}' in.fastaComment
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That looks like it should be plenty fast enough, more likely to be limited by the read speed of the hard drive than the speed of the code.Comment
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