Csplit Multifasta File Into A *Smaller Multifasta File
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Entering edit mode
9.4 years ago
neal.platt ▴ 230

I am trying to split a large multifasta file into several smaller mutlifasta files. I have seen several examples of csplit being used to split multifasta files into single fasta, but for our purposes this is less than ideal.

I have been using the following command:

  csplit -kf fastafile '%^>%' '/^>/' "{10}"

How would I modify this to generate a file with 10 fasta sequences rather than splitting at individual fasta headers (>).

Would awk be more useful?

Thanks for the help in advance.

split fasta • 4.7k views
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Entering edit mode
9.4 years ago

From your description I am not exactly sure how you want to split your file but there are a number of posts on splitting fasta files, perhaps those help

http://www.biostars.org/post/show/2226/how-to-split-a-multiple-fasta/

and

http://www.biostars.org/post/show/13270/how-to-split-one-big-sequence-file-into-multiple-files-with-less-than-1000-sequences-in-a-single-file/

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