It'd be nice to see some attempts you've made or to at least get some parameters like the size of the lists. In the absence of details, here's a few hints:

  1. Split the second file by the ">" at the beginning on a line. The ">" can easily be replaced on output.
  2. Turn this array into a "hash or arrays" (HoA). The key will be the sequence tag after the "R.fna." and the value will either be the raw sequence or the whole record (sans ">") if the "R.fna." isn't consistent. You can check the docs on HoA but the general idea is to use push when loading the hash values.
  3. Run through your first file and pull out all matches to the hash keys.
  4. Pick what sort of output format and remember to add the ">" to the start of each line.

In reply to Re: compare a list from one file with another text file by igelkott
in thread compare a list from one file with another text file by sm2004

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