UNIX for Advanced & Expert Users

>cel-let-7 MI0000001 Caenorhabditis elegans let-7 stem-loop
TACACTGTGGATCCGGTGAGGTAGTAGGTTGTATAGTTTGGAATATTACCACCGGTGAACTATGCAATTTTCTACCTTACCGGAGACAGAACTCTTCGA
>cel-lin-4 MI0000002 Caenorhabditis elegans lin-4 stem-loop
ATGCTTCCGGCCTGTTCCCTGAGACCTCAAGTGTGAGTGTACTATTGATGCTTCACACCTGGGCTCTCCGGGTACCAGGACGGTTTGAGCAGAT
>dps-mir-317 MI0001358 Drosophila pseudoobscura miR-317 stem-loop
TGCAACTGCCGTTGGGATACACCCTGTGCTCGCTTTGAATATGGTGCAAGCAAGTGAACACAGCTGGTGGTATCCAATGGCCGTTCTGCA
>dps-mir-318 MI0001359 Drosophila pseudoobscura miR-318 stem-loop
TTTATGGGATGCACCAAGTTCAGTTTTGTCACATTTCGAGCATCACTGGGCTTTGTTTATCTCATAAG
>dre-mir-7b MI0001360 Danio rerio miR-7b stem-loop
TGAACGCTGGCTTGCTTCTGTGTGGAAGACTTGTGATTTTGTTGTTGTTAGTTAGATGAAGTGACAACAAATCACGGTCTGCCCTACAGCACAGGCCCAGCATC

$ grep 'dre' hairpin.fa > dre.fa

>dre-mir-7b MI0001360 Danio rerio miR-7b stem-loop
>dre-mir-7a-1 MI0001361 Danio rerio miR-7a-1 stem-loop
>dre-mir-7a-2 MI0001362 Danio rerio miR-7a-2 stem-loop

awk 'END { 
   if (r) print r 
   }
/^>/ {
  if (r ~ p) 
    print r 
  r = x 
  }
{ 
  r = r ? r RS $0 : $0 
  }' p=dre infile

sed '/^>/N;s/\n/ /;/dps/!d' infile

sed '/^>/N;s/\n/ /;/dre/!d' infile