use warnings; use strict; { ## modify input record separator to read ## each FASTA record separately local $/ = '>'; ## test each record, printing out if it has ## pair field while (){ print $_ if ($_ =~ /pair:\d+/); } } __DATA__ >CVSF43567.d1 bg|346280 CGTAGCTGATGCTGTGCTGTTGTGTCGGGGGGATATATATATATATATGGGGTCGTAGTCGTAGCGCTAG TATGCTAGCAGCGTAGATGCTGATCGATGCTGATGCTGATCGTAGTCGTAGGCTAGTGCGATCGTAGTCG TAGTCGATGCTGATGCGTAGCTGATGTGCTGCTGATGCTAGTCGTCGTAGCTGATGCATGCTGATCGTAG TGCTCGATGCTAGTCGTAGTCGTAGTCGTAGCGACTGATGCGATCGTAGTCGGATGCTAGCACGTAGCTG GCTCGATGCTGATGCTGAT >CVSF10000.x1 bg|356789 pair:789860 ATGCGTAGCTGATGTGCTGCTGATGCTAGTCGTCGTAGCTGATGCATGCTGATCGTAGTGCTCGATGCTA GTCGTAGTCGTAGTCGTAGCGACTGATGCGATCGTAGTCGGATGATGCTGACTGATGCTGATCTGTACGT CGTAGCTGATGCATGCGCTAGTAGCT >CVSF10000.y1 bg|356790 pair:789859 GCTAGTCGATGCTGATGCTGTAGCTAGCGTAGTCGTACGCGCGCGCGCGCGTTTTTTGTGACGTCGTAGT CCGTAGCTGATGCGATGCTAGTGCTGTGTCAGCTGATGTCGTGTGTAGCTGATGCTGATCGTTCGTGTGT CGATGCTGATGCTAGTCGTAGTGTAT