use strict; use warnings; #my $count = 1; #my $file; my @files = ; foreach my $file(@files){ open (FILE,"$file") or die "$!"; my $outfile = $file."out"; open (OFILE,'>',"$outfile") or die "$!"; my $count = 1; while () { chomp; if( s/^>\S+/>contig_$count/) { $count++; } if( /^(\S+)$/) {print OFILE"$1\n\n"} } }