use strict;
use warnings;
my $idsfile = "sample_IDs.txt";
my $seqfile = "sample_reads.fasta";
my %ids  = ();

open (my $idfh, "<", $idsfile) or die "Can't open $idsfile - ", $!, "\n";
while(my $line = <$idfh>) {
  chomp $line;
  next unless $line;
  my @contents = split /\s/, $line;
  $ids{$contents[0]} += 1;
}
close $idfh;

local $/ = "\n>";  # read by FASTA record

open (my $fastafh, "<", $seqfile) or die "Can't open $seqfile - ", $!, "\n";
while (my $line = <$fastafh>) {
    chomp $line;
	next unless $line;
    my ($id) = $line =~ /^(\S+)/;  # parse ID as first word in FASTA header
	next unless $id;
    if ($ids{">" . $id}) {
        $line =~ s/^>*.+\n//;  # remove FASTA header
        $line =~ s/\n//g;  # remove endlines
        print "$line\n";
    }
}
close $fastafh;