use Bio::Seq;
use Bio::SeqIO;

while(my $fname = shift) {
  open(INSEQ, "<$fname") or die $!;
  my $seq;
  ## Grab all the sequence in a single string
  while(<INSEQ>) {
      chomp;
      $seq .= $_;
  }
  close INSEQ;
  my $fname =~ s{\.txt}{}; # strip .txt

  ## Create a new Bio::Seq object with your sequence
  my $seqobj = Bio::Seq->new(-display_id => $fname,
                             -seq  => $seq
                             );

  ## Write it out to filename.fa
  my $outfile = $fname . ".fa";
  my $seqout = Bio::SeqIO->new(-format => 'fasta',
                               -file   => "> $outfile",
                               );
  $seqout->write_seq($seqobj);
}