root > more translate2.pl
#!/usr/bin/perl -w
# Translates fasta DNA sequences to AA frame 1

use Bio::SeqIO;

my $file_in = shift
  or die "Usage: perl translate2.pl fastafilein";

my $seqin = Bio::SeqIO->new
  (-file => "$file_in", -format => "Fasta");

my $seqout = Bio::SeqIO->new
  (-file => ">translated.pep", -format => "Fasta");

#While there are sequences to be read from input file,
#translate the current sequence and write it to the output file.
while((my $seqobj = $seqin->next_seq())) {
  my $trans = $seqobj->translate;    # "translate" object
  $seqout->write_seq($trans);
  }

exit;

root > more orf15.tfa
>ORF15 BACKTRANSLATE of: : orf15.pep  check: 4419  from: 1  to: 485
AUGGAAGACGUUACCAACGAAGAAGUUUUCGAAAUGAUCGACUCCCGUACCGGUGUUCUG
AACGCUAACGACUGGAAAUCCCAGCUGCGUCGUUCCGCUACCACCCAGGCUCUGAAAAAA
ACCACCACCAACGCUGAAAUCAUCCUGUGCAACGACGAAUCCCUGAAAGGUCUGGUUCAG
UACGACGCUUUCGAAAAAGUUACCAAACUGAAACGUCUGCCGUACUGGCGUUCCAAAGGU
GACACCAACUACUACUGGGCUGACAUCGACACCACCCACGUUAUCUCCCACAUCGACAAA
CUGUACAACGUUCAGUUCUCCCGUGACCUGAUCGACACCGUUAUCGAAAAAGAAGCUUAC
CAGAACCGUUUCCACCCGAUCAAAUCCAUGAUCGAAUCCAAAUCCUGGGACGGUAUCAAA
CGUAUCGAAACCCUGUUCAUCGACUACCUGGGUGCUGAAGACAACCACUACAACCGUGAA
GUUACCAAAAAAUGGAUGAUGGGUGCUGUUGCUCGUAUCUACCAGCCGGGUAUCAAAUAC
GACUCCAUGAUCAUCCUGUACGGUGGUCAGGGUGUUGGUAAAUCCACCGCUGUUUCCAAA
CUGGGUGGUCACUGGUACAACCAGUCCAUCAAAACCUUCAAAGGUGACGAAGUUUACAAA
AAACUGCAGGGUUCCUGGAUCUGCGAAAUCGAAGAACUGUCCGCUUUCCAGAAAUCCACC
AUCGAAGACAUCAAAGGUUUCAUCUCCGCUAUCGUUGACAUCUACCGUGCUUCCUACGGU
AAACGUACCGAACGUCACCCGCGUCAGUGCGUUUUCGUUGGUACCACCAACAACUACGAA
UUCCUGAAAGACCAGACCGGUAACCGUCGUUUCUUCCCGAUCACCACCGACAAAAACAAA
GCUACCAAAUCCCCGUUCGACGACCUGACCCCGGACGUUGUUCAGCAGAUGUUCGCUGAA
GCUAAAGUUUACUUCGACGAAGACCCGACCGACAAAGCUCUGCUGCUGGACAAAGAAGCU
UCCGAAAUGGCUCUGAAAGUUCAGGAAGCUCACUCCGAAAAAGACGCUCUGGUUGGUGAA
AUCGAAGAAUUCCUGGAACGUCCGAUCCCGUCCGACUACUGGUACCGUACCCUGGAAGAA
AAACGUGUUUCCGCUCACGACGUUAUCGACCAGGACUACAUCAAACUGUACGGUGACGGU
AAACUGAUCGAACUGCCGAACACCAAACCGGGUGCUUACGUUUGGCGUGACAAAGUUUGC
UCCAUGGAAAUCUGGAAAGUUAUGAUGAAACGUGACGACCAGCCGCAGCAGCACCACCUG 
CGUAAAAUCGACAAAGCUCUGCGUAACACCAACUACUGCGACACCGUUAAAAAACAGACC
CGUUACGGUGAAGGUAUCGGUAAACAGUACGGUUUCUCCGUUGACCUGGCUUCCUACUAC
AAAAACCUGAAAGUU

root > perl translate2.pl orf15.tfa

root > more translated.pep
>ORF15 orf15.pep  check: 4419  from: 1  to: 485
MEDVTNEEVFEMIDSRTGVLNANDWKSQLRRSATTQALKKTTTNAEIILCNDESLKGLVQ
YDAFEKVTKLKRLPYWRSKGDTNYYWADIDTTHVISHIDKLYNVQFSRDLIDTVIEKEAY
QNRFHPIKSMIESKSWDGIKRIETLFIDYLGAEDNHYNREVTKKWMMGAVARIYQPGIKY
DSMIILYGGQGVGKSTAVSKLGGHWYNQSIKTFKGDEVYKKLQGSWICEIEELSAFQKST
IEDIKGFISAIVDIYRASYGKRTERHPRQCVFVGTTNNYEFLKDQTGNRRFFPITTDKNK
ATKSPFDDLTPDVVQQMFAEAKVYFDEDPTDKALLLDKEASEMALKVQEAHSEKDALVGE
IEEFLERPIPSDYWYRTLEEKRVSAHDVIDQDYIKLYGDGKLIELPNTKPGAYVWRDKVC
SMEIWKVMMKRDDQPQQHHLRKIDKALRNTNYCDTVKKQTRYGEGIGKQYGFSVDLASYY
KNLKV