lenti298 [~/perltest]>more translate.pl
#!/usr/bin/perl -w
# Translates fasta DNA sequences to AA frame 1

use Bio::SeqIO;

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

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

while((my $seqobj = $seqin->next_seq())) {
  my $trans = $seqobj->translate;    # "translate" object
  my $trans_seq = $trans->seq;       # sequence string
  my $trans_id = $trans->display_id; # ID string
  print ">$trans_id\n$trans_seq\n\n";
}
exit;
lenti299 [~/perltest]>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
lenti300 [~/perltest]>perl translate.pl orf15.tfa
>ORF15
MEDVTNEEVFEMIDSRTGVLNANDWKSQLRRSATTQALKKTTTNAEIILCNDESLKGLVQYDAFEKVTKLKRLPYWRSKG
DTNYYWADIDTTHVISHIDKLYNVQFSRDLIDTVIEKEAYQNRFHPIKSMIESKSWDGIKRIETLFIDYLGAEDNHYNRE
VTKKWMMGAVARIYQPGIKYDSMIILYGGQGVGKSTAVSKLGGHWYNQSIKTFKGDEVYKKLQGSWICEIEELSAFQKST
IEDIKGFISAIVDIYRASYGKRTERHPRQCVFVGTTNNYEFLKDQTGNRRFFPITTDKNKATKSPFDDLTPDVVQQMFAE
AKVYFDEDPTDKALLLDKEASEMALKVQEAHSEKDALVGEIEEFLERPIPSDYWYRTLEEKRVSAHDVIDQDYIKLYGDG
KLIELPNTKPGAYVWRDKVCSMEIWKVMMKRDDQPQQHHLRKIDKALRNTNYCDTVKKQTRYGEGIGKQYGFSVDLASYY
KNLKV

lenti301 [~/perltest]>