RobertCraven has asked for the wisdom of the Perl Monks concerning the following question:

Almighty Monks,

I am trying to translate a DNA sequence to a protein sequence using all 3 ORFs (same strand). However, when trying to pass options to the sequence object (like -frame => 1 or -complete => 1), the option is introduced into the object:

Source: 
use strict;
use warnings;
use Data::Dumper;
use Bio::Tools::CodonTable;
use Bio::Seq;

my $dna = 'ATGAAAGGAACATCCATTTTATTCAAAGCACCTCCAAACCTGCAATCCTAAGTTCCAGG
+CAACTCAATCCCAAAAATCCACTGTAGATGCCCAAAGGCTGGGGTGTTCGGTCTTCAACATTTTTGCCT
+TTGTGGCTCCCAGTCAAGATAGAGCTGCACCAAGTCCAATTCCATTCCTCATCACAGATGATTTTTTCT
+ACTTTAAGATCAGAACTATACAAGCTTCTTGCTTTGTGTCAGCATGCTGTTGTACCCATGGGCAAATTC
+TTAGGTAAGACAAAAACACAGTCCCAAGGGCAGGTAGTAATTTTTTCAGAAAAAGGTAAGGCAATCATT
+TATCTCAGTCTGCCCAGGACAGTCCCAATTTACACATGTATATTCTCCCAATCTGTAGGCTGTCTTTTC
+ATTTTGTTGATTATTTCACTTAATTTTTTATTATTTATTTATTTTATAGAGACAGATCTCATTATGTTG
+CCCAGGGTGATCCTTGATCTCCTGGCCTCAAGTGATCCTCCAACCTTGGTCTCCCAAAGTGCTGGGATT
+ACAGATGTGAACTACCACACCCAGTCAACGTGCAGAAGGTTTTCAGTTTGATGTAGTCTGATGTAGTCT
+CATGTATTTATCCTTCTTGTTGTTGCCTGAGCTTTTGGTGTGATATCCAAAAATATCATTGCCAAGATC
+AATATCAAGAAACTTTCCCCCTATGTTTCTTACAGAAATTTTATGGTTTCAGATTTTTCATCCATTTTG
+AGTATATTTGTGTGTATGATGTAAGATAAGGGTCCAGTCTCCCCAGTGTTGGATATCCAATTTTCATAA
+CACCATTTATTGAAGAGATTATTCTTTCTCCACTGTGTTTTCTTGATGTCCTTGTCAAAAATTAGTTGA
+CTTTTATATGCTTGGGTTTATTTCTGGGCTCTATTCTGTTTCATTGCTTTACATCTCTGTTTTCATGCC
+AGTGCCACAGTGTTTTGATTACTATAGCTTTGTAATATAATTTGAAATCAGAATGTGTAATACCTATAA
+CTTTGTTTTTTGCTCTAAAGATTTATTTATTTATTTATTTTTGCCATTTCAGGTCTTTTGTGGTTTCAT
+ATGAATTTCAGAATTGTTTTTCCTATTTCTGTGAAAAATGCCATTGACATTTTGATAGGGATTGTGTTG
+AATCTATATATTGCTTTGGATAGTATGGATG';

my $seq_obj = Bio::Seq->new(
    -seq => $dna,
    -alphabet => 'dna' );

my $prot_obj = $seq_obj->translate(-complete => 1); 

print $prot_obj->seq, "\n";

[download]
Output: 
MKGTSILFKAPPNLQS-completeVPGNSIPKIHCRCPKAGVFGLQHFCLCGSQSR-completeSCTK
+SNSIPHHR-completeFFLL-completeDQNYTSFLLCVSMLLYPWANS-completeVRQKHSPKG
+R-complete-completeFFQKKVRQSFISVCPGQSQFTHVYSPNL-completeAVFSFC-comple
+teLFHLIFYYLFIL-completeRQISLCCPG-completeSLISWPQVILQPWSPKVLGLQM-compl
+eteTTTPSQRAEGFQFDVV-completeCSLMYLSFLLLPELLV-completeYPKISLPRSISRNFPP
+MFLTEILWFQIFHPF-completeVYLCV-completeCKIRVQSPQCWISNFHNTIY-completeRD
+YSFSTVFS-completeCPCQKLVDFYMLGFISGLYSVSLLYISVFMPVPQCFDYYSFVI-complete
+FEIRMCNTYNFVFCSKDLFIYLFLPFQVFCGFI-completeISELFFLFL-completeKMPLTF-co
+mplete-completeGLC-completeIYILLWIVWM

[download]
Versions: 
Perl version v5.10.0
BioPerl 1.2.3

[download]

How do I correctly pass an option?
Any help is greatly appreciated!

Replies are listed 'Best First'.
Re: BioPerl translate sequence
by educated_foo (Vicar) on May 13, 2011 at 13:51 UTC
    It looks like it's using "-complete" to represent the stop codon. As is usually the case, for simple string manipulation it's easier and faster to take BioPerl out of the equation. All you need is a substitution and a lookup table: 
    my %prot = (
'TCA'=>'S','TCC'=>'S','TCG'=>'S','TCT'=>'S',
'TTC'=>'F','TTT'=>'F',
'TTA'=>'L','TTG'=>'L',
'TAC'=>'Y','TAT'=>'Y',
'TAA'=>'_','TAG'=>'_','TGA'=>'_',
'TGC'=>'C','TGT'=>'C',
'TGG'=>'W',
'CTA'=>'L','CTC'=>'L','CTG'=>'L','CTT'=>'L',
'CCA'=>'P','CCC'=>'P','CCG'=>'P','CCT'=>'P',
'CAC'=>'H','CAT'=>'H',
'CAA'=>'Q','CAG'=>'Q',
'CGA'=>'R','CGC'=>'R','CGG'=>'R','CGT'=>'R',
'ATA'=>'I','ATC'=>'I','ATT'=>'I',
'ATG'=>'M',
'ACA'=>'T','ACC'=>'T','ACG'=>'T','ACT'=>'T',
'AAC'=>'N','AAT'=>'N',
'AAA'=>'K','AAG'=>'K',
'AGC'=>'S','AGT'=>'S',
'AGA'=>'R','AGG'=>'R',
'GTA'=>'V','GTC'=>'V','GTG'=>'V','GTT'=>'V',
'GCA'=>'A','GCC'=>'A','GCG'=>'A','GCT'=>'A',
'GAC'=>'D','GAT'=>'D',
'GAA'=>'E','GAG'=>'E',
'GGA'=>'G','GGC'=>'G','GGG'=>'G','GGT'=>'G');

sub dna2prot
{
    my $dna = uc shift;
    $dna =~ y/ACGT//cd;
    map {
        s/(...)/$prot{$1}||'?'/eg; $_
    } $dna, ''.substr($dna,1), ''.substr($dna,2);
}

print "$_\n" for dna2prot($sequence)

    [download]
[reply]
[d/l]
      Thank you for the work of writing the hash, but unfortunately this code snippet will be only the beginning. There will be different codons involved, BLAST etc. . Instead of again reinventing the wheel like so many times before I'd like to use existing methods this time.
      Thanks again!
[reply]
Re: BioPerl translate sequence
by Anonymous Monk on May 13, 2011 at 13:56 UTC
    However, when trying to pass options to the sequence object (like -frame => 1 or -complete => 1), the option is introduced into the object: How do I correctly pass an option? Any help is greatly appreciated!

    What documentation are you referencing? See http://doc.bioperl.org/releases/bioperl-1.4/Bio/Perl.html#POD8 
     Title   : translate
 Usage   : $seqobj = translate($seq_or_string_scalar)

 Function: translates a DNA sequence object OR just a plain
           string of DNA to amino acids
 Returns : A Bio::Seq object

 Args    : Either a sequence object or a string of
           just DNA sequence characters
    So Bio::Seq->translate doesn't expect any kind of complete option

    I am trying to translate a DNA sequence to a protein sequence using all 3 ORFs (same strand).

    What? ORF sounds like something Pinky would say :D

[reply]
[d/l]
      Thank you for your answer. The idea is coming from here:

      BioPerl Wiki

      Gosh, have not seen Pinky in ages... :-D
      Not sure if he would have ever talked about ORFs ;)

[reply]

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