[Bioperl-l] Errors with Bio::Seq objects

Peng Zhou zhoupenggeni at gmail.com
Wed Jul 11 14:03:17 EDT 2012


Hi, 

I guess that's what the commands are supposed to do: the get_SeqFeatures() 
method return an array of Bio::SeqFeature objects, and the translate() 
method returns a Bio::Seq object. And you can't simply "print" an object in 
perl - you can "dump" it though:

$ perl -e ' use Bio::SeqIO; use Data::Dumper; my 
$seqio=Bio::SeqIO->new(-file=>shift); 
print Dumper($seqio->next_seq()->get_SeqFeatures()); ' nt.gb 

$ perl -e ' use Bio::SeqIO; use Data::Dumper; my 
$seqio=Bio::SeqIO->new(-file=>shift); 
print Dumper($seqio->next_seq()->translate()); ' nt.gb 

On Wednesday, July 11, 2012 12:31:37 PM UTC-5, De-Jian Zhao wrote:
>
> Hi, 
>
> I downloaded a nucleotide sequence from Genbank (file name: nt.gb) and 
> tested the Bio::SeqIO module as follows. The first 3 commands succeeded; 
> however the last 2 failed. 
>
> I think $seqio->next_seq() produces a Bio::Seq object which contains the 
> sequence, features and annotation (according to the DESCRIPTION of 
> "perldoc Bio::Seq") and thus the invocation of the methods 
> get_SeqFeatures() and translate() should be valid. However, the results 
> denied this idea. 
>
> Will anyone explain what happened to the last 2 commands? I have 
> encountered numerous cases of failures when testing the bioperl methods. 
> I want to translate the mRNA sequence and extract the sequence features. 
> What are the right commands? Thanks a lot! 
>
> Best, 
> Dejian 
>
>
>
> PS: The commands and results 
>
> $ perl -e ' use Bio::SeqIO; my $seqio=Bio::SeqIO->new(-file=>shift); 
> print $seqio->next_seq()->display_id(); ' nt.gb 
> NM_053056 
>
> $ perl -e ' use Bio::SeqIO; my $seqio=Bio::SeqIO->new(-file=>shift); 
> print $seqio->next_seq()->molecule(); ' nt.gb 
> mRNA 
>
> $ perl -e ' use Bio::SeqIO; my $seqio=Bio::SeqIO->new(-file=>shift); 
> print $seqio->next_seq()->subseq(1,6); ' nt.gb 
> CACACG 
>
> $ perl -e ' use Bio::SeqIO; my $seqio=Bio::SeqIO->new(-file=>shift); 
> print $seqio->next_seq()->get_SeqFeatures(); ' nt.gb 
> Bio::SeqFeature::Generic=HASH(0x20a30898)Bio::SeqFeature::Generic=HASH(0x20a30bb0)Bio::SeqFeature::Generic=HASH(0x20a30cd0)Bio::SeqFeature::Generic=HASH(0x20a317b0)Bio::SeqFeature::Generic=HASH(0x20a31720)Bio::SeqFeature::Generic=HASH(0x20a39a18)Bio::SeqFeature::Generic=HASH(0x20a317e0)Bio::SeqFeature::Generic=HASH(0x20a398b0)Bio::SeqFeature::Generic=HASH(0x20a39838)Bio::SeqFeature::Generic=HASH(0x20a39e98)Bio::SeqFeature::Generic=HASH(0x20a3b898)Bio::SeqFeature::Generic=HASH(0x20a3a120)Bio::SeqFeature::Generic=HASH(0x20a3bda8)Bio::SeqFeature::Generic=HASH(0x20a3c030)Bio::SeqFeature::Generic=HASH(0x20a3c2b8)Bio::SeqFeature::Generic=HASH(0x20a3be20)Bio::SeqFeature::Generic=HASH(0x20a3c0a8)Bio::SeqFeature::Generic=HASH(0x20a3bb98)Bio::SeqFeature::Generic=HASH(0x20a3c300)Bio::SeqFeature::Generic=HASH(0x20a3c588)Bio::SeqFeature::Generic=HASH(0x20a3d838)Bio::SeqFeature::Generic=HASH(0x20a3dfb8)Bio::SeqFeature::Generic=HASH(0x20a3dd18) 
>
>
> $ perl -e ' use Bio::SeqIO; my $seqio=Bio::SeqIO->new(-file=>shift); 
> print $seqio->next_seq()->translate(); ' nt.gb 
> Bio::Seq::RichSeq=HASH(0x20a3e7b0) 
>
>
>
>
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