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

[Brian Osborne]

Dejian,

These are not "failures". The get_SeqFeatures() and translate() methods will return Bio::Seq objects or a Bio::Seq object.

Start here:

www.bioperl.org/wiki/HOWTO:Beginners

Brian O.


On Jul 11, 2012, at 1:31 PM, 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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