[Bioperl-l] RE: How to check mRNA

[Heikki Lehvaslaiho]

You are absolutely right, Lifeng!

Looks like I better revert the genbank.pm back into the previous version.
Sorry folks!

Before I do anything in haste:

What shall we do with the embl parser? It gives out moltype:rna molecule:RNA
on cDNA entries e.g. t/data/ar.embl. According to logic Ewan explained, it
should be moltype:dna. I wonder what would break if I were to change it?

	-Heikki


Lifeng Tian wrote:
> 
> on 10/16/01 6:05 PM, Hong Lu at honglu69@altavista.com wrote:
> 
> > I want to differentiate mRNA sequence from other Sequences. I found
> > $seqobj->moltype will always give me 'dna' value even if the sequence is mRNA
> > type on the first line of genbank record.
> >
> > How to get the mRNA value fo error checking purpose?
> >
> > Henry Lu
> > Bioinformatics Scientist
> > Epigenesis Pharmaceuticals
> >
> >
> If you are using the standard way to request a stream object from
> Bio::SeqIO, then you should call:
> $seqobj->molecule(), instead of $seqobj->moltype.
> 
> In Bio::SeqIO::GenBank, you can find the seqobj is a Bio::Seq::RichSeq.
> $seqobj->moltype only contains DNA or Protein, and  the molecular types in
> Locus line can be accessed through  $seqobj->molecule().
> 
> ################example##########
> #!/usr/bin/perl -w
> 
> use Bio::SeqIO;
> 
> my $stream = Bio::SeqIO->new(-file=>$ARGV[0],
>     -format => "genbank");
> 
> while ( my $seq=$stream->next_seq() ) {
>     print "\nmoltype:",$seq->moltype();  #you get "dna"
> 
>     print "\nmolecule:",$seq->molecule(); #you get "mRNA"
> }
> ###########
> 
> Lifeng Tian
> Depart of Chemistry and Biochemistry
> Univ. of the Sciences in Philadelphia
> 
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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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