[Bioperl-l] How to check mRNA moltype?

[Heikki Lehvaslaiho]

Henry,

moltype() is the correct method. It works on EMBL sequences so it should on
GenBank, too. I had a look at the code and RNA option was completely
ignored. 
I rewrote the lines doing it and committed them to bioperl-live. I hope you
are using CVS and can see the changes immediately.

This fix should go into 07 branch, too, but first I'd like to get feedback
that the fix really works on larger data sets. I tried it only on t/data
examples.
Does anyone have a system handy to try this? The potential problem is that
it is  DNA/mRNA/... keyword is allowed to be missing completely from the
LOCUS line.


Incidentally, the LOCUS line is going to change slightly in GenBank
distributions in December. I tried the current parser on two examples
provided and it seems to keep on working properly. See
ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt

	-Heikki

Hong Lu 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
> 
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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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