[Bioperl-l] genbank parsing of multiple 'function' tags within primary tag

Surya Saha ss2489 at cornell.edu
Thu Sep 8 12:28:40 EDT 2011

You might want to explore using a hash of complex records that are very
similar to structures in C/C++. More info at


On Thu, Sep 8, 2011 at 12:14 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:

> I only had a quick look at your code, so maybe I'm missing something but
> you are currently pushing all products of all CDSs into the same array,
> i.e. you do not assign them to a datastructure that links a particular
> CDS to a list of products. You then use the same index to print out a
> locus from the @loci array and a product from @products, but the two
> will not match up because you will have more products than loci.
> That's right. Products are not the issue in this particular case, as it's
> E.coli and there's no alternate splicing as far as I know so there is a
> single product per gene. But there are plenty more 'function' qualifiers,
> for example, than loci. And I don't know how to create a data structure
> that
> will link a 'gene' (as primary tag) to all other qualifiers, whether they
> belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list