[Bioperl-l] genbank contig parses

[Richard Adams]

Sorry, I'm probably being too naive and jumping in with both feet, but
isn't this sort of approach possible, at least for Bio::Seq and
Bio::Seq::RichSeq objects?

1. to transfer features across to a "subseq obj" on the basis of whether
the feature
overlaps  or is contained in the subseq, and to revise the start/end
coordinates of the feature
in the subseq.

2. Transfer annotations en masse (as they usually refer to the whole
sequence) unless for example the reference field coordinates are outside
the desired range.

3. Assign a subseq identifier, e.g by the primary id tag or by appending
the sequence range to the
accession number.

Richard