[Biopython] Deprecate Bio.GenBank.Record based GenBank parser?
Peter Cock <[email protected]>
| Newsgroups | gmane.comp.python.bio.general |
|---|---|
| Message-ID | <CAKVJ-_7268frF+r3P_V5=em6z87JEWyiO4zU3nVsc4n=6jHGcQ@mail.gmail.com> |
Hello all, Am I right in thinking almost everyone working with GenBank or EMBL files in Biopython does so via Bio.Seq these days? Underneath, this calls the scanner/consumer parser defined in Bio.GenBank, where the scanner code breaks up the file into logical bits which are passed to a consumer which turns them into a Biopython data structure. For Bio.SeqIO, we build up a SeqRecord object, but there is an alternative consumer which builds up Bio.GenBank.Record objects instead. If you the Bio.GenBank.read(...) or Bio.GenBank.parse(...) functions you will get Bio.GenBank.Record objects which are a quite direct representation of the underlying data structure, and str(...) will give you a GenBank formatted string. Here for example, the feature locations are left as plain strings. Does anyone use the Bio.GenBank.Record based GenBank parser? Could we deprecate it (in favour of only using the GenBank parser via Bio.SeqIO)? This would mean in a few releases time, we could remove the old record class and potentially then simplify the GenBank/EMBL parsing. Peter _______________________________________________ Biopython mailing list - [email protected] http://mailman.open-bio.org/mailman/listinfo/biopython