Hi gang, One would be a better solution is extend SQLTable to be compatible with GFF3(or 2 or 1) schema. In our group, we're using UCSC's Genome Browser (BED/BEDgraph) and GBrowse-based browsers for viewing genomic features. We basically have two sets of databases which are SQLTable-compatible for pygr and another GFF3-compatible for GBrowse use.
The advantage of SQLTable is that it works on a 'single table' (simplicity) whereas GFF schema data is linked across multiple tables. We could extend the SQLTable class to specify the GFF 'source' attribute though and resolve the corresponding links to GFF's data table. By the way, we have several in-house tools for generating annotation databases from csv files: from cvs -> sql table -> pygr annotatino db. Could these tools be incorporated into pygr? Thanks, Paul On Thu, Aug 27, 2009 at 1:35 PM, jbiesinger <[email protected]>wrote: > > Off by one error. Forgot to add > > row_d['start'] = row_d['start'] - 1 > > in read_for_pygr in gffparser.py > > > -- Paul Rigor http://www.paulrigor.net/ http://www.ics.uci.edu/~prigor --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
