Hi Titus, I want to outline some suggestions for the 0.8 tutorials, to invite your feedback.
- Titus' alignment tutorial only covers pairwiseMode. I think we may want to add both a basic multiple sequence alignment example, and an example making use of the NLMSA.add_aligned_intervals() method. - we need to update this tutorial to reflect the new reporting of self- matches from pairwise NLMSA / blast. - Titus, will the "scalability" tutorial replace the existing annotation.rst tutorial, or will it be an *additional* tutorial? The code examples you posted seem to assume that the reader already knows all about Pygr annotation concepts, i.e. they already finished the existing annotation.rst tutorial... - in the scalability tutorial, we may want to showcase SQLTable with sqlite before showing the shelve variants. We want to encourage users to work with sqlite in preference to shelve (which newer versions of Python are not supporting solidly, due to the removal of bsddb from the Python standard library). - the sqlite code example can be made much simpler by using SQLiteServerInfo to connect to the database and SQLTable to create the table and save data to it. If Titus can push this tutorial to github, I can add appropriate modifications... - I'm wondering whether we need a "database tutorial" that illustrates Pygr's recommended ways to create and use data containers (via SQL, shelve etc.). Currently, there is some material hidden at the back of the worldbase tutorial, but I suspect nobody would know to look there for it. I could extract that material and add more, to create one tutorial that would cover all Pygr's "container classes". In the past, the docs tended to assume that a user already had a database stored in SQL or a shelve, and thus only showed how to work with *existing* databases. So I think we need new tutorial material showing how to create databases, and to highlight the "Pygr way" of doing this. Do people think it's a good idea to pull the database issues out as a separate tutorial? - I must confess I remain uncertain as to what exactly people want in the "gene build tutorial", partly because this overlaps the annotation tutorial (show how to store annotations for genes and exons), and partly because I'm probably the worst person in the world to understand "what confuses users about Pygr". Unless other people can give me some guidance, this tutorial will simply be: * based on the existing annotation tutorial, introducing Pygr annotation concepts; * add more code examples for actually *creating* new annotation databases to store genes and exons (the existing tutorial assumes the slice info is already stored in a db). * incorporate the GFF loading example submitted recently on this discussion group. We can't include this now, but I hope that discussions with UCSC will soon clarify the Ensembl to UCSC mapping question. In that case we could potentially add a code example showing how to access the Ensembl gene / exon annotations based on the UCSC mapping. But that will have to wait for a later point release. Please give me your feedback! If I haven't mentioned something you want, please speak up on this discussion group... -- Chris --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
