Also see: http://bcbio.wordpress.com/2009/04/05/more-python-gff-parsing-iterative-parsing-and-gff2-nested-features/
I didn't realize the power of GFF either until delving into the Sequence Ontology site. Also a neat new tool developed at my Alma Mater using GFF files: http://webgbrowse.cgb.indiana.edu/webgbrowse/cgi-bin/uploadData Kenny On Jun 16, 7:54 pm, Istvan Albert <[email protected]> wrote: > On Jun 16, 10:22 am, "C. Titus Brown" <[email protected]> wrote: > > > Questions & comments welcome! Watch the github space for updates and > > bugfixes. > > One possible issue with this approach is that it always unpacks all > fields, even if one has no interest in using them. Especially the > attribute columns are less frequently used but have a strong effect on > performance. > > This can lead to somewhat sluggish performance - most data sources > distribute GFF files that happen to store a lot of attributes - but > all the user is interested is separating by strand or operating on > intervals (at least this is very common in the type of analyses that I > run). The parser will be substantially slower (possibly one or two > orders of magnitude) than just splitting manually. A quick test (6 > attributes, 100K lines) finishes in 12 seconds vs 1 second a > csv.DictReader or 0.5 seconds for a csv.reader. As long as the GFF > files are short this is not really a problem, but for larger files it > will be noticeable. > > Thanks for the embedded links and docs in the code, those are very > useful, I learned some new things about GFF that I did not know > before. > > best, > > Istvan > > Not sure what the right solution is, maybe a flag that needs to be > turned on to get the attribute splitting behavior. --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
