No. I am building pairwise NLMSA from custom-made axtNet files. axtFiles are not that big but there are 14m sequences in it. It would take 2-3 hours for pygr to make .idDict and .seqIDdict. Namshin Kim
On Mon, Jun 29, 2009 at 11:15 AM, C. Titus Brown <[email protected]> wrote: > > On Mon, Jun 29, 2009 at 10:50:25AM +0900, Namshin Kim wrote: > -> I was wrong. You are right. I am testing using 14m sequences and Pygr > only > -> uses 1g memory. I am monitoring memory usage and let you know if I found > -> something strange. > > Are you aligning annotations or other sequences? > > -> BTW, I tried to use ScreedSequenceDB, which was working a month ago. > But, > -> this time, using the same script, I got following error message saying > there > -> is no 'name' attribute. I didn't do anything except updating pygr > (screed is > -> same). > > OK, I'll take a look! > > --t > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
