Excellent! Do you know about the -t / -t! regression test argument switches? Perfect for the kind of work you're doing here. xinteract -t! <args> to learn a test, xinteract -t <args> to verify that the results are the same as those produced in the -t! run.
Brian On Fri, Feb 5, 2010 at 10:03 AM, Dave Trudgian <[email protected]> wrote: > For info, I've modified the .pep.xml parsing into a single step, and on a > very small test dataset ASAPRatioProteinRatioParser run-time is down from > 19.8s to 0.8s. I'd expect the speed-up on a large dataset to be higher due > to the compound effects of more protein groups + bigger .pep.xml. > > Will tidy up the code and test thoroughly next week, and then share it. > > Cheers, > > DT > > Brian Pratt wrote: > >> Nothing to add! Dave has the right idea for a performance fix, and >> Natalie is correct about TPP being addicted to Boost already. >> >> Brian >> >> On Thu, Feb 4, 2010 at 2:37 PM, Natalie Tasman < >> [email protected]<mailto:[email protected]>> wrote: >> Hi Dave, Brian, >> >> Just jumping into comment on Boost. Yes, it is welcomed and in fact >> already used in the TPP (as well as the TPP-included ProteoWizard project); >> however, because the Boost API and process of building Boost libraries have >> not been particularly stable, we've found it necessary to fix the version of >> Boost that we work with. Our current version is 1.39.0. As long as you can >> test against that, you're contributes would be fine-- and no doubt very >> welcomed. >> >> -Natalie >> >> >> >> On 2/4/10 2:26 PM, Dave Trudgian wrote: >> Brian, >> >> Yup. I just discovered this too, as per other post. On our servers it's >> not disk-bound, as the 1.6GB .pep.xml is fully cached, but the continued >> rpeated slows things down. >> >> R.E. solutions for this, is Boost code welcomed in the main TPP tools? I >> think I can re-write using a single pass parse of the .pep.xml into a >> Boost.MultiIndex hash of structs/classes containing the required peptide >> info. >> >> DT >> >> Brian Pratt wrote: >> Looking at the code I can see where this would easily become diskbound for >> large data sets - it reads and rereads the same pepXML files repeatedly, but >> the effect is probably masked by disk cacheing up to a certain point. >> Somebody would need to write some logic for cacheing the file contents to >> speed this up properly. >> >> Brian >> >> On Thu, Feb 4, 2010 at 12:09 PM, Jake W <[email protected]<mailto: >> [email protected]> <mailto:[email protected]<mailto:[email protected]>>> >> wrote: >> >> I've seen the same thing. On datasets where >> ASAPRatioPeptideRatioParser completes in a few minutes, >> ASAPRatioProteinRatioParser can take an hour or so. This is on a >> Windows machine running TPP ver. 4.3.0. >> >> Jake >> >> -- >> You received this message because you are subscribed to the Google >> Groups "spctools-discuss" group. >> To post to this group, send email to >> [email protected]<mailto: >> [email protected]> >> <mailto:[email protected]<mailto: >> [email protected]>>. >> >> To unsubscribe from this group, send email to >> >> [email protected]<spctools-discuss%[email protected]> >> <mailto:spctools-discuss%[email protected]<spctools-discuss%[email protected]> >> > >> <mailto:spctools-discuss%[email protected]<spctools-discuss%[email protected]> >> <mailto:spctools-discuss%[email protected]<spctools-discuss%[email protected]>>>. >> >> >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected] >> <mailto:[email protected]>. >> >> To unsubscribe from this group, send email to >> [email protected]<spctools-discuss%[email protected]> >> <mailto:spctools-discuss%[email protected]<spctools-discuss%[email protected]> >> >. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected] >> <mailto:[email protected]>. >> >> To unsubscribe from this group, send email to >> [email protected]<spctools-discuss%[email protected]> >> <mailto:spctools-discuss%[email protected]<spctools-discuss%[email protected]> >> >. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]<spctools-discuss%[email protected]> >> . >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> > > -- > Dr. David Trudgian > Bioinformatician in Proteomics > University of Oxford > > Mon-Thu: CCMP, Roosevelt Drive > Tel: (+44) (01865 2)87784 > > Friday : Dunn School of Pathology, S. Parks Rd. > Tel: (+44) (01865 2)75557 > > > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" 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/spctools-discuss?hl=en.
