Thanks for the fix. I already checked one in like it into SVN a few weeks back. The upcoming release will avoid this problem.
-David On Tue, Jul 14, 2009 at 9:28 AM, Ping<yanpp...@gmail.com> wrote: > > Sure. I am not completely sure that my fix is correct. > > Under two functions: > > NonParametricDistribution::densityFit > NonParametricDistribution::varBWdensityFit > > I changed : > > (*d)[i] = (*d)[i] / k->size(); > > into: > > if ( k->size() == 0) > (*d)[i] = 0; > else > (*d)[i] = (*d)[i] / k->size(); > > > That is where I got the NAN error at the first point. > > Thanks, > > Ping > > > > > On Jul 14, 8:46 am, GATTACA <dfer...@umich.edu> wrote: >> Ping, >> >> Could you post what changes you made to the >> NonParametricDistribution.cxx to fix the NAN error? >> >> Thanks. >> >> On Jul 9, 1:21 pm, Ping <yanpp...@gmail.com> wrote: >> >> > Jimmy, >> >> > Thanks for your information. >> >> > I debug the TPP source code. There is a small bug inside the >> > NonParametricDistribution.cxx which causes theNANerror in the >> > previous tries. I fix it and the PeptideProphetParser is working fine >> > now. >> >> > Also after enabling InteractParser option -P as Davis suggested, I do >> > not need to replace the value in the "protein" with the first word >> > from the "protein_descr" in each search_hit entry. >> >> > Thanks again, >> >> > Ping >> >> > On Jul 6, 1:55 pm, Jimmy Eng <j...@systemsbiology.org> wrote: >> >> > > Has anyone been able to feedOMSSAnative pepXML output (using -op >> > > option) through PeptideProphet? I don't know if anyone has tested this >> > > or ifOMSSAhas only been tested using a separate converter. >> >> > > Replacing the protein word was to address the error message having no >> > > DECOY entries. This fix hopefully addressed that one point which is >> > > seems to have done. So to address the follow-up problem, minimally >> > > you'll want to include the diagnostic output from PeptideProphetParser >> > > in case anything obvious shows up from that info. Possibly you'll need >> > > to have a developer, who knows more than I do, take a closer look at >> > > your data. >> >> > > - Jimmy >> >> > > Ping wrote: >> > > > Jimmy, >> >> > > > As you suggested, I replace the value in the "protein" with the first >> > > > word from the "protein_descr" in each search_hit entry. But when I run >> > > > PeptideProphetParser, it still gives the error message: >> >> > > > ERROR:NANprobability density detected. Please alert the >> > > > developer !!! >> >> > > > Is there anything else I need to fix? >> >> > > > Thanks! >> >> > > > Ping >> >> > > > Here is the example of the result after I replace protein/ >> > > > protein_descr >> >> > > > for not decoy string, it looks like this: >> >> > > > <search_hit hit_rank="1" peptide="YPSRPLPPPPPFGLGFVPPPPPPYGPGR" >> > > > peptide_prev_aa="R" peptide_next_aa="I" protein="gi|73975149|ref| >> > > > XP_862242.1|" num_tot_proteins="3" num_matched_ions="15" >> > > > tot_num_ions="54" calc_neutral_pep_mass="2949.569" >> > > > massdiff="0.59985990298992" is_rejected="0" protein_descr="gi| >> > > > 73975149| >> > > > ref|XP_862242.1| PREDICTED: hypothetical protein XP_857149 isoform 2 >> > > > [Canis familiaris]" num_tol_term="2" num_missed_cleavages="0"> >> > > > <alternative_protein protein="gi|73975151|ref|XP_862273.1|" >> > > > protein_descr="gi|73975151|ref|XP_862273.1| PREDICTED: hypothetical >> > > > protein XP_857180 isoform 3 [Canis familiaris]"/> >> > > > <alternative_protein protein="gi|73975153|ref|XP_862298.1|" >> > > > protein_descr="gi|73975153|ref|XP_862298.1| PREDICTED: hypothetical >> > > > protein XP_857205 isoform 4 [Canis familiaris]"/> >> > > > <search_score name="pvalue" value="0.000002382663488"/> >> > > > <search_score name="expect" value="0.028320338214958"/> >> > > > </search_hit> >> >> > > > For decoy string, it looks like this: >> >> > > > <search_hit hit_rank="2" peptide="QESARYSAKVTVAGLEESATEAQQQIR" >> > > > peptide_prev_aa="K" peptide_next_aa="S" protein="decoy_2098 >> > > > 2" num_tot_proteins="1" num_matched_ions="17" tot_num_ions="52" >> > > > calc_neutral_pep_mass="2949.481" massdiff="0.9728599071700 >> > > > 05" is_rejected="0" protein_descr="decoy_20982"> >> > > > <search_score name="pvalue" value="0.000014221885248"/> >> > > > <search_score name="expect" value="0.168173793062284"/> >> > > > </search_hit> >> >> > > > On Jul 2, 4:44 pm, Jimmy Eng <j...@systemsbiology.org> wrote: >> > > >> Ping, >> >> > > >> I just downloadedOMSSA2.1.4 and tried the direct pep.xml export >> > > >> myself. I do see a problem with the resulting pep.xml file that the >> > > >> "-op" option generates that's causing the problem you're seeing. >> >> > > >> The key error message in your output is this: >> > > >> WARNING: No decoys with label DECOY were found in this dataset. >> >> > > >> Looking at the generated pep.xml files,OMSSAseems to be placing some >> > > >> number in the protein="" attribute of each search_hit element. >> > > >> Whereas >> > > >> PeptideProphet expects this protein attribute to contain some protein >> > > >> identifier that includes the DECOY string for those decoy matches. In >> > > >> the converters we use, the value of the protein attribute is the first >> > > >> word of the protein definition line. >> >> > > >> As for a fix, we need someone at NCBI to address this and hopefully >> > > >> someone here will contact them about this. For you in the short term, >> > > >> you're going to need a developer to modify you pep.xml files to >> > > >> replace >> > > >> the value in the "protein" attribute with the first word from the >> > > >> "protein_descr" attribute of each search_hit entry. >> >> > > >> - Jimmy >> >> > > >> Ping wrote: >> > > >>> Hi, >> > > >>> I am trying to run the xinteract on theomssapep.xml output files. my >> > > >>>omssa'sversion is 2.1.4, my TPP version is 4.2.1. But I couldn't get >> > > >>> it through. I search the old post, there is a similar post, but the >> > > >>> problem was solved by specifying enzyme to xinteract. >> > > >>> I tried it, but is still not working. InteractParse went through, but >> > > >>> PeptideProphetParser got stuck by a segmentation fault. >> > > >>> Any help would be greatly appreciated! >> > > >>> Many Thanks, >> > > >>> Ping >> > > >>> ***** output for interactParser and PeptideProphetParser >> > > >>> InteractParser 'interact.pep.xml' 'omssa.pep.xml' -L'7' -E'trypsin' >> > > >>> -C >> > > >>> -P >> > > >>> file 1: ParoSaliv_SHAM_03.pep.xml >> > > >>> processed altogether 2623 results >> > > >>> PeptideProphetParser 'interact.pep.xml' DECOY=DECOY MINPROB=0 >> > > >>> NONPARAM >> > > >>> Using Decoy Label "DECOY". >> > > >>> Using non-parametric distributions >> > > >>> (OMSSA) (minprob 0) >> > > >>> WARNING!! The discriminant function forOMSSAis not yet complete. It >> > > >>> is presented here to help facilitate trial and discussion. Reliance >> > > >>> on this code for publishable scientific results is not recommended. >> > > >>> init withOMSSATrypsin >> > > >>> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, >> > > >>> Ionization: >> > > >>> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN >> > > >>> PeptideProphet (TPP v4.2 JETSTREAM rev 1, Build 200905131510 >> > > >>> (linux)) akel...@isb >> > > >>> read in 75 1+, 1790 2+, 749 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >> > > >>> Initialising statistical models ... >> > > >>> WARNING: No decoys with label DECOY were found in this dataset. >> > > >>> reverting to fully unsupervised method. >> > > >>> Iterations: .........10.........20 >> > > >>> Segmentation fault > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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