Hi David, The patch works beautifully. Thanks for the fix.
Scott On Wed, Aug 5, 2009 at 9:24 AM, David Shteynberg < [email protected]> wrote: > Hi Scott, > > I just checked in a fix to this error in SVN. The problem was the spectrum > names were getting extra whitespace at the end in the .tandem files, which > were being propagated to the pepXML. The workaround that I committed trims > any extra whitespace surrounding the spectrum name. The fix is fairly > benign and I have verified that it works on your data. Please give it a > test and report back any issues. > > Thanks, > -David > > > > > On Wed, Jul 29, 2009 at 12:04 PM, Natalie Tasman < > [email protected]> wrote: > >> >> Hi Scott, >> >> Thanks for your feedback and I'm glad David is taking a look. I just >> want to remind everyone that svn trunk (which you're working with) is >> development code. If you want stable results stick with the official >> releases. >> >> -Natalie >> >> >> On Tue, Jul 28, 2009 at 6:35 PM, Scott >> Stansfield<[email protected]> wrote: >> > >> > Hi All, >> > >> > I've just my updated TPP (version 4.4) from the svn last night, >> > unfortunately when I run xinteract on my sets of TANDEM search results >> > "0" is returned for all peptide prophet probabilities for all >> > spectra. What's upsetting is it worked in the last version I had (TPP >> > 4.2.1), peptide prophet reports the models and the graphs for each >> > charge model are saved in the directory. Does anyone know where this >> > problem could have arisen? >> > >> > Cheers, >> > >> > Scott. >> > >> > I run xinteract on my files like this: >> > >> >>xinteract -OdP -dREV -p0 -eT -E20090409_1a_n1_v2 >> -N/data/tpp/data/processing/stansfie/20090409_1a_n1_v2/TANDEM.interact.pep.xml >> *.TANDEM.pep.xml >> > >> > bits of the TANDEM.interact.pep.xml output look like this: >> > >> > ...cropped... (there's a model) >> > >> > <roc_data_point min_prob="0.99" sensitivity="0.8941" error="0.0008" >> > num_corr="1501" num_incorr="1"/> >> > <roc_data_point min_prob="0.98" sensitivity="0.9298" error="0.0013" >> > num_corr="1561" num_incorr="2"/> >> > <roc_data_point min_prob="0.95" sensitivity="0.9651" error="0.0024" >> > num_corr="1620" num_incorr="4"/> >> > <roc_data_point min_prob="0.90" sensitivity="0.9835" error="0.0036" >> > num_corr="1651" num_incorr="6"/> >> > >> > ...cropped...(this should be better than zero since it's the largest >> > hyperscore in the dataset) >> > >> > </search_hit> >> > </search_result> >> > </spectrum_query> >> > <spectrum_query spectrum="20090409_1a_n1_K4-AMG_C10.01455.01455.3" >> > start_scan="95" end_scan="95" precursor_neutral_mass="2209.9282" >> > assumed_charge="3" index="1837" retention_time_sec="96.952" >> > experiment_label="20090409_1a_n1_v2"> >> > <search_result> >> > <search_hit hit_rank="1" peptide="LGEHNIDVLEGNEQFINAAK" >> > peptide_prev_aa="R" peptide_next_aa="I" protein="sp|TRYP_PIG|" >> > num_tot_proteins="3" num_matched_ions="25" tot_num_ions="76" >> > calc_neutral_pep_mass="2210.0967" massdiff="-0.169" num_tol_term="2" >> > num_missed_cleavages="0" is_rejected="0"> >> > <alternative_protein protein="sp|TRYP_PIG|" num_tol_term="2" >> > peptide_prev_aa="R" peptide_next_aa="I"/> >> > <alternative_protein protein="sp|TRYP_PIG|" num_tol_term="2" >> > peptide_prev_aa="R" peptide_next_aa="I"/> >> > <search_score name="hyperscore" value="977"/> >> > <search_score name="nextscore" value="412"/> >> > <search_score name="bscore" value="2"/> >> > <search_score name="yscore" value="2"/> >> > <search_score name="expect" value="0.0023"/> >> > <analysis_result analysis="peptideprophet"> >> > <peptideprophet_result probability="0" all_ntt_prob="(0,0,0)" >> > analysis="none"/> >> > </analysis_result> >> > </search_hit> >> > >> > ...cropped... >> > >> > > >> > >> >> >> > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
