You could work around that with sed, replacing all 'peptide_prev_aa=" is_rejected' with 'peptide_prev_aa="" is_rejected'.
But it's very strange that you see this at all. I don't see anywhere in the code that would write 'peptide_prev_aa but not peptide_next_aa and other attributes. On Fri, Sep 4, 2009 at 7:23 AM, nik <[email protected]> wrote: > > Hello, > > I generated *.pep.xml files from SEQUEST out files using OUT2XML.exe. > I generrate output for 1st two hits. However, for some search hits, I > see the probelm as explained below. > > For one sepctrum it generated following line for hit 2: > > <search_hit hit_rank="2" peptide="DNIQGITKPAIRR" peptide_prev_aa=" > is_rejected="0"> > > Because of such incorrect lines the XML reader cannot read the files > correctly (through Java or C#). Do you know how to fix such error > lines? > > Thanks, > ~Nikhil. > > Complete output as shown below: > > ************************* > <spectrum_query spectrum="2009_0813_04.10119.10119.2" > start_scan="10119" end_scan="10119" precursor_neutral_mass="1481.4557" > assumed_charge="2" index="139"> > <search_result> > <search_hit hit_rank="1" peptide="DNIQGITKPAIRR" > peptide_prev_aa="-" peptide_next_aa="-" protein="gi|28173560|ref| > NP_778224.1|" num_tot_proteins="14" num_matched_ions="14" > tot_num_ions="24" calc_neutral_pep_mass="1480.8475" > massdiff="+0.608260" num_tol_term="2" num_missed_cleavages="0" > is_rejected="0"> > <search_score name="xcorr" value="0.937"/> > <search_score name="deltacn" value="0.079"/> > <search_score name="deltacnstar" value="0.000"/> > <search_score name="spscore" value="249.4"/> > <search_score name="sprank" value="19"/> > </search_hit> > <search_hit hit_rank="2" peptide="DNIQGITKPAIRR" > peptide_prev_aa=" is_rejected="0"> > <search_score name="xcorr" value="0.000"/> > <search_score name="deltacn" value="0.079"/> > <search_score name="deltacnstar" value="0.000"/> > <search_score name="spscore" value="0.0"/> > <search_score name="sprank" value="0"/> > </search_hit> > </search_result> > </spectrum_query> > ***************************************************** > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
