Hi Dave, Thanks for finding and fixing this bug! Jimmy incorporated your changes into the code in trunk, and will be included with the next release. --Luis
On Tue, Aug 27, 2013 at 1:19 PM, Dave Trudgian < [email protected]> wrote: > I've come across an issue with InteractParser on some Comet data files. In > the PepXML that Comet produces sometimes the last > <search_result></search_result> block in the file is empty (no > peptide-spectrum match for the spectrum?). In this case InteractParser > fails to write the </msms_run_summary> and </analysis_summary> tags through > into the interact.pep.xml output. > > E.g. from Comet last 10 lines are: > > <search_score name="expect" value="0.00E+00"/> > </search_hit> > </search_result> > </spectrum_query> > <spectrum_query spectrum="HeLa_GluC_pH6_CID_3xload.37816.37816.6" > start_scan="37816" end_scan="37816" precursor_neutral_mass="7740.7671" > assumed_charge="6" index="32020" retention_time_sec="12964.2"> > <search_result> > </search_result> > </spectrum_query> > </msms_run_summary> > </msms_pipeline_analysis> > > After InteractParser this is truncated incorrectly to the last spectrum > query_block that had a search result, missing the final end tags to close > the pepxml. > > <search_score name="expect" value="0.00E+00"/> > </search_hit> > </search_result> > </spectrum_query> > > > I've put a quick and dirty fix in InteractParser.cxx after line 630 which > fixes this, and doesn't appear to break anything. Not sure this is the > correct way to do it given the rest of the parsing logic though: > > // DCT > // Always stop skipping if we hit an msms_run_summary closing tag. > // Fix for issue where end of file is not written if last search_result > // is empty, as observed on a Comet output file > if(! strcmp(tag->getName(), "msms_run_summary") ) { > if (tag->isEnd()) { > tag_cache->clear(); > output = True; > skip_hit = False; > skip_spec = False; > } > } > > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/groups/opt_out. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
