Hi Josh, Thanks for the bug report and patch. It will be included in our next release.
As for the extra "<kappa>" tags you get, how are you running the command? I have not been able to reproduce it with various configurations. For what it's worth, writeTraditional() is a template defined in Parser/Tag.cpp . I'd be glad to take a further look at it if you can send me the relevant files that expose this behavior. One thing I did notice while trying to repro this, is that Mascot2XML will sometimes pull the wrong protein description when one protein accession is a substring of another and the longer version is found earlier in the protein database. For example, the description for "IPI1234" might be filled in with the one for "DECOY_IPI1234" if that decoy entry comes first in the file. It also seems that Mascot itself does not fully report all of the possible proteins that a given peptide maps to (at least with a sample file I had). For these reasons, I would strongly suggest running RefreshParser after the conversion, and using the resulting file for downstream analysis. Cheers, --Luis On Wed, Sep 28, 2016 at 5:09 PM, Josh Eckels <[email protected]> wrote: > I'm working with some users who are generating a malformed pepXML file by > using Mascot2XML when the protein description includes special XML > characters, like < and >. The output pepXML file includes this text: > > ... > <alternative_protein protein="tr|A0N5G5|A0N5G5_HUMAN" > protein_descr="Rheumatoid factor D5 light chain (Fragment) OS=Homo sapiens > GN=V<kappa>3 PE=2 SV=1" num_tol_term="2" peptide_prev_aa="R" > peptide_next_aa="A"/> > <kappa> > <kappa> > <search_score name="ionscore" value="46.68"/> > ... > > Note the "<kappa>" that's included, unencoded in the value of > the protein_descr attribute. > > I'm attaching a patch, which uses the same encoding approach that's being > used for the primary protein identification as of 2010 with revision 4877. > > However, I'm also worried about the unclosed <kappa> tags immediately > afterwards. I assume that's coming from the modtags code a little later in > that same function. However, after a little poking around, I've been unable > to find the implementation of writeTraditional(). Anyone have ideas on what > might be going wrong here? > > Thanks, > Josh > > -- > 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 https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
