you can get trunk by subversion checkout: svn co https://sashimi.svn.sourceforge.net/svnroot/sashimi/trunk/trans_proteomic_pipeline tpp-trunk
or just visit the URL below and select 'Download GNU tarball': http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/ On Sun, Apr 18, 2010 at 7:49 PM, Simon Michnowicz <[email protected]> wrote: > Brian > that is great news! We have a user who is stumped on this, so I'd like > to get access to the trunk code. > I can not see it from http://sourceforge.net/projects/sashimi/files/ > Is there a way to get access to it? > > Thanks > Simon Michnowicz > > On Apr 17, 2:30 am, Brian Pratt <[email protected]> wrote: >> I actually fixed this back in February, but it's in the current ("trunk") >> code and not the 4.3 release. >> >> Brian >> >> On Thu, Apr 15, 2010 at 5:34 PM, Simon Michnowicz < >> >> >> >> >> >> [email protected]> wrote: >> > Brian >> > my apologies, the pepXML file was indeed broken. Mascot2XML took a >> > FASTA entry like >> > >tr|A0N7J4|V<beta>6-N-D<beta>-N-J<beta>1.1 protein (Fragment) Tax_Id=9606 >> > [Homo sapiens] >> >> > Into >> > <search_hit hit_rank="1" peptide="CASSSDR" peptide_prev_aa="-" >> > peptide_next_aa="A" protein="tr|A0N7J4|V<beta>6-N-D<beta>-N- >> > J<beta>1.1" num_tot_proteins="1" num_matched_ions="3" >> > tot_num_ions="12" calc_neutral_pep_mass="926.2242" massdiff="-0.3787" >> > num_tol_term="2" num_missed_cleavages="0" calc_pI="5.83" >> > is_rejected="0"> >> >> > Which breaks the pepXML viewer, and I imagine xinteract. >> >> > We have a version of Mascot2XML from TPP v4.3. Is there a more recent >> > version that might have a fix? >> >> > thanks >> > Simon Michnowicz >> >> > On Apr 16, 1:09 am, Brian Pratt <[email protected]> wrote: >> > > The defect is really somewhere upstream - whatever created the pepxml >> > files >> > > that went into xinteract should have escaped those characters. >> >> > > On Wed, Apr 14, 2010 at 11:25 PM, Simon Michnowicz < >> >> > > [email protected]> wrote: >> > > > Dear Group, >> > > > I am running a Peptide Prophet search but xinteract breaks. The error >> > > > message is : >> > > > "Syntax error parsing XML.not well-formed (invalid token)" >> >> > > > The offending line (in a peptide-xml file) is >> >> > > > <alternative_protein protein="tr|Q78E99|MRXR<gamma>" >> > > > protein_descr="homolog protein (Fragment) Tax_Id=10118 [Rattus sp]" >> > > > num_tol_term="2" peptide_prev_aa="K" peptide_next_aa="D"/> >> >> > > > Should the <gamma> entry should be <gamma> ?? >> > > > Is there an easy fix to this problem? >> > > > Thanks >> > > > Simon Michnowicz >> >> > > > -- >> > > > 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]<spctools-discuss%2Bunsubscrib >> > > > [email protected]><spctools-discuss%2Bunsubscrib >> > [email protected]> >> > > > . >> > > > For more options, visit this group at >> > > >http://groups.google.com/group/spctools-discuss?hl=en. >> >> > -- >> > 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]<spctools-discuss%2Bunsubscrib >> > [email protected]> >> > . >> > For more options, visit this group at >> >http://groups.google.com/group/spctools-discuss?hl=en. >> >> -- >> 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 >> athttp://groups.google.com/group/spctools-discuss?hl=en. > > -- > 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. > > -- 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.
