Hi Simon, Since xinteract can also run the <result>2XML converters (besides the prophets, etc), the -D option is required if you are trying to analyze a Mascot .dat file in this manner.
When otherwise specified, the RefreshParser step of xinteract uses the database given by the -D option, which adds its own <analysis> tag. This does not replace the <search_database> tag within pepXML, but rather adds its own <database_refresh_timestamp> tag wherein this new value is stored, and used by downstream tools. Hope this helps, --Luis On Sun, May 1, 2011 at 8:32 PM, Simon Michnowicz <[email protected] > wrote: > Luis > Thanks. Just one follow-on. > If the database is specified in the <result>2XML executable, what role > does the -D option play in xinteract? > Does it override the pepXML entry, or is it for something else? > thanks > Simon Michnowicz > > On Apr 30, 6:06 am, Luis Mendoza <[email protected]> > wrote: > > Hi Simon, > > This is unlikely to work, given that the pepXML format and other tools > tend > > to assume a single entry for the database field. One possible way around > > this is to create a single database by concatenating the entries of the > > target databases used in the Mascot search, and specify this in the -D > > parameter. > > > > Hope this helps! > > --Luis > > > > On Thu, Apr 28, 2011 at 12:57 AM, Simon Michnowicz < > > > > > > > > > > > > > > > > [email protected]> wrote: > > > Dear Group, > > > the new Mascot Server allows users to search multiple sequence > > > databases in a single search. > > > I was wondering if there were any issues with Mascot2Xml converting > > > the '.dat' result file of such a search? > > > (I am yet to produce such a .dat file, but will it ignore any entry > > > not found in the database specified by the -D parameter?) > > > > > 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]. > > > 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. > > -- 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.
