Thanks, Taejoon. You're awesome! Christine
On Thu, Apr 7, 2011 at 1:27 PM, Taejoon Kwon <[email protected] > wrote: > Here's my simple, crude python code to convert MSF to SQT format, and > I confirm that it can be converted to pepxml with TPP Sqt2XML script. > > Few things to mention: > > * Sqt2XML script truncate terminal AA at both ends, but MSF does not > have that info. So I put a dummy AA 'X' at both end. > * I still cannot find the AA modification info in MSF, so calculated > mass in ''Match' record can be incorrect depending on modification. > * deltaCn has various definitions (I didn't know that). > http://mspire.rubyforge.org/spec_id/srf.html > I took the original definition for this script. > > http://www.marcottelab.org/users/taejoon/MS/msf-to-sqt.py.txt > > You can run this with the following simple command (after changing > filename & permission, of course): > > ./msf-to-sqt.py my_file.msf > > I think there is an expert for this kind of task (inside TPP project). > I post this to save his/her time to dig MSF schema (that's what I did > yesterday). Of course I am happy to see him/her to take my code, and > make a single script to convert MSF to pepxml directly. :-) > > Cheers, > > Taejoon > > -- > 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. > > -- Christine Vogel, PhD NYU-Biology Center for Genomics & Systems Biology 12 Waverly Place, #403 (office) or 8th floor (mail) New York, NY 10003 phone: +1-212-998-3976 fax: +1-212-995-4015 http://www.nyu.edu/projects/vogel/ -- 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.
