Thanks Luis, that's helpful. For now I'll just use an older version of TPP to get the coverage values.
Cheers, Yasir On Tuesday, March 28, 2023 at 6:46:58 PM UTC-4 Luis Mendoza wrote: > Hello Yasir, > > We have recently identified a bug in ProteinProphet that mis-reports the > coverage as zero for all proteins. This affects TPP versions 6.1.0 and > 6.2.0. We will be releasing an update soon that corrects this and other > bugs. > > Even then, the value that is reported in protXML is the ratio of observed > amino acids to total. There is no simple way to get the coverage based on > the digestible portion of the protein, though we could think about adding > that as a feature. > > Let me know if you would like to get a preview version of just > ProteinProphet in advance of our release and I can post that separately, > just specify if you use Linux or Windows. Alternatively, if you have a > pre-6.1.0 version of TPP installed, you can run ProteinProphet and get the > coverage values reported. > > Cheers, > --Luis > > > On Tue, Mar 28, 2023 at 2:50 PM Yasir Ahmed <yaza...@gmail.com> wrote: > >> I guess I have another question about coverage: using ProtXMLViewer >> (which is similar to the output from ProteinProphet), the coverage values >> are almost always zero. For example, the example I show above has Obs/Dig >> of 82%, but is showing percent coverage to be zero in the ProteinProphet >> output. Any idea why? And can one get those Obs/Dig values? >> >> On Tuesday, March 28, 2023 at 5:23:06 PM UTC-4 Yasir Ahmed wrote: >> >>> Never mind, got it with ProtXMLViewer.pl (duh). >>> >>> On Tuesday, March 28, 2023 at 5:03:14 PM UTC-4 Yasir Ahmed wrote: >>> >>>> Greetings Friends, >>>> >>>> Is there a command line tool within the TPP that can output sequence >>>> residue coverage percentages (Obs/Tot)? I can get those for individual >>>> proteins using the ProtXMLViewer GUI (see attached image), but would like >>>> to do this for every protein in my database. >>>> >>>> Cheers, >>>> Yasir >>>> >>>> [image: Screen Shot 2023-03-28 at 4.29.18 PM.png] >>>> >>> -- >> 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 spctools-discu...@googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/bcc98ae1-0f89-4472-9a66-f0eeed496d5dn%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/bcc98ae1-0f89-4472-9a66-f0eeed496d5dn%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/597a9136-9dc6-4b7c-b5e1-110ab21277acn%40googlegroups.com.
