Sure thing. And to answer your original question: there is a command-line tool in TPP called batchcoverage (look in the bin/ directory) that calculates this residue coverage -- and is the one used by ProteinProphet to populate that attribute in protXML.
It needs an input file of the form: >PROTEIN_1 PEPTIDE ANOTHERONE ANDTHISONE >PROTEIN_2 ELVIS WASHERE >PROTEIN_3 ... And you run it by providing a reference fasta file location and output file name, like this: batchcoverage <database> <inputfile> <outputfile> The output file will contain a 2-column list of <protein> <coverage> values. Hope this helps, and stay tuned for updates! --Luis On Tue, Mar 28, 2023 at 3:59 PM Yasir Ahmed <yazah...@gmail.com> wrote: > 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 > <https://groups.google.com/d/msgid/spctools-discuss/597a9136-9dc6-4b7c-b5e1-110ab21277acn%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/CACyS9brLRhFpSNUyUOFssR5Tb4y_99_bDH2bfDOkO0sWduJvJQ%40mail.gmail.com.
