Hi, Thanks - that is what I was looking for. Have you tried to use pepXML input for the search parameters (similar to the one used by Omssa browser)? Best, Oded
On Aug 17, 5:56 pm, dctrud <[email protected]> wrote: > Hi Oded, > > We have OMSSA being called from a script, which generates a command > such as: > > omssacl -fm /cpfp_data/dev/submissions/500/560/B090717_002.mgf -d / > cpfp_data/temp_db/decoy_maxquant-kr-uniprot_sprot.v2009.04.23 -op / > cpfp_data/dev/search_results/2300/2334/B090717_002.pep.xml -he 1e6 -to > 0.5 -te 0.01 -e 0 -v 3 -mf 200 -mv 201,202,203 -mx /cpfp_data/dev/ > search_results/2300/2334/usermods.xml -hl 5 -zcc 1 -nt 4 > > The base_name in the resulting pepxml contains the .pep.xml extension, > which I don't think it should... so we then: > > sed -i 's/\.pep\.xml//ig' $pepxmlFile > > RefreshParser B090717_002.pep.xml /cpfp_data/temp_db/decoy_maxquant-kr- > uniprot_sprot.v2009.04.23.fasta > > xinteract -Ninteract.pep.xml -ESUB130 -p0 -eT -dDECOY -O-P-d-p-A > *.pep.xml > > This seems to work fine. I haven't seen any pp -2 score problems. > > DT --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
