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 -~----------~----~----~----~------~----~------~--~---
