Hi Jason, Thanks a lot! The scripts work very well. Exactly what I was looking for. Below I attached the information for a protein from a protXML file that contains XPRESS data. If you had a chance to modify the scripts that would be great. I am going to attempt it on my own as well, but you may be faster than me!
Thanks, Chris <protein_group group_number="1" probability="1.0000"> <protein protein_name="sp|O13297|CET1_YEAST" n_indistinguishable_proteins="1" probability="1.0000" percent_coverage="28.8" unique_stripped_peptides="ESTGHGSHSQKPK+IDPSFLNIIPDDDLTK+ISLNLELPVPDNDPPEK+LSEAANGSRPFAENLESDINQTETGQAAPIDNYK+LSSLSYEIFEGSK+QHRNLLSNGSPPMNDGSDANAK+RALSLDDLVNHDENEK+RDLEVLNEISASSKPSK+SYTDNPPQTK" group_sibling_id="a" total_number_peptides="6" pct_spectrum_ids="0.027" confidence="0.999"> <analysis_result analysis="xpress"> <XPressRatio ratio_mean="2.41" ratio_standard_dev="1.81" ratio_number_peptides="5" heavy2light_ratio_mean="0.42" heavy2light_ratio_standard_dev="0.31" peptide_string="LSEAANGSRPFAENLESDINQTETGQAAPIDNYK+LSSLSYEIFEGSK+ISLNLELPVPDNDPPEK+RALSLDDLVNHDENEK+IDPSFLNIIPDDDLTK"/> </analysis_result> <parameter name="prot_length" value="549"/> <annotation protein_description="mRNA-capping enzyme subunit beta OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CET1 PE=1 SV=2"/> <peptide peptide_sequence="LSEAANGSRPFAENLESDINQTETGQAAPIDNYK" charge="0" initial_probability="0.9974" nsp_adjusted_probability="0.9966" fpkm_adjusted_probability="0.9966" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="4.31" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="1.00" is_contributing_evidence="Y"> <indistinguishable_peptide peptide_sequence="LSEAANGSRPFAENLESDINQTETGQAAPIDNYK" charge="3" calc_neutral_pep_mass="3649.71"> </indistinguishable_peptide> </peptide> <peptide peptide_sequence="LSSLSYEIFEGSK" charge="0" initial_probability="0.9753" nsp_adjusted_probability="0.9680" fpkm_adjusted_probability="0.9680" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="4.33" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.98" is_contributing_evidence="Y"> <indistinguishable_peptide peptide_sequence="LSSLSYEIFEGSK" charge="2" calc_neutral_pep_mass="1458.72"> </indistinguishable_peptide> </peptide> <peptide peptide_sequence="ISLNLELPVPDNDPPEK" charge="0" initial_probability="0.9598" nsp_adjusted_probability="0.9482" fpkm_adjusted_probability="0.9482" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="4.35" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.96" is_contributing_evidence="Y"> <indistinguishable_peptide peptide_sequence="ISLNLELPVPDNDPPEK" charge="2" calc_neutral_pep_mass="1888.98"> </indistinguishable_peptide> </peptide> <peptide peptide_sequence="RALSLDDLVNHDENEK" charge="0" initial_probability="0.9368" nsp_adjusted_probability="0.9191" fpkm_adjusted_probability="0.9191" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="4.37" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.94" is_contributing_evidence="Y"> <indistinguishable_peptide peptide_sequence="RALSLDDLVNHDENEK" charge="3" calc_neutral_pep_mass="1866.91"> </indistinguishable_peptide> </peptide> <peptide peptide_sequence="IDPSFLNIIPDDDLTK" charge="0" initial_probability="0.9279" nsp_adjusted_probability="0.9079" fpkm_adjusted_probability="0.9079" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="4.38" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.93" is_contributing_evidence="Y"> <indistinguishable_peptide peptide_sequence="IDPSFLNIIPDDDLTK" charge="2" calc_neutral_pep_mass="1814.93"> </indistinguishable_peptide> </peptide> <peptide peptide_sequence="QHRNLLSNGSPPMNDGSDANAK" charge="0" initial_probability="0.3757" nsp_adjusted_probability="0.3713" fpkm_adjusted_probability="0.3713" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="4.93" n_sibling_peptides_bin="5" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.38" is_contributing_evidence="Y"> <indistinguishable_peptide peptide_sequence="QHRNLLSNGSPPMNDGSDANAK" charge="3" calc_neutral_pep_mass="2322.08"> </indistinguishable_peptide> </peptide> <peptide peptide_sequence="SYTDNPPQTK" charge="0" initial_probability="0.1341" nsp_adjusted_probability="0.1319" fpkm_adjusted_probability="0.1319" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="5.17" n_sibling_peptides_bin="5" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.13" is_contributing_evidence="N"> <indistinguishable_peptide peptide_sequence="SYTDNPPQTK" charge="2" calc_neutral_pep_mass="1191.54"> <modification_info modified_peptide="n[43]SYTDNPPQTK"/> </indistinguishable_peptide> </peptide> <peptide peptide_sequence="ESTGHGSHSQKPK" charge="0" initial_probability="0.0750" nsp_adjusted_probability="0.0737" fpkm_adjusted_probability="0.0737" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="5.31" n_sibling_peptides_bin="5" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.07" is_contributing_evidence="N"> <indistinguishable_peptide peptide_sequence="ESTGHGSHSQKPK" charge="2" calc_neutral_pep_mass="1378.66"> </indistinguishable_peptide> </peptide> <peptide peptide_sequence="RDLEVLNEISASSKPSK" charge="0" initial_probability="0.0543" nsp_adjusted_probability="0.0533" fpkm_adjusted_probability="0.0533" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="5.31" n_sibling_peptides_bin="5" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.05" is_contributing_evidence="N"> <indistinguishable_peptide peptide_sequence="RDLEVLNEISASSKPSK" charge="2" calc_neutral_pep_mass="1880.00"> <modification_info modified_peptide="RDLEVLNEISASSK[136]PSK"/> </indistinguishable_peptide> </peptide> </protein> </protein_group> On Friday, September 20, 2013 6:08:14 PM UTC+2, Jason Winget wrote: > > Chris, > I have a couple of simple python scripts for generating CSV output from > Pep or ProtXMLs. These should be relatively easy to modify to also output > XPRESS ratios. > You can find the code at https://github.com/jwinget/TPP_utilities if > you'd like to try yourself. > If I can find a ProtXML with the ratios in it, I'd be happy to take a stab > at making the modifications. > > Best, > Jason > > On Sunday, May 26, 2013 11:41:56 AM UTC-7, chr12is wrote: >> >> Hi All, >> >> I seem to be having an issue with getting my output in excel format. I am >> currently using TPP 4.6.2 on a linux cluster with CentOS. >> >> I generated my output.xml file using xinteract (running protein prophet >> as part of this command). The resulting output.prot.xml file from xinteract >> contains all the information I am interested in, including XPRESS ratios. >> However, I now want to take my result file elsewhere to do some analysis, >> such as R. To do this I would like to run some perl scripts on it, but >> parsing an XML file with perl is a bit tedious. As such, I would like to >> have it in Excel format so I can get the tab or comma delimited versions. >> >> I have tried to get the excel file using two options. This first is using >> the 'protxml2html.pl' script and passing it the excel option. It seems >> the XPRESS ratios are lost during this conversion. The html version doing >> this also does not contain the XPRESS ratios. >> >> The second option is to re-run protein prophet on the resulting >> interact.xml file and pass it the XPRESS option. It seems to work ok, but >> when it gets to XPRESS, and says 'importing XPRESS ratios', it completes >> almost instantly, and doesn't write the ratios to the file...otherwise the >> file is ok. >> >> I am working on a cluster purely through command line, so a fix that is >> based on this is desirable. >> >> Thanks for any suggestions you may have! >> >> Regards, >> Chris >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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