comparison test-data/small.prot.xml @ 0:956bfab63005 draft default tip

planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty

0:956bfab63005

<?xml version="1.0" encoding="UTF-8"?>
<protein_summary xmlns="http://regis-web.systemsbiology.net/protXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v6.xsd" summary_xml="/home/iracooke/venturiapg/search_results/Pirina/Pirina_pproph.prot.xml">
<protein_summary_header reference_database="/home/iracooke/venturiapg/vpirina6frame_decoy.fasta" residue_substitution_list="I -&gt; L" source_files="/home/iracooke/venturiapg/search_results/Pirina/Pirina_iproph.pep.xml" source_files_alt="/home/iracooke/venturiapg/search_results/Pirina/Pirina_iproph.pep.xml" min_peptide_probability="0.20" min_peptide_weight="0.50" num_predicted_correct_prots="1787.3" num_input_1_spectra="5700" num_input_2_spectra="24737" num_input_3_spectra="8680" num_input_4_spectra="714" num_input_5_spectra="124" initial_min_peptide_prob="0.05" total_no_spectrum_ids="28710.0" sample_enzyme="trypsin">
<program_details analysis="proteinprophet" time="2014-01-20T14:17:37" version=" Insilicos_LabKey_C++ (TPP v0.0 Development trunk rev 0, Build 201307090846 (linux))">
<proteinprophet_details occam_flag="Y" groups_flag="Y" degen_flag="Y" nsp_flag="Y" initial_peptide_wt_iters="2" nsp_distribution_iters="2" final_peptide_wt_iters="3">
      <nsp_information neighboring_bin_smoothing="Y">
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         <nsp_distribution bin_no="1" nsp_lower_bound_excl="0.00" nsp_upper_bound_incl="0.31" pos_freq="0.037" neg_freq="0.152" pos_to_neg_ratio="0.24"/>
         <nsp_distribution bin_no="2" nsp_lower_bound_excl="0.31" nsp_upper_bound_incl="1.00" pos_freq="0.077" neg_freq="0.032" pos_to_neg_ratio="2.42"/>
         <nsp_distribution bin_no="3" nsp_lower_bound_excl="1.00" nsp_upper_bound_incl="2.50" pos_freq="0.113" neg_freq="0.033" pos_to_neg_ratio="3.39"/>
         <nsp_distribution bin_no="4" nsp_lower_bound_excl="2.50" nsp_upper_bound_incl="4.63" pos_freq="0.123" neg_freq="0.032" pos_to_neg_ratio="3.91"/>
         <nsp_distribution bin_no="5" nsp_lower_bound_excl="4.63" nsp_upper_bound_incl="7.90" pos_freq="0.143" neg_freq="0.032" pos_to_neg_ratio="4.50"/>
         <nsp_distribution bin_no="6" nsp_lower_bound_excl="7.90" nsp_upper_bound_incl="14.92" pos_freq="0.196" neg_freq="0.041" pos_to_neg_ratio="4.78"/>
         <nsp_distribution bin_no="7" nsp_lower_bound_excl="14.92" nsp_upper_bound_excl="inf" pos_freq="0.254" neg_freq="0.054" pos_to_neg_ratio="4.72" alt_pos_to_neg_ratio="4.78"/>
      </nsp_information>
      <ni_information>
      </ni_information>
      <protein_summary_data_filter min_probability="0.00" sensitivity="1.000" false_positive_error_rate="0.835" predicted_num_correct="1787" predicted_num_incorrect="9044"/>
      <protein_summary_data_filter min_probability="0.10" sensitivity="1.000" false_positive_error_rate="0.235" predicted_num_correct="1787" predicted_num_incorrect="548"/>
      <protein_summary_data_filter min_probability="0.20" sensitivity="1.000" false_positive_error_rate="0.235" predicted_num_correct="1787" predicted_num_incorrect="548"/>
      <protein_summary_data_filter min_probability="0.30" sensitivity="0.956" false_positive_error_rate="0.151" predicted_num_correct="1709" predicted_num_incorrect="305"/>
      <protein_summary_data_filter min_probability="0.40" sensitivity="0.916" false_positive_error_rate="0.095" predicted_num_correct="1638" predicted_num_incorrect="171"/>
      <protein_summary_data_filter min_probability="0.50" sensitivity="0.887" false_positive_error_rate="0.063" predicted_num_correct="1585" predicted_num_incorrect="106"/>
      <protein_summary_data_filter min_probability="0.60" sensitivity="0.853" false_positive_error_rate="0.036" predicted_num_correct="1525" predicted_num_incorrect="58"/>
      <protein_summary_data_filter min_probability="0.70" sensitivity="0.826" false_positive_error_rate="0.020" predicted_num_correct="1477" predicted_num_incorrect="31"/>
      <protein_summary_data_filter min_probability="0.80" sensitivity="0.805" false_positive_error_rate="0.012" predicted_num_correct="1438" predicted_num_incorrect="18"/>
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      <protein_summary_data_filter min_probability="0.95" sensitivity="0.749" false_positive_error_rate="0.004" predicted_num_correct="1339" predicted_num_incorrect="5"/>
      <protein_summary_data_filter min_probability="0.96" sensitivity="0.738" false_positive_error_rate="0.003" predicted_num_correct="1318" predicted_num_incorrect="4"/>
      <protein_summary_data_filter min_probability="0.97" sensitivity="0.728" false_positive_error_rate="0.002" predicted_num_correct="1302" predicted_num_incorrect="3"/>
      <protein_summary_data_filter min_probability="0.98" sensitivity="0.711" false_positive_error_rate="0.002" predicted_num_correct="1272" predicted_num_incorrect="2"/>
      <protein_summary_data_filter min_probability="0.99" sensitivity="0.609" false_positive_error_rate="0.000" predicted_num_correct="1088" predicted_num_incorrect="0"/>
      <protein_summary_data_filter min_probability="1.00" sensitivity="0.164" false_positive_error_rate="0.000" predicted_num_correct="294" predicted_num_incorrect="0"/>
</proteinprophet_details>
</program_details>
</protein_summary_header>
<dataset_derivation generation_no="0">
</dataset_derivation>


<protein_group group_number="3" probability="1.0000">
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         <parameter name="prot_length" value="217"/>
         <annotation protein_description="513537 514187"/>
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            <annotation protein_description="513490 514190"/>
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         <peptide peptide_sequence="LIPDTTHLPSEPTTDILILPGGGPGAAAFVSSNSVQHLVR" charge="4" initial_probability="0.5417" nsp_adjusted_probability="0.8004" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.84" n_sibling_peptides_bin="3" n_instances="2" exp_tot_instances="0.81" is_contributing_evidence="Y" calc_neutral_pep_mass="4077.1555">
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      </protein>
</protein_group>



<protein_group group_number="7" probability="1.0000">
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         <parameter name="prot_length" value="402"/>
         <annotation protein_description="195564 196835"/>
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</protein_group>


























































































































































































































































































































<protein_group group_number="322" pseudo_name="29" probability="1.0000">
      
      <protein protein_name="lcl|scaffold10_frame_6_orf_3129" n_indistinguishable_proteins="1" probability="1.0000" percent_coverage="30.9" unique_stripped_peptides="ALLDDLPK+DREGLDAAAVVDR+EIQQYLAQFSSVSSPQFAVIK+ELFTDTGAGTLIR+LFLHENLK+LLEDAGVEPEYEEGIR+MFGDINLESQLK+NAVLGVLNQISSK+QLYDMGLYPVIVHGGGPQLNK+SSSVAIIHPDHLQR+VGGAILTDYLDSLVEALK+YATEENNQR" group_sibling_id="b" total_number_peptides="16" pct_spectrum_ids="0.095" confidence="1.000">
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         <annotation protein_description="346373 347986"/>
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