Mercurial > repos > iracooke > protk_proteogenomics
diff test-data/small.prot.xml @ 0:28067ed4ea0e draft
Docker support and update for protk 1.4
| author | iracooke |
|---|---|
| date | Thu, 26 Mar 2015 20:11:34 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.prot.xml Thu Mar 26 20:11:34 2015 -0400 @@ -0,0 +1,11012 @@ +<?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 -> 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"> + <nsp_distribution bin_no="0" nsp_lower_bound_incl="0.00" nsp_upper_bound_incl="0.00" pos_freq="0.057" neg_freq="0.625" pos_to_neg_ratio="0.09"/> + <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" 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