RubyGems - mspire - Versions diffs - 0.3.9 → 0.4.2 - Mend

mspire 0.3.9 → 0.4.2

Files changed (87) hide show

data/INSTALL +24 -7
data/README +15 -13
data/README.rdoc +18 -0
data/Rakefile +50 -14
data/bin/aafreqs.rb +0 -0
data/bin/bioworks2excel.rb +0 -0
data/bin/bioworks_to_pepxml.rb +2 -1
data/bin/bioworks_to_pepxml_gui.rb +0 -0
data/bin/fasta_shaker.rb +0 -0
data/bin/filter_and_validate.rb +0 -0
data/bin/gi2annot.rb +0 -0
data/bin/id_class_anal.rb +0 -0
data/bin/id_precision.rb +0 -0
data/bin/ms_to_lmat.rb +0 -0
data/bin/pepproph_filter.rb +0 -0
data/bin/protein_summary.rb +0 -0
data/bin/protxml2prots_peps.rb +0 -0
data/bin/raw_to_mzXML.rb +3 -3
data/bin/run_percolator.rb +122 -0
data/bin/sqt_group.rb +0 -0
data/bin/srf_group.rb +0 -0
data/changelog.txt +29 -0
data/lib/ms/gradient_program.rb +0 -1
data/lib/ms/msrun.rb +62 -29
data/lib/ms/parser/mzdata/axml.rb +55 -0
data/lib/ms/parser/mzdata/dom.rb +51 -36
data/lib/ms/parser/mzdata.rb +8 -2
data/lib/ms/parser/mzxml/axml.rb +59 -0
data/lib/ms/parser/mzxml/dom.rb +80 -57
data/lib/ms/parser/mzxml/hpricot.rb +1 -1
data/lib/ms/parser/mzxml/libxml.rb +6 -2
data/lib/ms/parser/mzxml.rb +110 -3
data/lib/ms/parser.rb +4 -4
data/lib/ms/precursor.rb +19 -4
data/lib/ms/scan.rb +7 -7
data/lib/ms/spectrum.rb +249 -58
data/lib/mspire.rb +1 -1
data/lib/spec_id/bioworks.rb +2 -2
data/lib/spec_id/precision/filter/cmdline.rb +8 -1
data/lib/spec_id/precision/prob/cmdline.rb +2 -2
data/lib/spec_id/precision/prob.rb +1 -0
data/lib/spec_id/proph/pep_summary.rb +3 -4
data/lib/spec_id/proph/prot_summary.rb +3 -3
data/lib/spec_id/protein_summary.rb +1 -1
data/lib/spec_id/sequest/pepxml.rb +5 -5
data/lib/spec_id/sqt.rb +4 -4
data/lib/spec_id/srf.rb +49 -8
data/lib/spec_id.rb +5 -0
data/lib/xml_style_parser.rb +16 -2
data/script/compile_and_plot_smriti_final.rb +0 -0
data/script/create_little_pepxml.rb +0 -0
data/script/degenerate_peptides.rb +0 -0
data/script/estimate_fpr_by_cysteine.rb +0 -0
data/script/extract_gradient_programs.rb +1 -1
data/script/find_cysteine_background.rb +0 -0
data/script/genuine_tps_and_probs.rb +0 -0
data/script/get_apex_values_rexml.rb +0 -0
data/script/mascot_fix_pepxml.rb +123 -0
data/script/msvis.rb +0 -0
data/script/mzXML2timeIndex.rb +0 -0
data/script/peps_per_bin.rb +0 -0
data/script/prep_dir.rb +0 -0
data/script/simple_protein_digestion.rb +0 -0
data/script/smriti_final_analysis.rb +0 -0
data/script/sqt_to_meta.rb +0 -0
data/script/top_hit_per_scan.rb +0 -0
data/script/toppred_to_yaml.rb +0 -0
data/script/tpp_installer.rb +0 -0
data/specs/bin/prob_validate_spec.rb +5 -2
data/specs/bin/protein_summary_spec.rb +5 -1
data/specs/ms/msrun_spec.rb +176 -133
data/specs/ms/parser_spec.rb +3 -3
data/specs/ms/spectrum_spec.rb +0 -2
data/specs/spec_id/precision/filter_spec.rb +4 -1
data/specs/spec_id/precision/prob_spec.rb +2 -2
data/specs/spec_id/sequest/pepxml_spec.rb +1 -1
data/specs/spec_id/sqt_spec.rb +5 -5
data/specs/spec_id/srf_spec.rb +56 -93
data/specs/spec_id/srf_spec_helper.rb +121 -284
data/specs/spec_id_spec.rb +3 -0
data/specs/transmem/toppred_spec.rb +1 -0
data/test_files/opd1_2runs_2mods/data/020.mzData.xml +683 -0
data/test_files/opd1_2runs_2mods/data/020.readw.mzXML +382 -0
data/test_files/opd1_2runs_2mods/data/040.mzData.xml +683 -0
data/test_files/opd1_2runs_2mods/data/040.readw.mzXML +382 -0
data/test_files/opd1_2runs_2mods/data/README.txt +6 -0
metadata +247 -229

data/test_files/opd1_2runs_2mods/data/040.readw.mzXML ADDED Viewed

@@ -0,0 +1,382 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<mzXML
+ xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_2.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_2.0 http://sashimi.sourceforge.net/schema_revision/mzXML_2.0/mzXML_idx_2.0.xsd">
+ <msRun scanCount="20"
+        startTime="PT0.00266667S"
+        endTime="PT28.86S">
+  <parentFile fileName="file://040.RAW"
+              fileType="RAWData"
+              fileSha1="b7a3d5361f87046e4c557fa6a1b2179123d00a06"/>
+  <msInstrument>
+	<msManufacturer category="msManufacturer" value="ThermoFinnigan"/>
+  	<msModel category="msModel" value="LCQ Deca XP"/>
+ 	<msIonisation category="msIonisation" value="ESI"/>
+	<msMassAnalyzer category="msMassAnalyzer" value="Ion Trap"/>
+	<msDetector category="msDetector" value="EMT"/>
+    <software type="acquisition"
+              name="Xcalibur"
+              version="1.3 SP 1"/>
+  </msInstrument>
+  <dataProcessing centroided="1">
+    <software type="conversion"
+              name="readw.exe"
+              version="1.1"/>
+  </dataProcessing>
+  <scan num="1"
+        msLevel="1"
+        peaksCount="667"
+        polarity="+"
+        scanType="ms"
+        retentionTime="PT0.16S"
+        lowMz="300.144"
+        highMz="1493.72"
+	basePeakMz="390.902"
+	basePeakIntensity="6.09196e+006"
+	totIonCurrent="8.53454e+007">
+    <peaks precision="32"
+           byteOrder="network"
+           pairOrder="m/z-int">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</peaks>
+  <scan num="2"
+        msLevel="2"
+        peaksCount="43"
+        polarity="+"
+        scanType="Full"
+        retentionTime="PT1.5S"
+        collisionEnergy="0"
+        lowMz="112.147"
+        highMz="407.847"
+	basePeakMz="149.062"
+	basePeakIntensity="2.11322e+006"
+	totIonCurrent="7.57247e+006">
+    <precursorMz precursorIntensity="6.09196e+006">390.9015503</precursorMz>
+    <peaks precision="32"
+           byteOrder="network"
+           pairOrder="m/z-int">QuBLbke4M4BC4dL8R8qeAELkAjpGiKAAQvmbmkThwABDFQ/qSgD7IEMWIUhH6JIAQyO7kEa6DABDJYnIRqMSAEMmxqJJrmr4QyevmEcR3ABDOL84RbkoAEM853BGq6YAQ0I3ZEYUfABDWoz8Rn0IAENh6MBGOzwAQ3Vh7kWmGABDgAm8Rc8YAEOApeBHFDYAQ4FPSkdg7QBDgaZmQIAAAEOCRzxJFwLgQ4LTPEg1s4BDgysyQYAAAEOI0NxGMhQAQ4qqNEdB/gBDiv7sR5vogEOLbMhJ3QfwQ4veckh2EwBDjD4sQOAAAEOUbP5HOh0AQ60YUkatqgBDtrasRwsUAEO3BSxHDhYAQ7hS0EXh+ABDuMf8R46NgEO5ixhHSPQAQ7pEWkdqQwBDuptMQKAAAEO7j/JF4qAAQ8NeNEa2aABDx7BSRPIgAEPLe95HQpQAQ8vsYEZo1AA=</peaks>
+  </scan>
+  <scan num="3"
+        msLevel="2"
+        peaksCount="84"
+        polarity="+"
+        scanType="Full"
+        retentionTime="PT2.31S"
+        collisionEnergy="0"
+        lowMz="320.948"
+        highMz="1124.79"
+	basePeakMz="990.001"
+	basePeakIntensity="690215"
+	totIonCurrent="1.82509e+006">
+    <precursorMz precursorIntensity="1.39509e+006">1121.981934</precursorMz>
+    <peaks precision="32"
+           byteOrder="network"
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+        polarity="+"
+        scanType="Full"
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+        collisionEnergy="0"
+        lowMz="422.191"
+        highMz="1324.08"
+	basePeakMz="1189.93"
+	basePeakIntensity="385568"
+	totIonCurrent="1.59692e+006">
+    <precursorMz precursorIntensity="629504">1321.930176</precursorMz>
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+           pairOrder="m/z-int">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</peaks>
+  </scan>
+  </scan>
+ </msRun>
+  <index name="scan">
+    <offset id="1">1149</offset>
+    <offset id="2">8648</offset>
+    <offset id="3">9609</offset>
+    <offset id="4">11001</offset>
+    <offset id="5">12243</offset>
+    <offset id="6">18312</offset>
+    <offset id="7">19271</offset>
+    <offset id="8">19834</offset>
+    <offset id="9">21391</offset>
+    <offset id="10">29831</offset>
+    <offset id="11">31129</offset>
+    <offset id="12">32798</offset>
+    <offset id="13">34133</offset>
+    <offset id="14">42129</offset>
+    <offset id="15">43631</offset>
+    <offset id="16">45217</offset>
+    <offset id="17">46436</offset>
+    <offset id="18">55005</offset>
+    <offset id="19">55969</offset>
+    <offset id="20">57368</offset>
+  </index>
+  <indexOffset>13321529</indexOffset>
+  <sha1>f18b190ad6aab59ad210af37397c9072d2383d63</sha1>
+</mzXML>

data/test_files/opd1_2runs_2mods/data/README.txt ADDED Viewed

@@ -0,0 +1,6 @@
+Some tags associated with the mzXML format are off because of the way we've modified the file to have only 20 scans!
+!!!! These are wrong!!!!
+<indexOffset>13623066</indexOffset>
+<sha1>f7c9ccdd385f0cfc124cc6d0ca3e2bb36e4a9090</sha1>