mspire 0.3.1 → 0.3.9

data/test_files/small.sqt

@@ -0,0 +1,87 @@
+H	SQTGenerator	mspire
+H	SQTGeneratorVersion	0.3.1
+H	Database	C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta
+H	FragmentMasses	AVG
+H	PrecursorMasses	AVG
+H	StartTime	
+H	Alg-MSModel	LCQ Deca XP
+H	DBLocusCount	4237
+H	Alg-FragMassTol	1.0000
+H	Alg-PreMassTol	25.0000
+H	Alg-IonSeries	0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
+H	Alg-PreMassUnits	ppm
+H	Alg-Enzyme	Trypsin(KR/P) (2)
+H	Comment	ultra small file created for testing
+H	Comment	Created from Bioworks .srf file
+H	DynamicMod	M*=+15.99940
+H	DynamicMod	STY#=+79.97990
+S	2	2	1	0.0	TESLA	390.92919921875	2653.90307617188	0.0	0
+S	3	3	1	0.0	TESLA	1121.94482421875	3283.54272460938	0.0	3
+M	1	1	1121.93902442	0.0	0.123464643955231	29.8535556793213	5	35	R.Y#RLGGS#T#K.K	U
+L	gi|16130113|ref|NP_416680.1|
+M	2	2	1121.96119642	0.795928299427032	0.0251956433057785	11.7253675460815	6	28	K.S#GNDLHY#R.G	U
+L	gi|16128318|ref|NP_414867.1|
+S	4	4	1	0.0	TESLA	1321.91357421875	3445.47338867188	0.0	0
+S	6	6	1	0.0	TESLA	391.016235351562	2796.34912109375	0.0	0
+S	7	7	1	0.0	TESLA	1221.97802734375	3769.00024414062	0.0	0
+S	8	8	1	0.0	TESLA	1322.00439453125	3935.37475585938	0.0	0
+S	10	10	1	0.0	TESLA	1121.91625976562	3106.53686523438	0.0	18
+M	1	5	1121.91159842	0.0	0.517962515354156	33.0886917114258	6	24	K.Y#DTEDY#R.H	U
+L	gi|16128388|ref|NP_414937.1|
+M	2	9	1121.91159842	0.17718294262886	0.426188379526138	28.0216407775879	6	24	K.Y#DT#EDYR.H	U
+L	gi|16128388|ref|NP_414937.1|
+M	3	3	1121.89096442	0.488175302743912	0.265105992555618	39.1714057922363	8	35	R.TTEKS#S#T#K.S	U
+L	gi|16130334|ref|NP_416903.1|
+M	4	2	1121.93902442	0.631783962249756	0.190722107887268	41.4820594787598	7	35	R.Y#RLGGS#T#K.K	U
+L	gi|16130113|ref|NP_416680.1|
+M	5	1	1121.89757842	0.707324922084808	0.15159472823143	41.5733528137207	8	30	R.FT#T#HGY#R.D	U
+L	gi|16129410|ref|NP_415968.1|
+M	6	13	1121.91159842	0.767382383346558	0.120487198233604	11.1207275390625	5	24	K.YDT#EDY#R.H	U
+L	gi|16128388|ref|NP_414937.1|
+M	7	14	1121.91785042	0.896376550197601	0.0536730699241161	6.10089921951294	4	25	R.NCY#Y#Y#R.E	U
+L	gi|16128767|ref|NP_415320.1|
+M	8	6	1121.89096442	0.931291460990906	0.0355884432792664	32.6543502807617	6	35	R.T#T#EKS#STK.S	U
+L	gi|16130334|ref|NP_416903.1|
+S	11	11	1	0.0	TESLA	1222.03955078125	3505.90185546875	0.0	6
+M	1	1	1222.02947242	0.0	0.258438050746918	134.970413208008	10	36	R.EDDS#PQGS#VK.A	U
+L	gi|16129012|ref|NP_415567.1|
+M	2	2	1222.04971442	0.24978731572628	0.193883508443832	59.2804641723633	8	32	R.S#YDT#EDGM*K.F	U
+L	gi|90111504|ref|NP_417349.4|
+M	3	2	1222.04971442	0.362763434648514	0.164686173200607	59.2804641723633	8	32	R.SY#DT#EDGM*K.F	U
+L	gi|90111504|ref|NP_417349.4|
+M	4	3	1222.05213042	0.740513622760773	0.067061148583889	45.5321998596191	7	35	K.QIT#T#Y#LDK.G	U
+L	gi|49176305|ref|YP_026198.1|
+S	14	14	1	0.0	TESLA	371.043518066406	3490.9755859375	0.0	0
+S	15	15	2	0.0	TESLA	814.180101299688	5307.74365234375	0.0	0
+S	15	15	3	0.0	TESLA	1220.76651363453	5307.74365234375	0.0	0
+S	16	16	1	0.0	TESLA	362.151611328125	4569.6455078125	0.0	0
+S	18	18	2	0.0	TESLA	616.584642315313	3327.263671875	0.0	4
+M	1	3	616.58129342	0.0	0.0607584044337273	8.33333301544189	1	12	K.S#KSSK.E	U
+L	gi|16129674|ref|NP_416233.1|
+S	18	18	3	0.0	TESLA	924.373325157969	3327.263671875	0.0	0
+S	19	19	1	0.0	TESLA	444.983337402344	1700.27795410156	0.0	0
+S	20	20	1	0.0	TESLA	361.671875	4756.20703125	0.0	0
+S	23	23	1	0.0	TESLA	1022.10571289062	3637.86059570312	0.0	41
+M	1	5	1022.11662242	0.0	0.725152492523193	73.9527359008789	6	24	-.MGT#TTM*GVK.L	U
+L	gi|16128980|ref|NP_415534.1|
+M	2	5	1022.11662242	0.0672458708286285	0.67638897895813	73.9527359008789	6	24	-.MGTT#TM*GVK.L	U
+L	gi|16128980|ref|NP_415534.1|
+M	3	3	1022.09997242	0.162994727492332	0.606956422328949	90.1473388671875	6	14	K.NQTNNRFK.T	U
+L	gi|16131314|ref|NP_417899.1|
+M	4	1	1022.11662242	0.169317632913589	0.602371394634247	127.829414367676	8	21	-.MT#M*NITSK.Q	U
+L	gi|16130518|ref|NP_417088.1|
+M	5	10	1022.11662242	0.205745562911034	0.57595556974411	60.3448905944824	5	24	-.MGTTT#M*GVK.L	U
+L	gi|16128980|ref|NP_415534.1|
+M	6	11	1022.11662242	0.264144241809845	0.533607602119446	60.1143188476562	5	21	-.MTM*NITS#K.Q	U
+L	gi|16130518|ref|NP_417088.1|
+M	7	8	1022.11662242	0.331606924533844	0.484686881303787	67.8056793212891	5	21	-.MTM*NIT#SK.Q	U
+L	gi|16130518|ref|NP_417088.1|
+M	8	16	1022.09807242	0.380560249090195	0.449188262224197	49.735767364502	5	21	-.MRTT#SFAK.V	U
+L	gi|16129390|ref|NP_415948.1|	Fake description
+M	9	15	1022.09674242	0.382012128829956	0.448135405778885	52.3407211303711	5	16	K.DVKFGNDAR.V	U
+L	gi|16131968|ref|NP_418567.1|	Fake description
+M	10	16	1022.09807242	0.398330867290497	0.436301857233047	49.735767364502	5	21	-.MRT#TSFAK.V	U
+L	gi|16129390|ref|NP_415948.1|
+S	24	24	1	0.0	TESLA	1422.02368164062	4142.11865234375	0.0	0
+S	26	26	1	0.0	TESLA	444.820556640625	1576.70617675781	0.0	0
+S	27	27	1	0.0	TESLA	393.008056640625	2896.16967773438	0.0	0

metadata

@@ -1,33 +1,62 @@
 --- !ruby/object:Gem::Specification 
-rubygems_version: 0.9.2
-specification_version: 1
 name: mspire
 version: !ruby/object:Gem::Version 
-  version: 0.3.1
-date: 2007-12-14 00:00:00 -06:00
-summary: Mass Spectrometry Proteomics Objects, Scripts, and Executables
-require_paths: 
-- lib
-email: jprince@icmb.utexas.edu
-homepage: http://mspire.rubyforge.org
-rubyforge_project: mspire
-description: mspire is for working with mass spectrometry proteomics data
-autorequire: 
-default_executable: 
-bindir: bin
-has_rdoc: true
-required_ruby_version: !ruby/object:Gem::Version::Requirement 
-  requirements: 
-  - - ">"
-    - !ruby/object:Gem::Version 
-      version: 0.0.0
-  version: 
+  version: 0.3.9
 platform: ruby
-signing_key: 
-cert_chain: 
-post_install_message: 
 authors: 
 - John Prince
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2008-01-24 00:00:00 -06:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: libjtp
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 0.2.13
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: axml
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 0.0.0
+    version: 
+description: mspire is for working with mass spectrometry proteomics data
+email: jprince@icmb.utexas.edu
+executables: 
+- aafreqs.rb
+- prob_validate.rb
+- gi2annot.rb
+- bioworks_to_pepxml_gui.rb
+- filter_and_validate.rb
+- pepproph_filter.rb
+- bioworks2excel.rb
+- srf_group.rb
+- raw_to_mzXML.rb
+- fasta_shaker.rb
+- sqt_group.rb
+- srf_to_sqt.rb
+- bioworks_to_pepxml.rb
+- id_precision.rb
+- protein_summary.rb
+- protxml2prots_peps.rb
+- ms_to_lmat.rb
+- id_class_anal.rb
+extensions: []
+
+extra_rdoc_files: 
+- README
+- INSTALL
+- LICENSE
 files: 
 - INSTALL
 - README
@@ -35,347 +64,337 @@ files:
 - LICENSE
 - changelog.txt
 - release_notes.txt
-- lib/spec_id
-- lib/align
-- lib/ms
-- lib/spec_id.rb
-- lib/fasta.rb
-- lib/align.rb
-- lib/sample_enzyme.rb
-- lib/ms.rb
-- lib/gi.rb
-- lib/roc.rb
-- lib/spec_id_xml.rb
-- lib/validator.rb
+- lib/scan_i.rb
+- lib/mspire.rb
 - lib/transmem
-- lib/transmem.rb
-- lib/xml_style_parser.rb
-- lib/xmlparser_wrapper.rb
-- lib/bsearch.rb
+- lib/transmem/phobius.rb
+- lib/transmem/toppred.rb
 - lib/group_by.rb
+- lib/align.rb
+- lib/sample_enzyme.rb
 - lib/xml.rb
-- lib/merge_deep.rb
-- lib/index_by.rb
-- lib/validator
-- lib/mspire.rb
-- lib/scan_i.rb
+- lib/fasta.rb
+- lib/spec_id_xml.rb
+- lib/spec_id
 - lib/spec_id/sequest.rb
+- lib/spec_id/digestor.rb
+- lib/spec_id/sqt.rb
+- lib/spec_id/proph
+- lib/spec_id/proph/pep_summary.rb
+- lib/spec_id/proph/prot_summary.rb
 - lib/spec_id/bioworks.rb
-- lib/spec_id/proph.rb
 - lib/spec_id/parser
-- lib/spec_id/srf.rb
-- lib/spec_id/aa_freqs.rb
+- lib/spec_id/parser/proph.rb
 - lib/spec_id/protein_summary.rb
+- lib/spec_id/aa_freqs.rb
 - lib/spec_id/precision
-- lib/spec_id/digestor.rb
-- lib/spec_id/proph
-- lib/spec_id/sequest
-- lib/spec_id/mass.rb
-- lib/spec_id/parser/proph.rb
 - lib/spec_id/precision/prob.rb
-- lib/spec_id/precision/filter
-- lib/spec_id/precision/filter.rb
-- lib/spec_id/precision/prob
 - lib/spec_id/precision/output.rb
-- lib/spec_id/precision/filter/interactive.rb
+- lib/spec_id/precision/filter
 - lib/spec_id/precision/filter/output.rb
+- lib/spec_id/precision/filter/interactive.rb
 - lib/spec_id/precision/filter/cmdline.rb
+- lib/spec_id/precision/filter.rb
+- lib/spec_id/precision/prob
 - lib/spec_id/precision/prob/output.rb
 - lib/spec_id/precision/prob/cmdline.rb
-- lib/spec_id/proph/pep_summary.rb
-- lib/spec_id/proph/prot_summary.rb
+- lib/spec_id/sequest
 - lib/spec_id/sequest/params.rb
 - lib/spec_id/sequest/pepxml.rb
+- lib/spec_id/proph.rb
+- lib/spec_id/mass.rb
+- lib/spec_id/srf.rb
+- lib/ms.rb
+- lib/gi.rb
+- lib/roc.rb
+- lib/index_by.rb
+- lib/validator
+- lib/validator/background.rb
+- lib/validator/aa_est.rb
+- lib/validator/cmdline.rb
+- lib/validator/aa.rb
+- lib/validator/digestion_based.rb
+- lib/validator/probability.rb
+- lib/validator/prot_from_pep.rb
+- lib/validator/q_value.rb
+- lib/validator/true_pos.rb
+- lib/validator/bias.rb
+- lib/validator/decoy.rb
+- lib/validator/transmem.rb
+- lib/spec_id.rb
+- lib/xml_style_parser.rb
+- lib/bsearch.rb
+- lib/validator.rb
+- lib/merge_deep.rb
+- lib/align
 - lib/align/chams.rb
-- lib/ms/converter
-- lib/ms/parser
-- lib/ms/spectrum.rb
-- lib/ms/gradient_program.rb
+- lib/ms
 - lib/ms/msrun.rb
-- lib/ms/precursor.rb
 - lib/ms/scan.rb
-- lib/ms/msrun_index.rb
-- lib/ms/parser.rb
+- lib/ms/converter
 - lib/ms/converter/mzxml.rb
-- lib/ms/parser/mzdata
+- lib/ms/msrun_index.rb
+- lib/ms/spectrum.rb
+- lib/ms/parser
 - lib/ms/parser/mzxml
-- lib/ms/parser/mzdata.rb
-- lib/ms/parser/mzxml.rb
-- lib/ms/parser/mzdata/libxml.rb
-- lib/ms/parser/mzdata/axml.rb
-- lib/ms/parser/mzdata/dom.rb
-- lib/ms/parser/mzxml/xmlparser.rb
-- lib/ms/parser/mzxml/libxml.rb
 - lib/ms/parser/mzxml/rexml.rb
+- lib/ms/parser/mzxml/libxml.rb
+- lib/ms/parser/mzxml/xmlparser.rb
+- lib/ms/parser/mzxml/dom.rb
 - lib/ms/parser/mzxml/regexp.rb
-- lib/ms/parser/mzxml/axml.rb
 - lib/ms/parser/mzxml/hpricot.rb
-- lib/ms/parser/mzxml/dom.rb
-- lib/transmem/toppred.rb
-- lib/transmem/phobius.rb
-- lib/validator/prot_from_pep.rb
-- lib/validator/true_pos.rb
-- lib/validator/aa.rb
-- lib/validator/decoy.rb
-- lib/validator/transmem.rb
-- lib/validator/cmdline.rb
-- lib/validator/bias.rb
-- lib/validator/background.rb
-- lib/validator/digestion_based.rb
-- lib/validator/probability.rb
-- bin/bioworks_to_pepxml_gui.rb
-- bin/gi2annot.rb
-- bin/protein_summary.rb
-- bin/ms_to_lmat.rb
+- lib/ms/parser/mzxml/axml.rb
+- lib/ms/parser/mzdata
+- lib/ms/parser/mzdata/libxml.rb
+- lib/ms/parser/mzdata/dom.rb
+- lib/ms/parser/mzdata/axml.rb
+- lib/ms/parser/mzdata.rb
+- lib/ms/parser/mzxml.rb
+- lib/ms/gradient_program.rb
+- lib/ms/parser.rb
+- lib/ms/precursor.rb
+- lib/xmlparser_wrapper.rb
+- lib/transmem.rb
 - bin/aafreqs.rb
-- bin/bioworks2excel.rb
+- bin/prob_validate.rb
+- bin/gi2annot.rb
+- bin/bioworks_to_pepxml_gui.rb
+- bin/filter_and_validate.rb
 - bin/pepproph_filter.rb
+- bin/bioworks2excel.rb
+- bin/srf_group.rb
+- bin/raw_to_mzXML.rb
 - bin/fasta_shaker.rb
+- bin/sqt_group.rb
+- bin/srf_to_sqt.rb
 - bin/bioworks_to_pepxml.rb
-- bin/protxml2prots_peps.rb
 - bin/id_precision.rb
+- bin/protein_summary.rb
+- bin/protxml2prots_peps.rb
+- bin/ms_to_lmat.rb
 - bin/id_class_anal.rb
-- bin/prob_validate.rb
-- bin/srf_to_sqt.rb
-- bin/filter_and_validate.rb
-- bin/srf_group.rb
-- bin/raw_to_mzXML.rb
+- script/histogram_probs.rb
+- script/extract_gradient_programs.rb
+- script/find_cysteine_background.rb
+- script/estimate_fpr_by_cysteine.rb
+- script/msvis.rb
+- script/toppred_to_yaml.rb
+- script/peps_per_bin.rb
 - script/create_little_pepxml.rb
-- script/mzXML2timeIndex.rb
+- script/sqt_to_meta.rb
+- script/compile_and_plot_smriti_final.rb
 - script/tpp_installer.rb
-- script/msvis.rb
-- script/histogram_probs.rb
-- script/prep_dir.rb
-- script/top_hit_per_scan.rb
 - script/genuine_tps_and_probs.rb
-- script/compile_and_plot_smriti_final.rb
-- script/simple_protein_digestion.rb
-- script/estimate_fpr_by_cysteine.rb
-- script/find_cysteine_background.rb
+- script/get_apex_values_rexml.rb
+- script/mzXML2timeIndex.rb
 - script/degenerate_peptides.rb
+- script/top_hit_per_scan.rb
+- script/prep_dir.rb
 - script/smriti_final_analysis.rb
-- script/toppred_to_yaml.rb
-- script/get_apex_values_rexml.rb
-- script/extract_gradient_programs.rb
-- specs/transmem_spec.rb
-- specs/roc_spec.rb
-- specs/ms
-- specs/load_bin_path.rb
-- specs/validator
-- specs/spec_helper.rb
-- specs/transmem
-- specs/spec_id
-- specs/spec_id_helper.rb
-- specs/fasta_spec.rb
+- script/simple_protein_digestion.rb
 - specs/gi_spec.rb
-- specs/bin
-- specs/validator_helper.rb
-- specs/merge_deep_spec.rb
-- specs/xml_spec.rb
-- specs/spec_id_spec.rb
+- specs/transmem
+- specs/transmem/phobius_spec.rb
+- specs/transmem/toppred_spec.rb
 - specs/align_spec.rb
-- specs/rspec_autotest.rb
-- specs/sample_enzyme_spec.rb
-- specs/spec_id_xml_spec.rb
-- specs/transmem_spec_shared.rb
-- specs/ms/gradient_program_spec.rb
-- specs/ms/msrun_spec.rb
-- specs/ms/parser_spec.rb
-- specs/ms/spectrum_spec.rb
-- specs/validator/background_spec.rb
-- specs/validator/decoy_spec.rb
-- specs/validator/transmem_spec.rb
-- specs/validator/true_pos_spec.rb
-- specs/validator/prot_from_pep_spec.rb
-- specs/validator/aa_spec.rb
-- specs/validator/fasta_helper.rb
-- specs/validator/bias_spec.rb
-- specs/transmem/toppred_spec.rb
-- specs/transmem/phobius_spec.rb
-- specs/spec_id/bioworks_spec.rb
-- specs/spec_id/aa_freqs_spec.rb
-- specs/spec_id/srf_spec.rb
-- specs/spec_id/precision
+- specs/fasta_spec.rb
+- specs/transmem_spec.rb
+- specs/spec_id
+- specs/spec_id/sequest_spec.rb
+- specs/spec_id/proph
+- specs/spec_id/proph/prot_summary_spec.rb
+- specs/spec_id/proph/pep_summary_spec.rb
+- specs/spec_id/protein_summary_spec.rb
 - specs/spec_id/srf_spec_helper.rb
-- specs/spec_id/sequest
 - specs/spec_id/digestor_spec.rb
-- specs/spec_id/protein_summary_spec.rb
-- specs/spec_id/proph
 - specs/spec_id/sqt_spec.rb
+- specs/spec_id/aa_freqs_spec.rb
+- specs/spec_id/srf_spec.rb
+- specs/spec_id/precision
 - specs/spec_id/precision/filter
+- specs/spec_id/precision/filter/cmdline_spec.rb
+- specs/spec_id/precision/filter/output_spec.rb
 - specs/spec_id/precision/prob_spec.rb
 - specs/spec_id/precision/filter_spec.rb
 - specs/spec_id/precision/prob_spec_helper.rb
-- specs/spec_id/precision/filter/cmdline_spec.rb
-- specs/spec_id/precision/filter/output_spec.rb
-- specs/spec_id/sequest/params_spec.rb
+- specs/spec_id/sequest
 - specs/spec_id/sequest/pepxml_spec.rb
-- specs/spec_id/proph/prot_summary_spec.rb
-- specs/spec_id/proph/pep_summary_spec.rb
-- specs/bin/filter_and_validate_spec.rb
-- specs/bin/fasta_shaker_spec.rb
+- specs/spec_id/sequest/params_spec.rb
+- specs/spec_id/bioworks_spec.rb
+- specs/spec_id_spec.rb
+- specs/roc_spec.rb
+- specs/spec_id_helper.rb
+- specs/merge_deep_spec.rb
+- specs/validator
+- specs/validator/aa_spec.rb
+- specs/validator/transmem_spec.rb
+- specs/validator/decoy_spec.rb
+- specs/validator/bias_spec.rb
+- specs/validator/true_pos_spec.rb
+- specs/validator/prot_from_pep_spec.rb
+- specs/validator/fasta_helper.rb
+- specs/validator/background_spec.rb
+- specs/validator/aa_est_spec.rb
+- specs/transmem_spec_shared.rb
+- specs/bin
+- specs/bin/ms_to_lmat_spec.rb
 - specs/bin/bioworks_to_pepxml_spec.rb
+- specs/bin/prob_validate_spec.rb
 - specs/bin/protein_summary_spec.rb
-- specs/bin/ms_to_lmat_spec.rb
+- specs/bin/fasta_shaker_spec.rb
 - specs/bin/filter_and_validate__multiple_vals_helper.yaml
-- specs/bin/prob_validate_spec.rb
-- test_files/4-03-03_mzXML
-- test_files/opd1
-- test_files/orbitrap_mzData
+- specs/bin/filter_and_validate_spec.rb
+- specs/rspec_autotest.rb
+- specs/xml_spec.rb
+- specs/spec_id_xml_spec.rb
+- specs/load_bin_path.rb
+- specs/sample_enzyme_spec.rb
+- specs/spec_helper.rb
+- specs/validator_helper.rb
+- specs/ms
+- specs/ms/msrun_spec.rb
+- specs/ms/spectrum_spec.rb
+- specs/ms/gradient_program_spec.rb
+- specs/ms/parser_spec.rb
+- test_files/toppred.small.out
+- test_files/bioworks_with_INV_small.xml
+- test_files/tf_bioworks2excel.bioXML
 - test_files/messups.fasta
-- test_files/small.fasta
-- test_files/toppred.xml.out
-- test_files/smallraw.RAW
 - test_files/bioworks_single_run_small.xml
-- test_files/tf_bioworks2excel.txt.actual
-- test_files/pepproph_small.xml
 - test_files/000_pepxml18_small.xml
-- test_files/tf_bioworks2excel.bioXML
-- test_files/bioworks31.params
-- test_files/bioworks_small.xml
-- test_files/bioworks32.params
+- test_files/toppred.xml.out
+- test_files/4-03-03_mzXML
+- test_files/4-03-03_mzXML/000.mzXML.timeIndex
+- test_files/4-03-03_mzXML/020.mzXML.timeIndex
+- test_files/bioworks_small.fasta
+- test_files/bioworks_small.toppred.out
+- test_files/opd1_020_beginning.RAW
+- test_files/phobius.small.noheader.txt
+- test_files/bioworks_small.phobius
+- test_files/corrupted_900.srf
+- test_files/phobius.small.small.txt
+- test_files/bioworks_small.params
+- test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes
+- test_files/pepproph_small.xml
+- test_files/yeast_gly_small-prot.xml
+- test_files/orbitrap_mzData
+- test_files/orbitrap_mzData/000_cut.xml
 - test_files/yeast_gly_small.xml
-- test_files/4-03-03_small.xml
-- test_files/bioworks_with_INV_small.xml
-- test_files/020a.mzXML.timeIndex
 - test_files/yeast_gly_small2.parentTimes
+- test_files/4-03-03_small.xml
+- test_files/tf_bioworks2excel.txt.actual
 - test_files/s01_anC1_ld020mM.meth
-- test_files/yeast_gly_small-prot.xml
-- test_files/bioworks-3.3_10prots.xml
-- test_files/4-03-03_small-prot.xml
-- test_files/bioworks33.params
 - test_files/head_of_7MIX.srf
-- test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes
+- test_files/bioworks31.params
+- test_files/bioworks32.params
+- test_files/validator_hits_separate
+- test_files/validator_hits_separate/bias_bioworks_small_HS.fasta
+- test_files/validator_hits_separate/bioworks_small_HS.xml
+- test_files/bioworks-3.3_10prots.xml
+- test_files/smallraw.RAW
+- test_files/bioworks_small.xml
 - test_files/bioworks_with_SHUFF_small.xml
-- test_files/toppred.small.out
-- test_files/phobius.small.small.txt
+- test_files/small.sqt
+- test_files/4-03-03_small-prot.xml
+- test_files/020a.mzXML.timeIndex
 - test_files/s01_anC1_ld020mM.key.txt
+- test_files/small.fasta
+- test_files/bioworks33.params
 - test_files/7MIX_STD_110802_1.sequest_params_fragment.srf
-- test_files/phobius.small.noheader.txt
-- test_files/interact-opd1_mods_small-prot.xml
-- test_files/corrupted_900.srf
-- test_files/validator_hits_separate
-- test_files/bioworks_small.phobius
-- test_files/bioworks_small.params
-- test_files/bioworks_small.toppred.out
-- test_files/bioworks_small.fasta
-- test_files/opd1_020_beginning.RAW
 - test_files/opd1_2runs_2mods
-- test_files/4-03-03_mzXML/000.mzXML.timeIndex
-- test_files/4-03-03_mzXML/020.mzXML.timeIndex
-- test_files/opd1/opd1_cat_inv_small-prot.xml
-- test_files/opd1/000.v2.1.mzXML.timeIndex
+- test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml
+- test_files/interact-opd1_mods_small-prot.xml
+- test_files/opd1
 - test_files/opd1/000.tpp_2.9.2.first10.xml
 - test_files/opd1/000_020-prot.png
-- test_files/opd1/twenty_scans.mzXML
-- test_files/opd1/000.my_answer.100lines.xml
-- test_files/opd1/twenty_scans_answ.lmat
-- test_files/opd1/twenty_scans_answ.lmata
-- test_files/opd1/000.tpp_1.2.3.first10.xml
+- test_files/opd1/sequest.3.2.params
 - test_files/opd1/sequest.3.1.params
-- test_files/opd1/000_020_3prots-prot.xml
 - test_files/opd1/twenty_scans.v2.1.mzXML
-- test_files/opd1/sequest.3.2.params
+- test_files/opd1/000.tpp_1.2.3.first10.xml
+- test_files/opd1/twenty_scans_answ.lmata
+- test_files/opd1/000.my_answer.100lines.xml
+- test_files/opd1/twenty_scans.mzXML
+- test_files/opd1/twenty_scans_answ.lmat
+- test_files/opd1/000.v2.1.mzXML.timeIndex
+- test_files/opd1/opd1_cat_inv_small-prot.xml
 - test_files/opd1/000_020_3prots-prot.mod_initprob.xml
-- test_files/orbitrap_mzData/000_cut.xml
-- test_files/validator_hits_separate/bioworks_small_HS.xml
-- test_files/validator_hits_separate/bias_bioworks_small_HS.fasta
-- test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml
-test_files: 
-- specs/transmem_spec.rb
-- specs/roc_spec.rb
-- specs/fasta_spec.rb
-- specs/gi_spec.rb
-- specs/merge_deep_spec.rb
-- specs/xml_spec.rb
-- specs/spec_id_spec.rb
-- specs/align_spec.rb
-- specs/sample_enzyme_spec.rb
-- specs/spec_id_xml_spec.rb
-- specs/ms/gradient_program_spec.rb
-- specs/ms/msrun_spec.rb
-- specs/ms/parser_spec.rb
-- specs/ms/spectrum_spec.rb
-- specs/validator/background_spec.rb
-- specs/validator/decoy_spec.rb
-- specs/validator/transmem_spec.rb
-- specs/validator/true_pos_spec.rb
-- specs/validator/prot_from_pep_spec.rb
-- specs/validator/aa_spec.rb
-- specs/validator/bias_spec.rb
-- specs/transmem/toppred_spec.rb
-- specs/transmem/phobius_spec.rb
-- specs/spec_id/bioworks_spec.rb
-- specs/spec_id/aa_freqs_spec.rb
-- specs/spec_id/srf_spec.rb
-- specs/spec_id/digestor_spec.rb
-- specs/spec_id/protein_summary_spec.rb
-- specs/spec_id/sqt_spec.rb
-- specs/spec_id/precision/prob_spec.rb
-- specs/spec_id/precision/filter_spec.rb
-- specs/spec_id/precision/filter/cmdline_spec.rb
-- specs/spec_id/precision/filter/output_spec.rb
-- specs/spec_id/sequest/params_spec.rb
-- specs/spec_id/sequest/pepxml_spec.rb
-- specs/spec_id/proph/prot_summary_spec.rb
-- specs/spec_id/proph/pep_summary_spec.rb
-- specs/bin/filter_and_validate_spec.rb
-- specs/bin/fasta_shaker_spec.rb
-- specs/bin/bioworks_to_pepxml_spec.rb
-- specs/bin/protein_summary_spec.rb
-- specs/bin/ms_to_lmat_spec.rb
-- specs/bin/prob_validate_spec.rb
+- test_files/opd1/000_020_3prots-prot.xml
+has_rdoc: true
+homepage: http://mspire.rubyforge.org
+post_install_message: 
 rdoc_options: 
 - --main
 - README
 - --title
 - mspire
-extra_rdoc_files: 
-- README
-- INSTALL
-- LICENSE
-executables: 
-- bioworks_to_pepxml_gui.rb
-- gi2annot.rb
-- protein_summary.rb
-- ms_to_lmat.rb
-- aafreqs.rb
-- bioworks2excel.rb
-- pepproph_filter.rb
-- fasta_shaker.rb
-- bioworks_to_pepxml.rb
-- protxml2prots_peps.rb
-- id_precision.rb
-- id_class_anal.rb
-- prob_validate.rb
-- srf_to_sqt.rb
-- filter_and_validate.rb
-- srf_group.rb
-- raw_to_mzXML.rb
-extensions: []
-
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
 requirements: 
 - "\"libxml\" is the prefered xml parser right now.  libxml, xmlparser, REXML and regular expressions are used as fallback in some routines."
 - some plotting functions will not be available without the "gnuplot" gem (and underlying gnuplot binary)
 - the "t2x" binary (in archive) or readw.exe is required to convert .RAW files to mzXML in some applications
 - "\"rake\" is useful for development"
 - "\"webgen (with gems redcloth and bluecloth) is necessary to build web pages"
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  name: libjtp
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Version::Requirement 
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        version: 0.2.12
-    version: 
-- !ruby/object:Gem::Dependency 
-  name: axml
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Version::Requirement 
-    requirements: 
-    - - ">"
-      - !ruby/object:Gem::Version 
-        version: 0.0.0
-    version: 
+rubyforge_project: mspire
+rubygems_version: 1.0.1
+signing_key: 
+specification_version: 2
+summary: Mass Spectrometry Proteomics Objects, Scripts, and Executables
+test_files: 
+- specs/gi_spec.rb
+- specs/transmem/phobius_spec.rb
+- specs/transmem/toppred_spec.rb
+- specs/align_spec.rb
+- specs/fasta_spec.rb
+- specs/transmem_spec.rb
+- specs/spec_id/sequest_spec.rb
+- specs/spec_id/proph/prot_summary_spec.rb
+- specs/spec_id/proph/pep_summary_spec.rb
+- specs/spec_id/protein_summary_spec.rb
+- specs/spec_id/digestor_spec.rb
+- specs/spec_id/sqt_spec.rb
+- specs/spec_id/aa_freqs_spec.rb
+- specs/spec_id/srf_spec.rb
+- specs/spec_id/precision/filter/cmdline_spec.rb
+- specs/spec_id/precision/filter/output_spec.rb
+- specs/spec_id/precision/prob_spec.rb
+- specs/spec_id/precision/filter_spec.rb
+- specs/spec_id/sequest/pepxml_spec.rb
+- specs/spec_id/sequest/params_spec.rb
+- specs/spec_id/bioworks_spec.rb
+- specs/spec_id_spec.rb
+- specs/roc_spec.rb
+- specs/merge_deep_spec.rb
+- specs/validator/aa_spec.rb
+- specs/validator/transmem_spec.rb
+- specs/validator/decoy_spec.rb
+- specs/validator/bias_spec.rb
+- specs/validator/true_pos_spec.rb
+- specs/validator/prot_from_pep_spec.rb
+- specs/validator/background_spec.rb
+- specs/validator/aa_est_spec.rb
+- specs/bin/ms_to_lmat_spec.rb
+- specs/bin/bioworks_to_pepxml_spec.rb
+- specs/bin/prob_validate_spec.rb
+- specs/bin/protein_summary_spec.rb
+- specs/bin/fasta_shaker_spec.rb
+- specs/bin/filter_and_validate_spec.rb
+- specs/xml_spec.rb
+- specs/spec_id_xml_spec.rb
+- specs/sample_enzyme_spec.rb
+- specs/ms/msrun_spec.rb
+- specs/ms/spectrum_spec.rb
+- specs/ms/gradient_program_spec.rb
+- specs/ms/parser_spec.rb