mspire 0.4.9 → 0.5.0

metadata

@@ -1,330 +1,68 @@
 --- !ruby/object:Gem::Specification 
 name: mspire
 version: !ruby/object:Gem::Version 
-  version: 0.4.9
+  version: 0.5.0
 platform: ruby
 authors: 
 - John Prince
+- Simon Chiang
 autorequire: 
 bindir: bin
 cert_chain: []
 
-date: 2010-01-06 00:00:00 -07:00
+date: 2008-11-20 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: libjtp
-  type: :runtime
+  name: tap
+  type: :development
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
     requirements: 
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.2.14
+        version: 0.11.2
     version: 
 - !ruby/object:Gem::Dependency 
-  name: axml
-  type: :runtime
+  name: minitest
+  type: :development
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
     requirements: 
-    - - ~>
+    - - "="
       - !ruby/object:Gem::Version 
-        version: 0.0.0
+        version: 1.3.0
     version: 
-- !ruby/object:Gem::Dependency 
-  name: arrayclass
-  type: :runtime
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        version: 0.1.0
-    version: 
-description: mspire is for working with mass spectrometry proteomics data
+description: A library for working with mass spectrometry proteomics data.
 email: jprince@icmb.utexas.edu
-executables: 
-- bioworks2excel.rb
-- protein_summary.rb
-- fasta_shaker.rb
-- srf_to_sqt.rb
-- pepproph_filter.rb
-- raw_to_mzXML.rb
-- sqt_group.rb
-- srf_group.rb
-- bioworks_to_pepxml_gui.rb
-- id_class_anal.rb
-- bioworks_to_pepxml.rb
-- run_percolator.rb
-- gi2annot.rb
-- id_precision.rb
-- filter_and_validate.rb
-- aafreqs.rb
-- ms_to_lmat.rb
-- protxml2prots_peps.rb
-- prob_validate.rb
+executables: []
+
 extensions: []
 
 extra_rdoc_files: 
-- README.rdoc
-files: 
-- INSTALL
-- README
-- README.rdoc
-- Rakefile
-- LICENSE
 - changelog.txt
-- release_notes.txt
-- lib/ms/parser/mzdata.rb
-- lib/ms/parser/mzdata/axml.rb
-- lib/ms/parser/mzdata/libxml.rb
-- lib/ms/parser/mzdata/dom.rb
-- lib/ms/parser/mzxml.rb
-- lib/ms/parser/mzxml/axml.rb
-- lib/ms/parser/mzxml/hpricot.rb
-- lib/ms/parser/mzxml/libxml.rb
-- lib/ms/parser/mzxml/dom.rb
-- lib/ms/parser/mzxml/regexp.rb
-- lib/ms/parser/mzxml/rexml.rb
-- lib/ms/parser/mzxml/xmlparser.rb
-- lib/ms/spectrum.rb
-- lib/ms/msrun.rb
-- lib/ms/parser.rb
-- lib/ms/msrun_index.rb
-- lib/ms/converter/mzxml.rb
-- lib/ms/scan.rb
-- lib/ms/precursor.rb
-- lib/ms/gradient_program.rb
-- lib/align/chams.rb
-- lib/group_by.rb
-- lib/mspire.rb
-- lib/spec_id/protein_summary.rb
-- lib/spec_id/parser/proph.rb
-- lib/spec_id/mass.rb
-- lib/spec_id/srf.rb
-- lib/spec_id/proph/prot_summary.rb
-- lib/spec_id/proph/pep_summary.rb
-- lib/spec_id/precision/filter/cmdline.rb
-- lib/spec_id/precision/filter/interactive.rb
-- lib/spec_id/precision/filter/output.rb
-- lib/spec_id/precision/prob/cmdline.rb
-- lib/spec_id/precision/prob/output.rb
-- lib/spec_id/precision/prob.rb
-- lib/spec_id/precision/output.rb
-- lib/spec_id/precision/filter.rb
-- lib/spec_id/proph.rb
-- lib/spec_id/bioworks.rb
-- lib/spec_id/sequest/params.rb
-- lib/spec_id/sequest/pepxml.rb
-- lib/spec_id/digestor.rb
-- lib/spec_id/sequest.rb
-- lib/spec_id/sqt.rb
-- lib/spec_id/aa_freqs.rb
-- lib/pi_zero.rb
-- lib/align.rb
-- lib/scan_i.rb
-- lib/validator.rb
-- lib/spec_id.rb
-- lib/archive/targz.rb
-- lib/qvalue.rb
+- LICENSE
+- README
+files: 
 - lib/ms.rb
-- lib/core_extensions.rb
-- lib/bsearch.rb
-- lib/roc.rb
-- lib/sample_enzyme.rb
-- lib/spec_id_xml.rb
-- lib/xmlparser_wrapper.rb
-- lib/fasta.rb
-- lib/transmem/toppred.rb
-- lib/transmem/phobius.rb
-- lib/index_by.rb
-- lib/transmem.rb
-- lib/gi.rb
-- lib/xml_style_parser.rb
-- lib/merge_deep.rb
-- lib/validator/bias.rb
-- lib/validator/aa_est.rb
-- lib/validator/cmdline.rb
-- lib/validator/background.rb
-- lib/validator/digestion_based.rb
-- lib/validator/decoy.rb
-- lib/validator/true_pos.rb
-- lib/validator/aa.rb
-- lib/validator/q_value.rb
-- lib/validator/probability.rb
-- lib/validator/transmem.rb
-- lib/validator/prot_from_pep.rb
-- lib/xml.rb
-- bin/bioworks2excel.rb
-- bin/protein_summary.rb
-- bin/fasta_shaker.rb
-- bin/srf_to_sqt.rb
-- bin/pepproph_filter.rb
-- bin/raw_to_mzXML.rb
-- bin/sqt_group.rb
-- bin/srf_group.rb
-- bin/bioworks_to_pepxml_gui.rb
-- bin/id_class_anal.rb
-- bin/bioworks_to_pepxml.rb
-- bin/run_percolator.rb
-- bin/gi2annot.rb
-- bin/id_precision.rb
-- bin/filter_and_validate.rb
-- bin/aafreqs.rb
-- bin/ms_to_lmat.rb
-- bin/protxml2prots_peps.rb
-- bin/prob_validate.rb
-- script/mascot_fix_pepxml.rb
-- script/extract_gradient_programs.rb
-- script/smriti_final_analysis.rb
-- script/prep_dir.rb
-- script/toppred_to_yaml.rb
-- script/sqt_to_meta.rb
-- script/compile_and_plot_smriti_final.rb
-- script/find_cysteine_background.rb
-- script/estimate_fpr_by_cysteine.rb
-- script/top_hit_per_scan.rb
-- script/msvis.rb
-- script/histogram_probs.rb
-- script/genuine_tps_and_probs.rb
-- script/get_apex_values_rexml.rb
-- script/simple_protein_digestion.rb
-- script/mzXML2timeIndex.rb
-- script/peps_per_bin.rb
-- script/tpp_installer.rb
-- script/degenerate_peptides.rb
-- script/create_little_pepxml.rb
-- specs/ms/msrun_spec.rb
-- specs/ms/parser_spec.rb
-- specs/ms/spectrum_spec.rb
-- specs/ms/gradient_program_spec.rb
-- specs/spec_id/sqt_spec.rb
-- specs/spec_id/protein_summary_spec.rb
-- specs/spec_id/aa_freqs_spec.rb
-- specs/spec_id/proph/pep_summary_spec.rb
-- specs/spec_id/proph/prot_summary_spec.rb
-- specs/spec_id/bioworks_spec.rb
-- specs/spec_id/srf_spec.rb
-- specs/spec_id/precision/filter/output_spec.rb
-- specs/spec_id/precision/filter/cmdline_spec.rb
-- specs/spec_id/precision/prob_spec_helper.rb
-- specs/spec_id/precision/prob_spec.rb
-- specs/spec_id/precision/filter_spec.rb
-- specs/spec_id/srf_spec_helper.rb
-- specs/spec_id/sequest/params_spec.rb
-- specs/spec_id/sequest/pepxml_spec.rb
-- specs/spec_id/digestor_spec.rb
-- specs/spec_id/sequest_spec.rb
-- specs/xml_spec.rb
-- specs/roc_spec.rb
-- specs/merge_deep_spec.rb
-- specs/sample_enzyme_spec.rb
-- specs/gi_spec.rb
-- specs/transmem_spec_shared.rb
-- specs/validator_helper.rb
-- specs/pi_zero_spec.rb
-- specs/load_bin_path.rb
-- specs/spec_id_helper.rb
-- specs/bin/filter_and_validate_spec.rb
-- specs/bin/fasta_shaker_spec.rb
-- specs/bin/protein_summary_spec.rb
-- specs/bin/prob_validate_spec.rb
-- specs/bin/ms_to_lmat_spec.rb
-- specs/bin/filter_and_validate__multiple_vals_helper.yaml
-- specs/bin/bioworks_to_pepxml_spec.rb
-- specs/align_spec.rb
-- specs/spec_id_xml_spec.rb
-- specs/transmem_spec.rb
-- specs/spec_helper.rb
-- specs/transmem/toppred_spec.rb
-- specs/transmem/phobius_spec.rb
-- specs/qvalue_spec.rb
-- specs/rspec_autotest.rb
-- specs/fasta_spec.rb
-- specs/spec_id_spec.rb
-- specs/validator/aa_spec.rb
-- specs/validator/prot_from_pep_spec.rb
-- specs/validator/bias_spec.rb
-- specs/validator/decoy_spec.rb
-- specs/validator/background_spec.rb
-- specs/validator/fasta_helper.rb
-- specs/validator/true_pos_spec.rb
-- specs/validator/transmem_spec.rb
-- specs/validator/aa_est_spec.rb
-- test_files/yeast_gly_small2.parentTimes
-- test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes
-- test_files/validator_hits_separate/bias_bioworks_small_HS.fasta
-- test_files/validator_hits_separate/bioworks_small_HS.xml
-- test_files/tf_bioworks2excel.bioXML
-- test_files/phobius.small.small.txt
-- test_files/bioworks_with_SHUFF_small.xml
-- test_files/4-03-03_small.xml
-- test_files/toppred.small.out
-- test_files/yeast_gly_small-prot.xml
-- test_files/bioworks32.params
-- test_files/tf_bioworks2excel.txt.actual
-- test_files/bioworks_with_INV_small.xml
-- test_files/bioworks_single_run_small.xml
-- test_files/bioworks_small.xml
-- test_files/bioworks_small.phobius
-- test_files/bioworks31.params
-- test_files/s01_anC1_ld020mM.key.txt
-- test_files/7MIX_STD_110802_1.sequest_params_fragment.srf
-- test_files/opd1_020_beginning.RAW
-- test_files/yeast_gly_small.xml
-- test_files/opd1/000.tpp_2.9.2.first10.xml
-- test_files/opd1/sequest.3.2.params
-- test_files/opd1/000.my_answer.100lines.xml
-- test_files/opd1/twenty_scans.v2.1.mzXML
-- test_files/opd1/000_020-prot.png
-- test_files/opd1/opd1_cat_inv_small-prot.xml
-- test_files/opd1/000.tpp_1.2.3.first10.xml
-- test_files/opd1/sequest.3.1.params
-- test_files/opd1/twenty_scans.mzXML
-- test_files/opd1/000_020_3prots-prot.mod_initprob.xml
-- test_files/opd1/twenty_scans_answ.lmata
-- test_files/opd1/000.v2.1.mzXML.timeIndex
-- test_files/opd1/twenty_scans_answ.lmat
-- test_files/opd1/000_020_3prots-prot.xml
-- test_files/small.sqt
-- test_files/pepproph_small.xml
-- test_files/phobius.small.noheader.txt
-- test_files/4-03-03_small-prot.xml
-- test_files/interact-opd1_mods_small-prot.xml
-- test_files/messups.fasta
-- test_files/toppred.xml.out
-- test_files/bioworks33.params
-- test_files/020a.mzXML.timeIndex
-- test_files/bioworks_small.toppred.out
-- test_files/bioworks_small.params
-- test_files/head_of_7MIX.srf
-- test_files/s01_anC1_ld020mM.meth
-- test_files/000_pepxml18_small.xml
-- test_files/orbitrap_mzData/000_cut.xml
-- test_files/bioworks_small.fasta
-- test_files/small.fasta
-- test_files/bioworks-3.3_10prots.xml
-- test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml
-- test_files/opd1_2runs_2mods/data/040.readw.mzXML
-- test_files/opd1_2runs_2mods/data/040.mzData.xml
-- test_files/opd1_2runs_2mods/data/020.readw.mzXML
-- test_files/opd1_2runs_2mods/data/020.mzData.xml
-- test_files/opd1_2runs_2mods/data/README.txt
-- test_files/smallraw.RAW
-- test_files/4-03-03_mzXML/020.mzXML.timeIndex
-- test_files/4-03-03_mzXML/000.mzXML.timeIndex
-- test_files/corrupted_900.srf
+- lib/ms/calc.rb
+- lib/ms/data.rb
+- lib/ms/data/interleaved.rb
+- lib/ms/data/transposed.rb
+- lib/ms/data/simple.rb
+- lib/ms/data/lazy_io.rb
+- lib/ms/data/lazy_string.rb
+- lib/ms/format/format_error.rb
+- lib/ms/support/binary_search.rb
+- lib/ms/spectrum.rb
+- changelog.txt
+- LICENSE
+- README
 has_rdoc: true
 homepage: http://mspire.rubyforge.org
-licenses: []
-
 post_install_message: 
-rdoc_options: 
-- --main
-- README.rdoc
-- --title
-- mspire
+rdoc_options: []
+
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
@@ -339,62 +77,12 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !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"
+requirements: []
+
 rubyforge_project: mspire
-rubygems_version: 1.3.5
+rubygems_version: 1.3.0
 signing_key: 
-specification_version: 3
+specification_version: 2
 summary: Mass Spectrometry Proteomics Objects, Scripts, and Executables
-test_files: 
-- specs/ms/msrun_spec.rb
-- specs/ms/parser_spec.rb
-- specs/ms/spectrum_spec.rb
-- specs/ms/gradient_program_spec.rb
-- specs/spec_id/sqt_spec.rb
-- specs/spec_id/protein_summary_spec.rb
-- specs/spec_id/aa_freqs_spec.rb
-- specs/spec_id/proph/pep_summary_spec.rb
-- specs/spec_id/proph/prot_summary_spec.rb
-- specs/spec_id/bioworks_spec.rb
-- specs/spec_id/srf_spec.rb
-- specs/spec_id/precision/filter/output_spec.rb
-- specs/spec_id/precision/filter/cmdline_spec.rb
-- specs/spec_id/precision/prob_spec.rb
-- specs/spec_id/precision/filter_spec.rb
-- specs/spec_id/sequest/params_spec.rb
-- specs/spec_id/sequest/pepxml_spec.rb
-- specs/spec_id/digestor_spec.rb
-- specs/spec_id/sequest_spec.rb
-- specs/xml_spec.rb
-- specs/roc_spec.rb
-- specs/merge_deep_spec.rb
-- specs/sample_enzyme_spec.rb
-- specs/gi_spec.rb
-- specs/pi_zero_spec.rb
-- specs/bin/filter_and_validate_spec.rb
-- specs/bin/fasta_shaker_spec.rb
-- specs/bin/protein_summary_spec.rb
-- specs/bin/prob_validate_spec.rb
-- specs/bin/ms_to_lmat_spec.rb
-- specs/bin/bioworks_to_pepxml_spec.rb
-- specs/align_spec.rb
-- specs/spec_id_xml_spec.rb
-- specs/transmem_spec.rb
-- specs/transmem/toppred_spec.rb
-- specs/transmem/phobius_spec.rb
-- specs/qvalue_spec.rb
-- specs/fasta_spec.rb
-- specs/spec_id_spec.rb
-- specs/validator/aa_spec.rb
-- specs/validator/prot_from_pep_spec.rb
-- specs/validator/bias_spec.rb
-- specs/validator/decoy_spec.rb
-- specs/validator/background_spec.rb
-- specs/validator/true_pos_spec.rb
-- specs/validator/transmem_spec.rb
-- specs/validator/aa_est_spec.rb
+test_files: []
+

data/INSTALL

@@ -1,58 +0,0 @@
-
-Prerequisites
--------------
-
-Much of the package will work without any prerequisites at all.  Some functionality may require addition ruby packages or other converters.
-
-* libjtp - generic library installed automatically if you install mspire with rubygems (or 'gem install libjtp')
-
-### XML parsing:
-
-* [xmlparser](http://www.yoshidam.net/Ruby.html) (comes with one-click Windows; on Ubuntu: 'sudo apt-get libxml-parser-ruby1.8')
-* [axml](http://axml.rubyforge.org/) dom wrapper for xmlparser. ('gem install axml')
-
-### Optional:
-* ['t2x'](archive/t2x) linux executable to convert .RAW files (Xcalibur 1.x) to version 1 mzXML files
-* [libxml](http://libxml.rubyforge.org/) can use instead of xmlparser.  In Ubuntu: sudo apt-get install libxml2 libxml2-dev ; sudo gem install libxml-ruby --remote
-* [gnuplot](http://rgplot.rubyforge.org/) ('gem install gnuplot').  For some plotting.  Of course, you'll need [gnuplot](http://www.gnuplot.info/) before this package will work.  Under one-click installer for windows this package requires a little configuration.  It works with no configuration on cygwin (or linux).
-
-Installation
-------------
-
-    gem install mspire
-
-See [installation under cygwin](cygwin.html) if you're on Windows.
-
-Development
------------
-
-NOTE: If you are interested in becoming a developer on this project (i.e., write access to the repository) please [contact me](http://rubyforge.org/users/jtprince/)
-
-
-anonymous svn checkout:
-
-    svn checkout svn://rubyforge.org/var/svn/mspire
-
-prerequisites: 
-
-* [rake](http://rake.rubyforge.org/) (with rubygems: 'gem install rake --remote')
-* [rspec](http://rspec.info/) (with rubygems: 'gem install rspec --remote')
-
-Use rake:
-
-    % rake -T
-    rake clean              # Remove any temporary products.
-    rake html_docs          # creates docs in doc/html
-    rake package            # Build all the packages
-    rake test               # Run tests
-    rake test_ind           # Run unit tests individual on each test
-    rake upload_docs        # create and upload docs to server
-    ...etc...
-
-    run tests: rake spec
-         (or): rake specl
-
-    run tests with large files: rake spec SPEC_LARGE=t
-
-    run test on one file: rake spec SPEC=specs/{path_to_spec_file}
-

data/README.rdoc

@@ -1,18 +0,0 @@
-
-= mspire
-
-mass spectrometry proteomics in ruby
-
-Please refer to the latest Documentation[http://mspire.rubyforge.org]
-
-Please see Installation[http://mspire.rubyforge.org/install/index.html]
-
-== Data Models and Examples
-
-Object models and usage examples are online:
-
-[MS::MSRun] http://mspire.rubyforge.org/ms/msrun.html
-[SpecID] http://mspire.rubyforge.org/spec_id/spec_id.html
-[SRF] http://mspire.rubyforge.org/spec_id/srf.html
-[False Identification Rate Determination] http://mspire.rubyforge.org/spec_id/fir/index.html
-[OBI-Warp] http://mspire.rubyforge.org/ms/obiwarp.html