--- !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: 
platform: ruby
signing_key: 
cert_chain: 
post_install_message: 
authors: 
- John Prince
files: 
- INSTALL
- README
- Rakefile
- 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/transmem
- lib/transmem.rb
- lib/xml_style_parser.rb
- lib/xmlparser_wrapper.rb
- lib/bsearch.rb
- lib/group_by.rb
- lib/xml.rb
- lib/merge_deep.rb
- lib/index_by.rb
- lib/validator
- lib/mspire.rb
- lib/scan_i.rb
- lib/spec_id/sequest.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/protein_summary.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/output.rb
- lib/spec_id/precision/filter/cmdline.rb
- 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/params.rb
- lib/spec_id/sequest/pepxml.rb
- lib/align/chams.rb
- lib/ms/converter
- lib/ms/parser
- lib/ms/spectrum.rb
- lib/ms/gradient_program.rb
- lib/ms/msrun.rb
- lib/ms/precursor.rb
- lib/ms/scan.rb
- lib/ms/msrun_index.rb
- lib/ms/parser.rb
- lib/ms/converter/mzxml.rb
- lib/ms/parser/mzdata
- 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/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
- bin/aafreqs.rb
- bin/bioworks2excel.rb
- bin/pepproph_filter.rb
- bin/fasta_shaker.rb
- bin/bioworks_to_pepxml.rb
- bin/protxml2prots_peps.rb
- bin/id_precision.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/create_little_pepxml.rb
- script/mzXML2timeIndex.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/degenerate_peptides.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
- 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/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/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/precision/filter
- 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/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/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
- 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/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/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/bioworks_with_SHUFF_small.xml
- test_files/toppred.small.out
- test_files/phobius.small.small.txt
- test_files/s01_anC1_ld020mM.key.txt
- 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/opd1/000.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.3.1.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_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
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: []

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: