mspire 0.4.7 → 0.4.9

data/changelog.txt

@@ -221,3 +221,7 @@ filter)
 ## version 0.4.7
 1. Added ability to quickly grab sequest params out of a .SRF file
 2. Added helpful runtime error if print_duplicate_references is 0.
+
+## version 0.4.9
+1. quiet some unneeded output and fixed truncation of filenames with '.'
+inside them.

data/lib/mspire.rb

@@ -1,4 +1,4 @@
 
 module Mspire
-  Version = '0.4.7'
+  Version = '0.4.9'
 end

data/lib/spec_id/sequest/pepxml.rb

@@ -767,8 +767,8 @@ Default_Options = {
   # given any kind of filename (from windows or whatever)
   # returns the base of the filename with no file extension
   def self.base_name_noext(file)
-    file.gsub!("\\", '/')
-    File.basename(file).sub(/\.[\w^\.]+$/, '')
+    basename = file.split(/[\/\\]/).last
+    basename.chomp(File.extname(basename))
   end
 
 

data/lib/spec_id/srf.rb

@@ -853,7 +853,6 @@ class SRF::OUT::Pep
   end
 
   def self.read_extra_references(fh, num_extra_references, pep_hits, global_ref_hash)
-    p num_extra_references
     num_extra_references.times do
       # 80 bytes total (with index number)
       pep = pep_hits[fh.read(8).unpack('x4I').first - 1]

data/lib/validator/transmem.rb

@@ -136,7 +136,7 @@ class Validator::Transmem::Protein < Validator::DigestionBased
     prts = pep.prots
     prts_w_keys = 0
     sum_of_fractions = 0.0
-    prts.each do |prot| 
+    prts.each do |prot|
       key = @transmem_index.reference_to_key(prot.reference)
       ans = @transmem_index.avg_overlap(key, pep.aaseq, :fraction)
       if ans

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: mspire
 version: !ruby/object:Gem::Version 
-  version: 0.4.7
+  version: 0.4.9
 platform: ruby
 authors: 
 - John Prince
@@ -9,11 +9,12 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2008-11-06 00:00:00 -07:00
+date: 2010-01-06 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: libjtp
+  type: :runtime
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
     requirements: 
@@ -23,6 +24,7 @@ dependencies:
     version: 
 - !ruby/object:Gem::Dependency 
   name: axml
+  type: :runtime
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
     requirements: 
@@ -32,6 +34,7 @@ dependencies:
     version: 
 - !ruby/object:Gem::Dependency 
   name: arrayclass
+  type: :runtime
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
     requirements: 
@@ -42,25 +45,25 @@ dependencies:
 description: mspire is for working with mass spectrometry proteomics data
 email: jprince@icmb.utexas.edu
 executables: 
-- gi2annot.rb
-- protxml2prots_peps.rb
-- filter_and_validate.rb
-- raw_to_mzXML.rb
-- run_percolator.rb
+- bioworks2excel.rb
+- protein_summary.rb
+- fasta_shaker.rb
 - srf_to_sqt.rb
-- prob_validate.rb
+- pepproph_filter.rb
+- raw_to_mzXML.rb
+- sqt_group.rb
 - srf_group.rb
-- ms_to_lmat.rb
-- protein_summary.rb
 - bioworks_to_pepxml_gui.rb
 - id_class_anal.rb
+- bioworks_to_pepxml.rb
+- run_percolator.rb
+- gi2annot.rb
 - id_precision.rb
-- sqt_group.rb
+- filter_and_validate.rb
 - aafreqs.rb
-- pepproph_filter.rb
-- bioworks2excel.rb
-- bioworks_to_pepxml.rb
-- fasta_shaker.rb
+- ms_to_lmat.rb
+- protxml2prots_peps.rb
+- prob_validate.rb
 extensions: []
 
 extra_rdoc_files: 
@@ -73,278 +76,249 @@ files:
 - LICENSE
 - changelog.txt
 - release_notes.txt
-- lib/ms
-- lib/ms/parser
-- lib/ms/parser/mzxml
-- lib/ms/parser/mzxml/rexml.rb
-- lib/ms/parser/mzxml/libxml.rb
-- lib/ms/parser/mzxml/xmlparser.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/ms/parser/mzdata
-- lib/ms/parser/mzdata/libxml.rb
+- 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/mzdata.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/gradient_program.rb
-- lib/ms/precursor.rb
-- lib/ms/msrun_index.rb
 - lib/ms/parser.rb
-- lib/ms/spectrum.rb
-- lib/ms/converter
+- lib/ms/msrun_index.rb
 - lib/ms/converter/mzxml.rb
 - lib/ms/scan.rb
-- lib/core_extensions.rb
-- lib/scan_i.rb
-- lib/fasta.rb
-- lib/qvalue.rb
-- lib/roc.rb
-- lib/spec_id.rb
-- lib/xml.rb
+- lib/ms/precursor.rb
+- lib/ms/gradient_program.rb
+- lib/align/chams.rb
 - lib/group_by.rb
-- lib/index_by.rb
-- lib/sample_enzyme.rb
-- lib/transmem
-- lib/transmem/phobius.rb
-- lib/transmem/toppred.rb
-- lib/ms.rb
-- lib/pi_zero.rb
-- lib/spec_id
-- lib/spec_id/srf.rb
-- lib/spec_id/sequest.rb
-- lib/spec_id/parser
+- lib/mspire.rb
+- lib/spec_id/protein_summary.rb
 - lib/spec_id/parser/proph.rb
-- lib/spec_id/sequest
-- lib/spec_id/sequest/params.rb
-- lib/spec_id/sequest/pepxml.rb
-- lib/spec_id/precision
-- lib/spec_id/precision/filter.rb
-- lib/spec_id/precision/prob.rb
-- lib/spec_id/precision/output.rb
-- lib/spec_id/precision/filter
-- lib/spec_id/precision/filter/interactive.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
 - lib/spec_id/precision/prob/cmdline.rb
 - lib/spec_id/precision/prob/output.rb
-- lib/spec_id/mass.rb
-- lib/spec_id/proph
-- lib/spec_id/proph/pep_summary.rb
-- lib/spec_id/proph/prot_summary.rb
-- lib/spec_id/protein_summary.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/aa_freqs.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/bioworks.rb
-- lib/merge_deep.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
+- 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/align
-- lib/align/chams.rb
-- lib/validator.rb
 - lib/gi.rb
-- lib/validator
-- lib/validator/prot_from_pep.rb
-- lib/validator/aa.rb
-- lib/validator/decoy.rb
-- lib/validator/true_pos.rb
+- lib/xml_style_parser.rb
+- lib/merge_deep.rb
+- lib/validator/bias.rb
 - lib/validator/aa_est.rb
-- lib/validator/probability.rb
 - lib/validator/cmdline.rb
-- lib/validator/digestion_based.rb
-- lib/validator/transmem.rb
-- lib/validator/bias.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/xml_style_parser.rb
-- lib/mspire.rb
-- lib/archive
-- lib/archive/targz.rb
-- lib/spec_id_xml.rb
-- lib/bsearch.rb
-- bin/gi2annot.rb
-- bin/protxml2prots_peps.rb
-- bin/filter_and_validate.rb
-- bin/raw_to_mzXML.rb
-- bin/run_percolator.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/prob_validate.rb
+- bin/pepproph_filter.rb
+- bin/raw_to_mzXML.rb
+- bin/sqt_group.rb
 - bin/srf_group.rb
-- bin/ms_to_lmat.rb
-- bin/protein_summary.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/sqt_group.rb
+- bin/filter_and_validate.rb
 - bin/aafreqs.rb
-- bin/pepproph_filter.rb
-- bin/bioworks2excel.rb
-- bin/bioworks_to_pepxml.rb
-- bin/fasta_shaker.rb
-- script/estimate_fpr_by_cysteine.rb
-- script/toppred_to_yaml.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/mzXML2timeIndex.rb
-- script/genuine_tps_and_probs.rb
-- script/histogram_probs.rb
-- script/find_cysteine_background.rb
-- script/degenerate_peptides.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/tpp_installer.rb
-- script/mascot_fix_pepxml.rb
+- script/find_cysteine_background.rb
+- script/estimate_fpr_by_cysteine.rb
 - script/top_hit_per_scan.rb
-- script/create_little_pepxml.rb
-- script/smriti_final_analysis.rb
-- script/get_apex_values_rexml.rb
-- script/sqt_to_meta.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
-- specs/ms
-- specs/ms/gradient_program_spec.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/msrun_spec.rb
-- specs/merge_deep_spec.rb
-- specs/qvalue_spec.rb
-- specs/spec_helper.rb
-- specs/fasta_spec.rb
-- specs/transmem
-- specs/transmem/phobius_spec.rb
-- specs/transmem/toppred_spec.rb
-- specs/align_spec.rb
-- specs/spec_id_helper.rb
-- specs/transmem_spec.rb
-- specs/spec_id
+- 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/sqt_spec.rb
-- specs/spec_id/sequest
-- specs/spec_id/sequest/pepxml_spec.rb
-- specs/spec_id/sequest/params_spec.rb
-- specs/spec_id/precision
-- specs/spec_id/precision/filter_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
-- specs/spec_id/precision/filter/cmdline_spec.rb
-- specs/spec_id/precision/filter/output_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/srf_spec.rb
+- specs/spec_id/precision/filter_spec.rb
 - specs/spec_id/srf_spec_helper.rb
-- specs/spec_id/sequest_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/aa_freqs_spec.rb
-- specs/rspec_autotest.rb
-- specs/pi_zero_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/transmem_spec_shared.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_spec.rb
-- specs/validator
-- specs/validator/true_pos_spec.rb
-- specs/validator/aa_est_spec.rb
-- specs/validator/background_spec.rb
-- specs/validator/bias_spec.rb
-- specs/validator/transmem_spec.rb
-- specs/validator/prot_from_pep_spec.rb
-- specs/validator/decoy_spec.rb
-- specs/validator/aa_spec.rb
-- specs/validator/fasta_helper.rb
-- specs/bin
-- specs/bin/filter_and_validate__multiple_vals_helper.yaml
-- specs/bin/protein_summary_spec.rb
+- specs/spec_id_helper.rb
 - specs/bin/filter_and_validate_spec.rb
-- specs/bin/ms_to_lmat_spec.rb
 - specs/bin/fasta_shaker_spec.rb
-- specs/bin/bioworks_to_pepxml_spec.rb
+- specs/bin/protein_summary_spec.rb
 - specs/bin/prob_validate_spec.rb
-- specs/roc_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/validator_helper.rb
-- test_files/020a.mzXML.timeIndex
+- 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/bioworks_single_run_small.xml
-- test_files/bioworks_with_INV_small.xml
-- test_files/validator_hits_separate
-- test_files/validator_hits_separate/bioworks_small_HS.xml
+- test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes
 - test_files/validator_hits_separate/bias_bioworks_small_HS.fasta
-- test_files/opd1
-- test_files/opd1/twenty_scans_answ.lmata
+- 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/opd1/000.v2.1.mzXML.timeIndex
+- 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_020_3prots-prot.mod_initprob.xml
+- test_files/opd1/000.tpp_1.2.3.first10.xml
 - test_files/opd1/sequest.3.1.params
-- test_files/opd1/000_020-prot.png
 - test_files/opd1/twenty_scans.mzXML
-- test_files/opd1/twenty_scans.v2.1.mzXML
-- test_files/opd1/000.tpp_1.2.3.first10.xml
-- test_files/opd1/000_020_3prots-prot.xml
-- test_files/opd1/000.my_answer.100lines.xml
+- 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/sequest.3.2.params
-- test_files/bioworks_small.xml
-- test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes
-- test_files/bioworks_with_SHUFF_small.xml
-- test_files/yeast_gly_small.xml
-- test_files/bioworks_small.toppred.out
-- test_files/4-03-03_small-prot.xml
-- test_files/bioworks32.params
-- test_files/bioworks_small.fasta
+- test_files/opd1/000_020_3prots-prot.xml
+- test_files/small.sqt
 - test_files/pepproph_small.xml
-- test_files/4-03-03_mzXML
-- test_files/4-03-03_mzXML/020.mzXML.timeIndex
-- test_files/4-03-03_mzXML/000.mzXML.timeIndex
-- test_files/smallraw.RAW
-- test_files/toppred.small.out
-- test_files/head_of_7MIX.srf
-- test_files/bioworks-3.3_10prots.xml
-- test_files/interact-opd1_mods_small-prot.xml
-- test_files/s01_anC1_ld020mM.meth
 - test_files/phobius.small.noheader.txt
-- test_files/opd1_020_beginning.RAW
+- 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/4-03-03_small.xml
-- test_files/bioworks_small.phobius
-- test_files/phobius.small.small.txt
-- test_files/tf_bioworks2excel.bioXML
-- test_files/000_pepxml18_small.xml
 - test_files/bioworks33.params
-- test_files/tf_bioworks2excel.txt.actual
-- test_files/s01_anC1_ld020mM.key.txt
+- test_files/020a.mzXML.timeIndex
+- test_files/bioworks_small.toppred.out
 - test_files/bioworks_small.params
-- test_files/yeast_gly_small-prot.xml
-- test_files/messups.fasta
-- test_files/orbitrap_mzData
+- 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/7MIX_STD_110802_1.sequest_params_fragment.srf
-- test_files/bioworks31.params
-- test_files/small.sqt
+- test_files/bioworks_small.fasta
 - test_files/small.fasta
-- test_files/opd1_2runs_2mods
+- test_files/bioworks-3.3_10prots.xml
 - test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml
-- test_files/opd1_2runs_2mods/data
-- test_files/opd1_2runs_2mods/data/README.txt
+- 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/040.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
 has_rdoc: true
 homepage: http://mspire.rubyforge.org
+licenses: []
+
 post_install_message: 
 rdoc_options: 
 - --main
@@ -372,55 +346,55 @@ requirements:
 - "\"rake\" is useful for development"
 - "\"webgen (with gems redcloth and bluecloth) is necessary to build web pages"
 rubyforge_project: mspire
-rubygems_version: 1.1.1
+rubygems_version: 1.3.5
 signing_key: 
-specification_version: 2
+specification_version: 3
 summary: Mass Spectrometry Proteomics Objects, Scripts, and Executables
 test_files: 
-- specs/ms/gradient_program_spec.rb
+- specs/ms/msrun_spec.rb
 - specs/ms/parser_spec.rb
 - specs/ms/spectrum_spec.rb
-- specs/ms/msrun_spec.rb
-- specs/merge_deep_spec.rb
-- specs/qvalue_spec.rb
-- specs/fasta_spec.rb
-- specs/transmem/phobius_spec.rb
-- specs/transmem/toppred_spec.rb
-- specs/align_spec.rb
-- specs/transmem_spec.rb
-- specs/spec_id/protein_summary_spec.rb
-- specs/spec_id/bioworks_spec.rb
+- specs/ms/gradient_program_spec.rb
 - specs/spec_id/sqt_spec.rb
-- specs/spec_id/sequest/pepxml_spec.rb
-- specs/spec_id/sequest/params_spec.rb
-- specs/spec_id/precision/filter_spec.rb
-- specs/spec_id/precision/prob_spec.rb
-- specs/spec_id/precision/filter/cmdline_spec.rb
-- specs/spec_id/precision/filter/output_spec.rb
-- specs/spec_id/proph/prot_summary_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/sequest_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/aa_freqs_spec.rb
-- specs/pi_zero_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/spec_id_spec.rb
-- specs/validator/true_pos_spec.rb
-- specs/validator/aa_est_spec.rb
-- specs/validator/background_spec.rb
-- specs/validator/bias_spec.rb
-- specs/validator/transmem_spec.rb
-- specs/validator/prot_from_pep_spec.rb
-- specs/validator/decoy_spec.rb
-- specs/validator/aa_spec.rb
-- specs/bin/protein_summary_spec.rb
+- specs/pi_zero_spec.rb
 - specs/bin/filter_and_validate_spec.rb
-- specs/bin/ms_to_lmat_spec.rb
 - specs/bin/fasta_shaker_spec.rb
-- specs/bin/bioworks_to_pepxml_spec.rb
+- specs/bin/protein_summary_spec.rb
 - specs/bin/prob_validate_spec.rb
-- specs/roc_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