mspire 0.4.9 → 0.5.0
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- data/README +27 -17
- data/changelog.txt +31 -62
- data/lib/ms/calc.rb +32 -0
- data/lib/ms/data/interleaved.rb +60 -0
- data/lib/ms/data/lazy_io.rb +73 -0
- data/lib/ms/data/lazy_string.rb +15 -0
- data/lib/ms/data/simple.rb +59 -0
- data/lib/ms/data/transposed.rb +41 -0
- data/lib/ms/data.rb +57 -0
- data/lib/ms/format/format_error.rb +12 -0
- data/lib/ms/spectrum.rb +25 -384
- data/lib/ms/support/binary_search.rb +126 -0
- data/lib/ms.rb +10 -10
- metadata +38 -350
- data/INSTALL +0 -58
- data/README.rdoc +0 -18
- data/Rakefile +0 -330
- data/bin/aafreqs.rb +0 -23
- data/bin/bioworks2excel.rb +0 -14
- data/bin/bioworks_to_pepxml.rb +0 -148
- data/bin/bioworks_to_pepxml_gui.rb +0 -225
- data/bin/fasta_shaker.rb +0 -5
- data/bin/filter_and_validate.rb +0 -5
- data/bin/gi2annot.rb +0 -14
- data/bin/id_class_anal.rb +0 -112
- data/bin/id_precision.rb +0 -172
- data/bin/ms_to_lmat.rb +0 -67
- data/bin/pepproph_filter.rb +0 -16
- data/bin/prob_validate.rb +0 -6
- data/bin/protein_summary.rb +0 -6
- data/bin/protxml2prots_peps.rb +0 -32
- data/bin/raw_to_mzXML.rb +0 -55
- data/bin/run_percolator.rb +0 -122
- data/bin/sqt_group.rb +0 -26
- data/bin/srf_group.rb +0 -27
- data/bin/srf_to_sqt.rb +0 -40
- data/lib/align/chams.rb +0 -78
- data/lib/align.rb +0 -154
- data/lib/archive/targz.rb +0 -94
- data/lib/bsearch.rb +0 -120
- data/lib/core_extensions.rb +0 -16
- data/lib/fasta.rb +0 -626
- data/lib/gi.rb +0 -124
- data/lib/group_by.rb +0 -10
- data/lib/index_by.rb +0 -11
- data/lib/merge_deep.rb +0 -21
- data/lib/ms/converter/mzxml.rb +0 -77
- data/lib/ms/gradient_program.rb +0 -170
- data/lib/ms/msrun.rb +0 -244
- data/lib/ms/msrun_index.rb +0 -108
- data/lib/ms/parser/mzdata/axml.rb +0 -67
- data/lib/ms/parser/mzdata/dom.rb +0 -175
- data/lib/ms/parser/mzdata/libxml.rb +0 -7
- data/lib/ms/parser/mzdata.rb +0 -31
- data/lib/ms/parser/mzxml/axml.rb +0 -70
- data/lib/ms/parser/mzxml/dom.rb +0 -182
- data/lib/ms/parser/mzxml/hpricot.rb +0 -253
- data/lib/ms/parser/mzxml/libxml.rb +0 -19
- data/lib/ms/parser/mzxml/regexp.rb +0 -122
- data/lib/ms/parser/mzxml/rexml.rb +0 -72
- data/lib/ms/parser/mzxml/xmlparser.rb +0 -248
- data/lib/ms/parser/mzxml.rb +0 -282
- data/lib/ms/parser.rb +0 -108
- data/lib/ms/precursor.rb +0 -25
- data/lib/ms/scan.rb +0 -81
- data/lib/mspire.rb +0 -4
- data/lib/pi_zero.rb +0 -244
- data/lib/qvalue.rb +0 -161
- data/lib/roc.rb +0 -187
- data/lib/sample_enzyme.rb +0 -160
- data/lib/scan_i.rb +0 -21
- data/lib/spec_id/aa_freqs.rb +0 -170
- data/lib/spec_id/bioworks.rb +0 -497
- data/lib/spec_id/digestor.rb +0 -138
- data/lib/spec_id/mass.rb +0 -179
- data/lib/spec_id/parser/proph.rb +0 -335
- data/lib/spec_id/precision/filter/cmdline.rb +0 -218
- data/lib/spec_id/precision/filter/interactive.rb +0 -134
- data/lib/spec_id/precision/filter/output.rb +0 -148
- data/lib/spec_id/precision/filter.rb +0 -637
- data/lib/spec_id/precision/output.rb +0 -60
- data/lib/spec_id/precision/prob/cmdline.rb +0 -160
- data/lib/spec_id/precision/prob/output.rb +0 -94
- data/lib/spec_id/precision/prob.rb +0 -249
- data/lib/spec_id/proph/pep_summary.rb +0 -104
- data/lib/spec_id/proph/prot_summary.rb +0 -484
- data/lib/spec_id/proph.rb +0 -4
- data/lib/spec_id/protein_summary.rb +0 -489
- data/lib/spec_id/sequest/params.rb +0 -316
- data/lib/spec_id/sequest/pepxml.rb +0 -1458
- data/lib/spec_id/sequest.rb +0 -33
- data/lib/spec_id/sqt.rb +0 -349
- data/lib/spec_id/srf.rb +0 -973
- data/lib/spec_id.rb +0 -778
- data/lib/spec_id_xml.rb +0 -99
- data/lib/transmem/phobius.rb +0 -147
- data/lib/transmem/toppred.rb +0 -368
- data/lib/transmem.rb +0 -157
- data/lib/validator/aa.rb +0 -48
- data/lib/validator/aa_est.rb +0 -112
- data/lib/validator/background.rb +0 -77
- data/lib/validator/bias.rb +0 -95
- data/lib/validator/cmdline.rb +0 -431
- data/lib/validator/decoy.rb +0 -107
- data/lib/validator/digestion_based.rb +0 -70
- data/lib/validator/probability.rb +0 -51
- data/lib/validator/prot_from_pep.rb +0 -234
- data/lib/validator/q_value.rb +0 -32
- data/lib/validator/transmem.rb +0 -272
- data/lib/validator/true_pos.rb +0 -46
- data/lib/validator.rb +0 -197
- data/lib/xml.rb +0 -38
- data/lib/xml_style_parser.rb +0 -119
- data/lib/xmlparser_wrapper.rb +0 -19
- data/release_notes.txt +0 -2
- data/script/compile_and_plot_smriti_final.rb +0 -97
- data/script/create_little_pepxml.rb +0 -61
- data/script/degenerate_peptides.rb +0 -47
- data/script/estimate_fpr_by_cysteine.rb +0 -226
- data/script/extract_gradient_programs.rb +0 -56
- data/script/find_cysteine_background.rb +0 -137
- data/script/genuine_tps_and_probs.rb +0 -136
- data/script/get_apex_values_rexml.rb +0 -44
- data/script/histogram_probs.rb +0 -61
- data/script/mascot_fix_pepxml.rb +0 -123
- data/script/msvis.rb +0 -42
- data/script/mzXML2timeIndex.rb +0 -25
- data/script/peps_per_bin.rb +0 -67
- data/script/prep_dir.rb +0 -121
- data/script/simple_protein_digestion.rb +0 -27
- data/script/smriti_final_analysis.rb +0 -103
- data/script/sqt_to_meta.rb +0 -24
- data/script/top_hit_per_scan.rb +0 -67
- data/script/toppred_to_yaml.rb +0 -47
- data/script/tpp_installer.rb +0 -249
- data/specs/align_spec.rb +0 -79
- data/specs/bin/bioworks_to_pepxml_spec.rb +0 -79
- data/specs/bin/fasta_shaker_spec.rb +0 -259
- data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +0 -199
- data/specs/bin/filter_and_validate_spec.rb +0 -180
- data/specs/bin/ms_to_lmat_spec.rb +0 -34
- data/specs/bin/prob_validate_spec.rb +0 -86
- data/specs/bin/protein_summary_spec.rb +0 -14
- data/specs/fasta_spec.rb +0 -354
- data/specs/gi_spec.rb +0 -22
- data/specs/load_bin_path.rb +0 -7
- data/specs/merge_deep_spec.rb +0 -13
- data/specs/ms/gradient_program_spec.rb +0 -77
- data/specs/ms/msrun_spec.rb +0 -498
- data/specs/ms/parser_spec.rb +0 -92
- data/specs/ms/spectrum_spec.rb +0 -87
- data/specs/pi_zero_spec.rb +0 -115
- data/specs/qvalue_spec.rb +0 -39
- data/specs/roc_spec.rb +0 -251
- data/specs/rspec_autotest.rb +0 -149
- data/specs/sample_enzyme_spec.rb +0 -126
- data/specs/spec_helper.rb +0 -135
- data/specs/spec_id/aa_freqs_spec.rb +0 -52
- data/specs/spec_id/bioworks_spec.rb +0 -148
- data/specs/spec_id/digestor_spec.rb +0 -75
- data/specs/spec_id/precision/filter/cmdline_spec.rb +0 -20
- data/specs/spec_id/precision/filter/output_spec.rb +0 -31
- data/specs/spec_id/precision/filter_spec.rb +0 -246
- data/specs/spec_id/precision/prob_spec.rb +0 -44
- data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
- data/specs/spec_id/proph/pep_summary_spec.rb +0 -98
- data/specs/spec_id/proph/prot_summary_spec.rb +0 -128
- data/specs/spec_id/protein_summary_spec.rb +0 -189
- data/specs/spec_id/sequest/params_spec.rb +0 -68
- data/specs/spec_id/sequest/pepxml_spec.rb +0 -374
- data/specs/spec_id/sequest_spec.rb +0 -38
- data/specs/spec_id/sqt_spec.rb +0 -246
- data/specs/spec_id/srf_spec.rb +0 -172
- data/specs/spec_id/srf_spec_helper.rb +0 -139
- data/specs/spec_id_helper.rb +0 -33
- data/specs/spec_id_spec.rb +0 -366
- data/specs/spec_id_xml_spec.rb +0 -33
- data/specs/transmem/phobius_spec.rb +0 -425
- data/specs/transmem/toppred_spec.rb +0 -298
- data/specs/transmem_spec.rb +0 -60
- data/specs/transmem_spec_shared.rb +0 -64
- data/specs/validator/aa_est_spec.rb +0 -66
- data/specs/validator/aa_spec.rb +0 -40
- data/specs/validator/background_spec.rb +0 -67
- data/specs/validator/bias_spec.rb +0 -122
- data/specs/validator/decoy_spec.rb +0 -51
- data/specs/validator/fasta_helper.rb +0 -26
- data/specs/validator/prot_from_pep_spec.rb +0 -141
- data/specs/validator/transmem_spec.rb +0 -146
- data/specs/validator/true_pos_spec.rb +0 -58
- data/specs/validator_helper.rb +0 -33
- data/specs/xml_spec.rb +0 -12
- data/test_files/000_pepxml18_small.xml +0 -206
- data/test_files/020a.mzXML.timeIndex +0 -4710
- data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +0 -3973
- data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +0 -3872
- data/test_files/4-03-03_small-prot.xml +0 -321
- data/test_files/4-03-03_small.xml +0 -3876
- data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
- data/test_files/bioworks-3.3_10prots.xml +0 -5999
- data/test_files/bioworks31.params +0 -77
- data/test_files/bioworks32.params +0 -62
- data/test_files/bioworks33.params +0 -63
- data/test_files/bioworks_single_run_small.xml +0 -7237
- data/test_files/bioworks_small.fasta +0 -212
- data/test_files/bioworks_small.params +0 -63
- data/test_files/bioworks_small.phobius +0 -109
- data/test_files/bioworks_small.toppred.out +0 -2847
- data/test_files/bioworks_small.xml +0 -5610
- data/test_files/bioworks_with_INV_small.xml +0 -3753
- data/test_files/bioworks_with_SHUFF_small.xml +0 -2503
- data/test_files/corrupted_900.srf +0 -0
- data/test_files/head_of_7MIX.srf +0 -0
- data/test_files/interact-opd1_mods_small-prot.xml +0 -304
- data/test_files/messups.fasta +0 -297
- data/test_files/opd1/000.my_answer.100lines.xml +0 -101
- data/test_files/opd1/000.tpp_1.2.3.first10.xml +0 -115
- data/test_files/opd1/000.tpp_2.9.2.first10.xml +0 -126
- data/test_files/opd1/000.v2.1.mzXML.timeIndex +0 -3748
- data/test_files/opd1/000_020-prot.png +0 -0
- data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +0 -62
- data/test_files/opd1/000_020_3prots-prot.xml +0 -62
- data/test_files/opd1/opd1_cat_inv_small-prot.xml +0 -139
- data/test_files/opd1/sequest.3.1.params +0 -77
- data/test_files/opd1/sequest.3.2.params +0 -62
- data/test_files/opd1/twenty_scans.mzXML +0 -418
- data/test_files/opd1/twenty_scans.v2.1.mzXML +0 -382
- data/test_files/opd1/twenty_scans_answ.lmat +0 -0
- data/test_files/opd1/twenty_scans_answ.lmata +0 -9
- data/test_files/opd1_020_beginning.RAW +0 -0
- data/test_files/opd1_2runs_2mods/data/020.mzData.xml +0 -683
- data/test_files/opd1_2runs_2mods/data/020.readw.mzXML +0 -382
- data/test_files/opd1_2runs_2mods/data/040.mzData.xml +0 -683
- data/test_files/opd1_2runs_2mods/data/040.readw.mzXML +0 -382
- data/test_files/opd1_2runs_2mods/data/README.txt +0 -6
- data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +0 -753
- data/test_files/orbitrap_mzData/000_cut.xml +0 -1920
- data/test_files/pepproph_small.xml +0 -4691
- data/test_files/phobius.small.noheader.txt +0 -50
- data/test_files/phobius.small.small.txt +0 -53
- data/test_files/s01_anC1_ld020mM.key.txt +0 -25
- data/test_files/s01_anC1_ld020mM.meth +0 -0
- data/test_files/small.fasta +0 -297
- data/test_files/small.sqt +0 -87
- data/test_files/smallraw.RAW +0 -0
- data/test_files/tf_bioworks2excel.bioXML +0 -14340
- data/test_files/tf_bioworks2excel.txt.actual +0 -1035
- data/test_files/toppred.small.out +0 -416
- data/test_files/toppred.xml.out +0 -318
- data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +0 -7
- data/test_files/validator_hits_separate/bioworks_small_HS.xml +0 -5651
- data/test_files/yeast_gly_small-prot.xml +0 -265
- data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +0 -6
- data/test_files/yeast_gly_small.xml +0 -3807
- data/test_files/yeast_gly_small2.parentTimes +0 -6
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require 'rexml/document'
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require 'hash_by'
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require 'instance_var_set_from_hash'
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require 'axml'
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require 'spec_id'
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require 'arrayclass'
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require 'spec_id/parser/proph'
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module SpecID ; end
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module SpecID::Prot ; end
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module SpecID::Pep ; end
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module Proph
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class ProtSummary
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include SpecID
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# if you get this match it's a protein prophet file and the version is the
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# first match!
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Filetype_and_version_re_old = /ProteinProphet_v([\.\d]+)\.dtd/ # gives 1.9 or what else?
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Filetype_and_version_re_new = /protXML_v([\.\d]+)\.xsd/ # gives 4 right now
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# inherits prots and peps
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# the protein groups
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attr_accessor :prot_groups
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attr_accessor :version
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def hi_prob_best ; true end
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5.times do
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answer =
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$1.dup
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elsif line =~ Filetype_and_version_re_old
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$1.dup
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end
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break if answer
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end
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end
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raise(ArgumentError, "couldn't detect version in #{file}") unless answer
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answer
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end
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def initialize(file=nil)
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if file
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@version = get_version(file)
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#@prot_groups = ProtSummary::Parser.new.parse_file(file)
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SpecID::Parser::ProtProph.new(:spec_id).parse(file, :spec_id => self)
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end
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end
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# returns a set of unique proteins
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def unique_prots(prot_groups)
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prot_groups.each do |pg|
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all_prots << prt
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end
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end
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end
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end
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class ProtSummary::Parser
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attr_accessor :prot_groups
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def initialize(file=nil, with_peps=false, tp='axml')
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if file
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end
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# returns an array of protein_groups
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def parse_file(file, with_peps=false, tp='axml')
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File.open(file) do |fh|
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@prot_groups = _parse_for_prot_groups(fh, with_peps, tp)
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end
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@prot_groups
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end
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# returns an array of ProtGroup objects
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def _parse_for_prot_groups(stream, with_peps=false, tp='axml')
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prtgrps = []
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case tp
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when 'axml'
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root = AXML.parse(stream)
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root.protein_group.each do |protein_group|
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pg = ProtGroup.new(protein_group.attrs) do
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protein_group.map do |protein|
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Prot.new(protein.attrs)
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end
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end
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prtgrps << pg
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end
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end
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prtgrps
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end
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end # ProtSummary::Parser
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class ProtGroup
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attr_accessor :group_number, :probability, :prots
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def initialize(args=nil)
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@prots = []
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if args
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instance_var_set_from_hash(args)
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end
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if block_given?
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@prots = yield
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end
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end
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end
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end # Proph
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Proph::Prot = Arrayclass.new(%w(protein_name probability n_indistinguishable_proteins percent_coverage unique_stripped_peptides group_sibling_id total_number_peptides pct_spectrum_ids description peps q_value))
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# note that 'description' is found in the element 'annotation', attribute 'protein_description'
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# NOTE!: unique_stripped peptides is an array rather than + joined string
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class Proph::Prot
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include SpecID::Prot
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# returns protein_name
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def name ; self[0] end
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def reference ; self[0] end
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def first_entry ; self[0] end # the name is also the first_entry
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end
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139
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#def to_s
|
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# '<Prot: protein_name=' + @protein_name + ' ' + 'probability=' + @probability.to_s + '>'
|
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#end
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142
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|
143
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# this is a pep from a -prot.xml file
|
144
|
-
|
145
|
-
Proph::Prot::Pep = Arrayclass.new(%w(peptide_sequence charge initial_probability nsp_adjusted_probability weight is_nondegenerate_evidence n_enzymatic_termini n_sibling_peptides n_sibling_peptides_bin n_instances is_contributing_evidence calc_neutral_pep_mass modification_info prots q_value))
|
146
|
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|
147
|
-
class Proph::Prot::Pep
|
148
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include SpecID::Pep
|
149
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|
150
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alias_method :mod_info, :modification_info
|
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alias_method :mod_info=, :modification_info=
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|
153
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def aaseq ; self[0] end
|
154
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def probability ; self[3] end
|
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|
156
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end # class Pep
|
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|
158
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=begin
|
159
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#attr_accessor :sequence, :probability, :filenames, :charge, :precursor_neutral_mass, :nsp_cutoff, :scans
|
160
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#attr_writer :arithmetic_avg_scan_by_parent_time
|
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|
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|
162
|
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#def initialize(args=nil)
|
163
|
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# if args
|
164
|
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# @sequence = args[:sequence]
|
165
|
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# @probability = args[:probability] ## nsp prob
|
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# @filenames = args[:filenames]
|
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# @charge = args[:charge]
|
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|
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# @nsp_cutoff = args[:nsp_cutoff]
|
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# if args.key?(:scans)
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# @scans = args[:scans]
|
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# else
|
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|
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# @scans = [] ## this is set later if needed
|
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|
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# end
|
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# else
|
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# @scans = []
|
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|
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# end
|
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#end
|
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|
179
|
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# filter peptides based on the number of scans
|
180
|
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# if a peptide has more than max_dups scans, the peptide is tossed
|
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|
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# note that multiple scans that were used as a single dtafile scan
|
182
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# will be counted as a single scan for these purposes!
|
183
|
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# (easy, since they are stored as a single item in the array of scans)
|
184
|
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def self.filter_by_max_dup_scans(max_dups=nil, peps=nil)
|
185
|
-
if max_dups
|
186
|
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new_peps = []
|
187
|
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peps.each do |pep|
|
188
|
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unless pep.scans.size > max_dups
|
189
|
-
new_peps << pep
|
190
|
-
end
|
191
|
-
end
|
192
|
-
new_peps
|
193
|
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else
|
194
|
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peps.dup
|
195
|
-
end
|
196
|
-
end
|
197
|
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|
198
|
-
|
199
|
-
## from the list of scans, creates a scan object whose time is the
|
200
|
-
## arithmetic mean of the parent scans (based on prec_inten) and whose
|
201
|
-
## prec_mz is the avg of all prec_mz's. num is nil, charge is the first
|
202
|
-
def arithmetic_avg_scan_by_parent_time
|
203
|
-
unless @arithmetic_avg_scan_by_parent_time
|
204
|
-
flat_scans = @scans.flatten
|
205
|
-
|
206
|
-
# new_prec_mz
|
207
|
-
prec_mz_sum = 0.0
|
208
|
-
prec_inten_sum = 0.0
|
209
|
-
times = []
|
210
|
-
intens = []
|
211
|
-
tot_inten = 0.0
|
212
|
-
flat_scans.each do |c|
|
213
|
-
prec_inten = c.prec_inten
|
214
|
-
prec_inten_sum += prec_inten
|
215
|
-
prec_mz_sum += c.prec_mz
|
216
|
-
tot_inten += prec_inten
|
217
|
-
times << c.parent.time
|
218
|
-
intens << prec_inten
|
219
|
-
end
|
220
|
-
new_prec_mz = prec_mz_sum / flat_scans.size
|
221
|
-
new_prec_inten = prec_inten_sum / flat_scans.size
|
222
|
-
|
223
|
-
fraction_inten = []
|
224
|
-
intens.each do |inten|
|
225
|
-
fraction_inten.push( inten/tot_inten )
|
226
|
-
end
|
227
|
-
|
228
|
-
new_time = 0.0
|
229
|
-
(0...times.size).each do |i|
|
230
|
-
new_time += times[i] * fraction_inten[i]
|
231
|
-
end
|
232
|
-
|
233
|
-
@arithmetic_avg_scan_by_parent_time = MS::Scan.new( nil, @scans.first.ms_level, new_time, new_prec_mz, new_prec_inten )
|
234
|
-
|
235
|
-
end
|
236
|
-
@arithmetic_avg_scan_by_parent_time
|
237
|
-
end
|
238
|
-
|
239
|
-
def to_s
|
240
|
-
'<Pep seq=' + @sequence + ' ' + 'prob=' + @probability.to_s + ' charge=' + @charge + '>'
|
241
|
-
end
|
242
|
-
|
243
|
-
def has_dta?(dta_filename)
|
244
|
-
if @filenames
|
245
|
-
@filenames.each do |fn|
|
246
|
-
if dta_filename == fn
|
247
|
-
return true
|
248
|
-
end
|
249
|
-
end
|
250
|
-
end
|
251
|
-
return false
|
252
|
-
end
|
253
|
-
|
254
|
-
|
255
|
-
# Given a list of peptides, returns only those unique based on
|
256
|
-
# sequence/charge
|
257
|
-
def self.uniq_by_seqcharge(peptides)
|
258
|
-
# @TODO: this could be done with one fewer traversals, but it is beautiful
|
259
|
-
peptides.hash_by(:sequence, :charge).collect do |k,v|
|
260
|
-
v.first
|
261
|
-
end
|
262
|
-
end
|
263
|
-
=end
|
264
|
-
|
265
|
-
|
266
|
-
|
267
|
-
|
268
|
-
|
269
|
-
=begin
|
270
|
-
|
271
|
-
# Class for parsing the peptide prophet output files in various ways
|
272
|
-
class Proph::Pep::Parser < Parser
|
273
|
-
|
274
|
-
# parse_type = "rexml" | "regex"
|
275
|
-
# regex's are about 50 times faster but are not guaranteed to work
|
276
|
-
# seq charge hash is keyed on an array -> [sequence,charge]
|
277
|
-
# @TODO: implement parsing on this with xmlparser
|
278
|
-
def dta_filenames_by_seq_charge(pep_xml_file, parse_type="rexml")
|
279
|
-
seq_charge_hash = Hash.new {|hash,key| hash[key] = [] }
|
280
|
-
case parse_type
|
281
|
-
when "rexml"
|
282
|
-
#puts "READING: " + pep_xml_file + " ..."
|
283
|
-
doc = REXML::Document.new File.new(pep_xml_file)
|
284
|
-
|
285
|
-
## Create a hash of peptides based on sequence_charge (takes an array)
|
286
|
-
doc.elements.each("msms_pipeline_analysis/msms_run_summary/search_result") do |result|
|
287
|
-
pep_charge = result.attributes['assumed_charge']
|
288
|
-
filename = result.attributes['spectrum']
|
289
|
-
result.elements.to_a('search_hit').each do |hit|
|
290
|
-
pep_seq = hit.attributes['peptide']
|
291
|
-
seq_charge = [pep_seq, pep_charge]
|
292
|
-
seq_charge_hash[seq_charge] << filename
|
293
|
-
end
|
294
|
-
end
|
295
|
-
seq_charge_hash
|
296
|
-
when "regex"
|
297
|
-
#puts "READING: " + pep_xml_file + " ..."
|
298
|
-
## Create a hash of peptides based on sequence_charge (takes an array)
|
299
|
-
|
300
|
-
## file from peptideAtlas:
|
301
|
-
search_result_regex1 = /<spectrum_query spectrum="(.*\.\d+\.\d+\.\d)".* assumed_charge="(\d)"/o
|
302
|
-
search_result_regex2 = /<search_result sxpectrum="(.*\.\d+\.\d+\.\d)".* assumed_charge="(\d)"/o
|
303
|
-
search_hit_regex = /<search_hit .*peptide="(\w+)" /o
|
304
|
-
|
305
|
-
peptide_h = {}
|
306
|
-
filename = nil
|
307
|
-
pep_charge = nil
|
308
|
-
File.open(pep_xml_file).each do |line|
|
309
|
-
if line =~ search_result_regex1
|
310
|
-
filename = $1.dup
|
311
|
-
pep_charge = $2.dup
|
312
|
-
elsif line =~ search_result_regex2
|
313
|
-
filename = $1.dup
|
314
|
-
pep_charge = $2.dup
|
315
|
-
end
|
316
|
-
if line =~ search_hit_regex
|
317
|
-
pep_seq = $1.dup
|
318
|
-
seq_charge = [pep_seq, pep_charge]
|
319
|
-
seq_charge_hash[seq_charge] << filename
|
320
|
-
end
|
321
|
-
end
|
322
|
-
end
|
323
|
-
seq_charge_hash
|
324
|
-
end
|
325
|
-
|
326
|
-
# drops all search_hits that have peptideprophet probability < min_val
|
327
|
-
# and drops any search_results that end up with 0 search_hits
|
328
|
-
def filter_by_min_pep_prob(file, outfile, min_val)
|
329
|
-
root = root_el(file)
|
330
|
-
|
331
|
-
d_search_hit = nil
|
332
|
-
d_search_result = nil
|
333
|
-
root.children.each do |child1|
|
334
|
-
if child1.name == 'msms_run_summary'
|
335
|
-
d_search_result = []
|
336
|
-
child1.children.each do |child2|
|
337
|
-
if child2.name == 'search_result'
|
338
|
-
#puts "size before: " + child2.size.to_s
|
339
|
-
d_search_hit = []
|
340
|
-
child2.children.each do |child3|
|
341
|
-
if child3.name == 'search_hit'
|
342
|
-
child3.children.each do |child4|
|
343
|
-
if child4.name == 'peptideprophet_result'
|
344
|
-
if child4.attrs["probability"].to_f < min_val
|
345
|
-
#puts "dropping probability: #{child4.attrs["probability"]}"
|
346
|
-
d_search_hit << child3
|
347
|
-
else
|
348
|
-
#puts "keeping probability: #{child4.attrs["probability"]}"
|
349
|
-
end
|
350
|
-
end
|
351
|
-
end
|
352
|
-
end
|
353
|
-
end
|
354
|
-
d_search_hit.each do |to_drop|
|
355
|
-
to_drop.drop
|
356
|
-
end
|
357
|
-
#puts "size after: " + child2.size.to_s
|
358
|
-
if child2.size == 0
|
359
|
-
d_search_result << child2
|
360
|
-
end
|
361
|
-
end
|
362
|
-
end
|
363
|
-
d_search_result.each do |to_drop|
|
364
|
-
to_drop.drop
|
365
|
-
end
|
366
|
-
end
|
367
|
-
end
|
368
|
-
|
369
|
-
File.open(outfile, "w") do |fh|
|
370
|
-
fh.print root.to_s
|
371
|
-
end
|
372
|
-
end
|
373
|
-
end # Pep::Parser
|
374
|
-
|
375
|
-
|
376
|
-
# Class for parsing the '*-prot.xml' files in different ways
|
377
|
-
class Proph::Prot::Parser < Parser
|
378
|
-
|
379
|
-
attr_accessor :prots
|
380
|
-
attr_writer :peps
|
381
|
-
|
382
|
-
def initialize
|
383
|
-
@prots = []
|
384
|
-
end
|
385
|
-
|
386
|
-
# returns all the peptides from prots
|
387
|
-
def peps
|
388
|
-
unless @peps
|
389
|
-
@peps = []
|
390
|
-
@prots.each do |prot|
|
391
|
-
@peps.push(*(prot.peps))
|
392
|
-
end
|
393
|
-
end
|
394
|
-
@peps
|
395
|
-
end
|
396
|
-
|
397
|
-
|
398
|
-
# sets and returns an array of Prot objects
|
399
|
-
# parse_type = "rexml" | "regex"
|
400
|
-
def get_prots_and_peps(protxmlfile, prot_prob_cutoff=1.0, pep_init_prob_cutoff=1.0, pep_nsp_prob_cutoff=1.0, parse_type="rexml")
|
401
|
-
## ensure these are all floats
|
402
|
-
(prot_prob_cutoff, pep_init_prob_cutoff, pep_nsp_prob_cutoff) = [prot_prob_cutoff, pep_init_prob_cutoff, pep_nsp_prob_cutoff].collect do |cutoff|
|
403
|
-
cutoff.to_f
|
404
|
-
end
|
405
|
-
|
406
|
-
case parse_type
|
407
|
-
when "rexml"
|
408
|
-
doc = REXML::Document.new File.new(protxmlfile)
|
409
|
-
doc.elements.each("protein_summary/protein_group/protein") do |elem|
|
410
|
-
if elem.attributes['probability'].to_f >= prot_prob_cutoff
|
411
|
-
prob = elem.attributes['probability'].to_f
|
412
|
-
name= elem.attributes['protein_name']
|
413
|
-
curr_prot = Prot.new({:probability => prob, :protein_name => name, :cutoff => prot_prob_cutoff})
|
414
|
-
peptides = []
|
415
|
-
elem.elements.to_a('peptide').each do |pep|
|
416
|
-
if pep.attributes['nsp_adjusted_probability'].to_f >= pep_nsp_prob_cutoff && pep.attributes['initial_probability'].to_f >= pep_init_prob_cutoff
|
417
|
-
nsp_prob = pep.attributes['nsp_adjusted_probability'].to_f
|
418
|
-
sequence = pep.attributes['peptide_sequence']
|
419
|
-
charge = pep.attributes['charge']
|
420
|
-
pnm = pep.attributes['precursor_neutral_mass']
|
421
|
-
peptides.push(Pep.new(:probability => nsp_prob, :sequence => sequence, :charge => charge, :precursor_neutral_mass => pnm, :nsp_cutoff => pep_nsp_prob_cutoff))
|
422
|
-
end
|
423
|
-
## Only take proteins with peptides!
|
424
|
-
if peptides.size > 0
|
425
|
-
curr_prot.peps = peptides
|
426
|
-
@prots << curr_prot
|
427
|
-
end
|
428
|
-
end
|
429
|
-
end
|
430
|
-
end
|
431
|
-
when "regex"
|
432
|
-
prot_regex = /<protein protein_name="(.*)?" n_indistinguishable_proteins(.*)/o
|
433
|
-
prot_prob_regex = /probability="([\d\.]+)"/o
|
434
|
-
pep_regex = /<peptide peptide_sequence="(\w+)?"(.*)/o
|
435
|
-
pep_else_regex = /charge="(\d)" initial_probability="([\d\.]+)" nsp_adjusted_probability="([\d\.]+)"/o
|
436
|
-
|
437
|
-
curr_prot = nil
|
438
|
-
peptides = []
|
439
|
-
File.open(protxmlfile).each do |line|
|
440
|
-
if line =~ prot_regex
|
441
|
-
prob = nil
|
442
|
-
name = $1.dup
|
443
|
-
rest = $2
|
444
|
-
if rest =~ prot_prob_regex
|
445
|
-
prob = $1.dup
|
446
|
-
end
|
447
|
-
if curr_prot
|
448
|
-
if curr_prot.probability.to_f >= prot_prob_cutoff
|
449
|
-
if peptides.size > 0
|
450
|
-
curr_prot.peps = peptides
|
451
|
-
@prots.push(curr_prot)
|
452
|
-
end
|
453
|
-
end
|
454
|
-
end
|
455
|
-
curr_prot = Prot.new({:probability => prob, :protein_name => name, :cutoff => prot_prob_cutoff})
|
456
|
-
peptides = []
|
457
|
-
end
|
458
|
-
if line =~ pep_regex
|
459
|
-
sequence = $1.dup
|
460
|
-
rest = $2
|
461
|
-
if rest =~ pep_else_regex
|
462
|
-
charge = $1
|
463
|
-
init_prob = $2
|
464
|
-
nsp_prob = $3
|
465
|
-
if nsp_prob.to_f >= pep_nsp_prob_cutoff && init_prob.to_f >= pep_init_prob_cutoff
|
466
|
-
peptides.push(Pep.new(:probability => nsp_prob, :sequence => sequence, :charge => charge, :nsp_cutoff => pep_nsp_prob_cutoff))
|
467
|
-
end
|
468
|
-
end
|
469
|
-
end
|
470
|
-
# get the last one:
|
471
|
-
if curr_prot && curr_prot.probability.to_f > prot_prob_cutoff && peptides.size > 0
|
472
|
-
curr_prot.peps = peptides
|
473
|
-
@prots.push(curr_prot)
|
474
|
-
end
|
475
|
-
end
|
476
|
-
end
|
477
|
-
@prots
|
478
|
-
end
|
479
|
-
|
480
|
-
end # Prot::Parser
|
481
|
-
|
482
|
-
################ --END
|
483
|
-
|
484
|
-
=end
|
data/lib/spec_id/proph.rb
DELETED