RubyGems - mspire - Versions diffs - 0.5.0 → 0.6.1 - Mend

mspire 0.5.0 → 0.6.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (107) hide show

data/README.rdoc +24 -0
data/Rakefile +51 -0
data/VERSION +1 -0
data/lib/cv/description.rb +18 -0
data/lib/cv/param.rb +33 -0
data/lib/cv.rb +3 -0
data/lib/io/bookmark.rb +13 -0
data/lib/merge.rb +7 -0
data/lib/ms/cvlist.rb +76 -0
data/lib/ms/digester.rb +245 -0
data/lib/ms/fasta.rb +86 -0
data/lib/ms/ident/peptide/db.rb +243 -0
data/lib/ms/ident/peptide.rb +72 -0
data/lib/ms/ident/peptide_hit/qvalue.rb +56 -0
data/lib/ms/ident/peptide_hit.rb +26 -0
data/lib/ms/ident/pepxml/modifications.rb +83 -0
data/lib/ms/ident/pepxml/msms_pipeline_analysis.rb +70 -0
data/lib/ms/ident/pepxml/msms_run_summary.rb +82 -0
data/lib/ms/ident/pepxml/parameters.rb +14 -0
data/lib/ms/ident/pepxml/sample_enzyme.rb +165 -0
data/lib/ms/ident/pepxml/search_database.rb +49 -0
data/lib/ms/ident/pepxml/search_hit/modification_info.rb +79 -0
data/lib/ms/ident/pepxml/search_hit.rb +144 -0
data/lib/ms/ident/pepxml/search_result.rb +35 -0
data/lib/ms/ident/pepxml/search_summary.rb +92 -0
data/lib/ms/ident/pepxml/spectrum_query.rb +85 -0
data/lib/ms/ident/pepxml.rb +112 -0
data/lib/ms/ident/protein.rb +33 -0
data/lib/ms/ident/protein_group.rb +80 -0
data/lib/ms/ident/search.rb +114 -0
data/lib/ms/ident.rb +37 -0
data/lib/ms/isotope/aa.rb +59 -0
data/lib/ms/mascot.rb +6 -0
data/lib/ms/mass/aa.rb +79 -0
data/lib/ms/mass.rb +55 -0
data/lib/ms/mzml/index_list.rb +98 -0
data/lib/ms/mzml/plms1.rb +34 -0
data/lib/ms/mzml.rb +197 -0
data/lib/ms/obo.rb +38 -0
data/lib/ms/plms1.rb +156 -0
data/lib/ms/quant/qspec/protein_group_comparison.rb +22 -0
data/lib/ms/quant/qspec.rb +112 -0
data/lib/ms/spectrum.rb +154 -8
data/lib/ms.rb +3 -10
data/lib/msplat.rb +2 -0
data/lib/obo/ims.rb +5 -0
data/lib/obo/ms.rb +7 -0
data/lib/obo/ontology.rb +41 -0
data/lib/obo/unit.rb +5 -0
data/lib/openany.rb +23 -0
data/lib/write_file_or_string.rb +18 -0
data/obo/ims.obo +562 -0
data/obo/ms.obo +11677 -0
data/obo/unit.obo +2563 -0
data/spec/ms/cvlist_spec.rb +60 -0
data/spec/ms/digester_spec.rb +351 -0
data/spec/ms/fasta_spec.rb +100 -0
data/spec/ms/ident/peptide/db_spec.rb +108 -0
data/spec/ms/ident/pepxml/sample_enzyme_spec.rb +181 -0
data/spec/ms/ident/pepxml/search_hit/modification_info_spec.rb +37 -0
data/spec/ms/ident/pepxml_spec.rb +442 -0
data/spec/ms/ident/protein_group_spec.rb +68 -0
data/spec/ms/mass_spec.rb +8 -0
data/spec/ms/mzml/index_list_spec.rb +122 -0
data/spec/ms/mzml/plms1_spec.rb +62 -0
data/spec/ms/mzml_spec.rb +50 -0
data/spec/ms/plms1_spec.rb +38 -0
data/spec/ms/quant/qspec_spec.rb +25 -0
data/spec/msplat_spec.rb +24 -0
data/spec/obo_spec.rb +25 -0
data/spec/spec_helper.rb +25 -0
data/spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta +69 -0
data/spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml +728 -0
data/spec/testfiles/ms/mzml/j24z.idx_comp.3.mzML +271 -0
data/spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML +330 -0
data/spec/testfiles/ms/quant/kill_extra_tabs.rb +13 -0
data/spec/testfiles/ms/quant/max_quant_output.provenance.txt +15 -0
data/spec/testfiles/ms/quant/max_quant_output.txt +199 -0
data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv +199 -0
data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp +199 -0
data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv +199 -0
data/spec/testfiles/ms/quant/pdcd5_final.txt +199 -0
data/spec/testfiles/ms/quant/pdcd5_final.txt_qspecgp +0 -0
data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.CSV.csv +199 -0
data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.csv +199 -0
data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.csv +199 -0
data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv +199 -0
data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp +199 -0
data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv +199 -0
data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.txt +199 -0
data/spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt +134 -0
data/spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt_qspecgp +134 -0
data/spec/testfiles/ms/quant/remove_rest_of_proteins.rb +13 -0
data/spec/testfiles/ms/quant/unlog_transform.rb +13 -0
data/spec/testfiles/plms1/output.key +0 -0
metadata +157 -40
data/README +0 -77
data/changelog.txt +0 -196
data/lib/ms/calc.rb +0 -32
data/lib/ms/data/interleaved.rb +0 -60
data/lib/ms/data/lazy_io.rb +0 -73
data/lib/ms/data/lazy_string.rb +0 -15
data/lib/ms/data/simple.rb +0 -59
data/lib/ms/data/transposed.rb +0 -41
data/lib/ms/data.rb +0 -57
data/lib/ms/format/format_error.rb +0 -12
data/lib/ms/support/binary_search.rb +0 -126

data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.CSV.csv ADDED Viewed

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data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.csv ADDED Viewed

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