mspire 0.8.4 → 0.8.5
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- data/README.md +1 -1
- data/VERSION +1 -1
- data/lib/mspire/fasta.rb +5 -27
- data/lib/mspire/ident/peptide/db/creator.rb +248 -0
- data/lib/mspire/ident/peptide/db/io.rb +62 -0
- data/lib/mspire/ident/peptide/db.rb +18 -225
- data/lib/mspire/ident/peptide_hit/qvalue.rb +3 -2
- data/schema/peptide_hit_qvalues.pqh.tsv +5 -0
- data/script/mascot_dat_to_peptide_hit_qvalues.rb +118 -0
- data/spec/mspire/ident/peptide/db/creator_spec.rb +65 -0
- data/spec/mspire/ident/peptide/db/io_spec.rb +21 -0
- data/spec/mspire/ident/peptide/db_spec.rb +7 -97
- data/spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.PEPTIDE_CENTRIC.yml +728 -0
- data/spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml +728 -728
- metadata +9 -2
metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: mspire
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.8.
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4
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+
version: 0.8.5
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5
5
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prerelease:
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6
6
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platform: ruby
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7
7
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authors:
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@@ -10,7 +10,7 @@ authors:
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10
10
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autorequire:
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11
11
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bindir: bin
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12
12
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cert_chain: []
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13
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-
date: 2012-
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13
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+
date: 2012-10-10 00:00:00.000000000 Z
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14
14
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dependencies:
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15
15
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- !ruby/object:Gem::Dependency
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16
16
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name: nokogiri
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@@ -223,6 +223,8 @@ files:
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223
223
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- lib/mspire/ident.rb
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224
224
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- lib/mspire/ident/peptide.rb
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225
225
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- lib/mspire/ident/peptide/db.rb
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226
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+
- lib/mspire/ident/peptide/db/creator.rb
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|
227
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+
- lib/mspire/ident/peptide/db/io.rb
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226
228
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- lib/mspire/ident/peptide_hit.rb
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|
227
229
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- lib/mspire/ident/peptide_hit/qvalue.rb
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228
230
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- lib/mspire/ident/pepxml.rb
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@@ -307,7 +309,9 @@ files:
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307
309
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- obo/ims.obo
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|
308
310
|
- obo/ms.obo
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|
309
311
|
- obo/unit.obo
|
|
312
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+
- schema/peptide_hit_qvalues.pqh.tsv
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|
310
313
|
- script/download_uniprotkb_db.rb
|
|
314
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+
- script/mascot_dat_to_peptide_hit_qvalues.rb
|
|
311
315
|
- script/mzml_read_binary.rb
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|
312
316
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- script/quant_compare_direct_injections.rb
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|
313
317
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- spec/cv/param_spec.rb
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@@ -318,6 +322,8 @@ files:
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|
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318
322
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- spec/mspire/digester_spec.rb
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319
323
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- spec/mspire/error_rate/qvalue_spec.rb
|
|
320
324
|
- spec/mspire/fasta_spec.rb
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|
325
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+
- spec/mspire/ident/peptide/db/creator_spec.rb
|
|
326
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+
- spec/mspire/ident/peptide/db/io_spec.rb
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|
321
327
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- spec/mspire/ident/peptide/db_spec.rb
|
|
322
328
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- spec/mspire/ident/pepxml/sample_enzyme_spec.rb
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|
323
329
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- spec/mspire/ident/pepxml/search_hit/modification_info_spec.rb
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@@ -349,6 +355,7 @@ files:
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349
355
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- spec/obo_spec.rb
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|
350
356
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- spec/spec_helper.rb
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|
351
357
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- spec/testfiles/continuous_binary.tmp.ibd
|
|
358
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+
- spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.PEPTIDE_CENTRIC.yml
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|
352
359
|
- spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.fasta
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|
353
360
|
- spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
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|
354
361
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- spec/testfiles/mspire/imzml/1_BB7_SIM_478.5.CHECK.ibd
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