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
  1. data/README.rdoc +24 -0
  2. data/Rakefile +51 -0
  3. data/VERSION +1 -0
  4. data/lib/cv/description.rb +18 -0
  5. data/lib/cv/param.rb +33 -0
  6. data/lib/cv.rb +3 -0
  7. data/lib/io/bookmark.rb +13 -0
  8. data/lib/merge.rb +7 -0
  9. data/lib/ms/cvlist.rb +76 -0
  10. data/lib/ms/digester.rb +245 -0
  11. data/lib/ms/fasta.rb +86 -0
  12. data/lib/ms/ident/peptide/db.rb +243 -0
  13. data/lib/ms/ident/peptide.rb +72 -0
  14. data/lib/ms/ident/peptide_hit/qvalue.rb +56 -0
  15. data/lib/ms/ident/peptide_hit.rb +26 -0
  16. data/lib/ms/ident/pepxml/modifications.rb +83 -0
  17. data/lib/ms/ident/pepxml/msms_pipeline_analysis.rb +70 -0
  18. data/lib/ms/ident/pepxml/msms_run_summary.rb +82 -0
  19. data/lib/ms/ident/pepxml/parameters.rb +14 -0
  20. data/lib/ms/ident/pepxml/sample_enzyme.rb +165 -0
  21. data/lib/ms/ident/pepxml/search_database.rb +49 -0
  22. data/lib/ms/ident/pepxml/search_hit/modification_info.rb +79 -0
  23. data/lib/ms/ident/pepxml/search_hit.rb +144 -0
  24. data/lib/ms/ident/pepxml/search_result.rb +35 -0
  25. data/lib/ms/ident/pepxml/search_summary.rb +92 -0
  26. data/lib/ms/ident/pepxml/spectrum_query.rb +85 -0
  27. data/lib/ms/ident/pepxml.rb +112 -0
  28. data/lib/ms/ident/protein.rb +33 -0
  29. data/lib/ms/ident/protein_group.rb +80 -0
  30. data/lib/ms/ident/search.rb +114 -0
  31. data/lib/ms/ident.rb +37 -0
  32. data/lib/ms/isotope/aa.rb +59 -0
  33. data/lib/ms/mascot.rb +6 -0
  34. data/lib/ms/mass/aa.rb +79 -0
  35. data/lib/ms/mass.rb +55 -0
  36. data/lib/ms/mzml/index_list.rb +98 -0
  37. data/lib/ms/mzml/plms1.rb +34 -0
  38. data/lib/ms/mzml.rb +197 -0
  39. data/lib/ms/obo.rb +38 -0
  40. data/lib/ms/plms1.rb +156 -0
  41. data/lib/ms/quant/qspec/protein_group_comparison.rb +22 -0
  42. data/lib/ms/quant/qspec.rb +112 -0
  43. data/lib/ms/spectrum.rb +154 -8
  44. data/lib/ms.rb +3 -10
  45. data/lib/msplat.rb +2 -0
  46. data/lib/obo/ims.rb +5 -0
  47. data/lib/obo/ms.rb +7 -0
  48. data/lib/obo/ontology.rb +41 -0
  49. data/lib/obo/unit.rb +5 -0
  50. data/lib/openany.rb +23 -0
  51. data/lib/write_file_or_string.rb +18 -0
  52. data/obo/ims.obo +562 -0
  53. data/obo/ms.obo +11677 -0
  54. data/obo/unit.obo +2563 -0
  55. data/spec/ms/cvlist_spec.rb +60 -0
  56. data/spec/ms/digester_spec.rb +351 -0
  57. data/spec/ms/fasta_spec.rb +100 -0
  58. data/spec/ms/ident/peptide/db_spec.rb +108 -0
  59. data/spec/ms/ident/pepxml/sample_enzyme_spec.rb +181 -0
  60. data/spec/ms/ident/pepxml/search_hit/modification_info_spec.rb +37 -0
  61. data/spec/ms/ident/pepxml_spec.rb +442 -0
  62. data/spec/ms/ident/protein_group_spec.rb +68 -0
  63. data/spec/ms/mass_spec.rb +8 -0
  64. data/spec/ms/mzml/index_list_spec.rb +122 -0
  65. data/spec/ms/mzml/plms1_spec.rb +62 -0
  66. data/spec/ms/mzml_spec.rb +50 -0
  67. data/spec/ms/plms1_spec.rb +38 -0
  68. data/spec/ms/quant/qspec_spec.rb +25 -0
  69. data/spec/msplat_spec.rb +24 -0
  70. data/spec/obo_spec.rb +25 -0
  71. data/spec/spec_helper.rb +25 -0
  72. data/spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta +69 -0
  73. data/spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml +728 -0
  74. data/spec/testfiles/ms/mzml/j24z.idx_comp.3.mzML +271 -0
  75. data/spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML +330 -0
  76. data/spec/testfiles/ms/quant/kill_extra_tabs.rb +13 -0
  77. data/spec/testfiles/ms/quant/max_quant_output.provenance.txt +15 -0
  78. data/spec/testfiles/ms/quant/max_quant_output.txt +199 -0
  79. data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv +199 -0
  80. data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp +199 -0
  81. data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv +199 -0
  82. data/spec/testfiles/ms/quant/pdcd5_final.txt +199 -0
  83. data/spec/testfiles/ms/quant/pdcd5_final.txt_qspecgp +0 -0
  84. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.CSV.csv +199 -0
  85. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.csv +199 -0
  86. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.csv +199 -0
  87. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv +199 -0
  88. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp +199 -0
  89. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv +199 -0
  90. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.txt +199 -0
  91. data/spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt +134 -0
  92. data/spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt_qspecgp +134 -0
  93. data/spec/testfiles/ms/quant/remove_rest_of_proteins.rb +13 -0
  94. data/spec/testfiles/ms/quant/unlog_transform.rb +13 -0
  95. data/spec/testfiles/plms1/output.key +0 -0
  96. metadata +157 -40
  97. data/README +0 -77
  98. data/changelog.txt +0 -196
  99. data/lib/ms/calc.rb +0 -32
  100. data/lib/ms/data/interleaved.rb +0 -60
  101. data/lib/ms/data/lazy_io.rb +0 -73
  102. data/lib/ms/data/lazy_string.rb +0 -15
  103. data/lib/ms/data/simple.rb +0 -59
  104. data/lib/ms/data/transposed.rb +0 -41
  105. data/lib/ms/data.rb +0 -57
  106. data/lib/ms/format/format_error.rb +0 -12
  107. data/lib/ms/support/binary_search.rb +0 -126
data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.txt ADDED
@@ -0,0 +1,199 @@
1
+ protid protLen 0 0 0 1 1 1
2
+ P16104;Q96QV6;A4FTV9;B2R5B3;P04908;P0C0S8;P20671;Q08AJ9;Q6FI13;Q7L7L0;Q93077;Q16777;Q9BTM1;A3KPC7;Q96KK5;Q99878;C9JE22;Q9BTM1-2;B2R5B6;Q8IUE6;P0C0S5;Q71UI9;C9J0D1;A6NN01;B4E0B3;A6NKY0;A6NFA8;C9J386;A8MQC5 1 -10.1748 21.57658 -11.79741 21.6756 -13.53891 21.91554
3
+ P04406;Q2TSD0;E7EUT4;E7EUT5;Q0QET7;A4UCT1;E7EPW1;Q5ZEY3 1 20.84445 20.82648 20.52258 20.91634 21.22588 20.78532
4
+ P29590;P29590-7;Q9BZY1;P29590-11;P29590-8;P29590-3;P29590-6;Q15156;P29590-13;P29590-9;P29590-5;E9PG00;P29590-2;P29590-12;Q59H09;P29590-4;A4VCI9;E9PBR7;P29590-10;P29590-14;Q59GQ8;Q05835 1 -10.73202 -11.98464 -10.42344 -7.477787 -14.00278 -11.96467
5
+ A5JHP3;P81605;Q53YJ2 1 21.5695 21.77989 -12.43826 21.44081 21.40561 20.8966
6
+ Q92794;A5PKX7;A5PLL3 1 -9.716413 -3.583641 -17.64762 -8.342788 -10.27187 -16.43587
7
+ A5YM50;Q15907;Q5U0I1;Q6FHR0;B4DMK0;B4DMN1;Q6FI42;P62491;B4DT13;B4DQU5 1 22.25381 22.27523 22.3938 20.48886 20.20729 20.32608
8
+ Q14315;Q14315-2;E9KL45;P21333;P21333-2;B2ZZ83;Q60FE5;Q60FE6;Q5HY54;O75369;Q60FE7;O75369-2;O75369-3;O75369-6;A6NDY9;B2ZZ80;O75369-4;O75369-5 1 17.14967 -13.14418 -10.14975 -9.094846 -11.56903 -9.011176
9
+ A6NE09;P08865;C9J9K3;Q96RS2;C9JQR9 1 19.60259 20.11426 19.26591 19.04354 18.54808 -15.37007
10
+ B4DUT8;Q53GK7;Q6FHC3;Q6FHE4;Q99439;B4DDF4;A6NFI4 1 -11.94525 -10.09451 -13.05105 -8.697504 -3.733516 -15.28478
11
+ P30044;A6NG06;B7ZLJ4;P30044-2;A6NC19;B7ZVW3 1 19.97519 20.10917 19.06863 18.47908 18.01149 18.66837
12
+ A6NHL2;A6NHL2-2 1 -12.56135 -7.988067 -13.00901 -9.405752 -14.37151 16.64005
13
+ Q8NI27;Q8NI27-2;E9PHG2;Q5JZ13;A6PVD0 1 -18.3428 -5.515328 -11.6108 -14.80355 -7.519837 -10.10585
14
+ A8K0T9;P52907 1 -8.070804 19.27394 18.9881 -16.03139 -4.297441 -12.72701
15
+ B2R8N1;Q53QS9;Q99627;E9PGT6;A8K1H6 1 -6.645485 -3.159239 -6.579911 -7.806178 -10.67114 16.4076
16
+ A8K220;A8K486;P62937;B2RE56;B4DM82;C9J5S7;Q71V99;Q567Q0;E5RIZ5 1 22.1986 22.38929 22.38087 21.16944 21.32592 21.29418
17
+ A8K2X8;E7ENZ3;B4DYC8;B4DE30;B4DYD8;Q96GI1;B4DZY9;Q9HB74;D6RIZ7 1 21.44294 21.35676 21.02439 27.51676 27.83744 27.34908
18
+ A8K3K1;P68032;P68133;B7Z6P1;D2JYH4;P62736;P63267;A6NL76;Q5T8M8;B3KW67;B3KUD3;Q5T8M7;B4DUI8;Q13707;E7EQV5;Q7Z7J6;B4E315;E9PG30;B7Z6I1;Q5T9N7;C9JFL5;B8ZZJ2;C9JZR7;C9JUM1;B3KPP5;C9JTX5;Q562L3;Q562M3;Q562M5;Q562N2;Q562P8;Q562Q0;Q562Q2;Q562Q4;Q562Q6;Q562Q8;Q562Q9;Q562R0;Q562R5;Q562R6;Q562T0;Q562T3;Q562T4;Q562T5;Q562T6;Q562T8;Q562U0;Q562U1;Q562W2;Q562X0;Q562X1;Q562X2;Q562X4;Q562X6;Q562X7;Q562Y4;Q562Y8;A0AUL6 1 -8.780886 -17.22744 -11.99804 -11.46239 -9.619148 -16.34999
19
+ A8K4I2;P16403;P16402;A3R0T7;A3R0T8;B2R984;P10412;Q4VB24;Q02539;A1L407;P22492 1 20.76418 20.74993 21.21561 21.25678 21.20574 20.81245
20
+ Q99615;A8K4T2;Q59EH7;B7Z9W6;Q7Z784;B4DKK3 1 -10.2706 18.26467 -12.02999 -12.49216 -4.80777 -9.250307
21
+ B4DSZ4;E7EWS7;A8K4W8;P68036;B4DDG1 1 19.52338 19.43561 19.70301 18.72341 19.21295 19.45617
22
+ A8K4Z4;P05388;Q53HW2;Q8NHW5;B4E3D5;Q3B7A4;Q6NSF2;Q53HK9 1 17.82607 -15.11839 -13.71657 -9.695791 -14.91231 -20.01069
23
+ Q59EJ3;A8K5I0;P08107;B4DNT8;B4DWK5;B4DI39;B4E3B6;B4DFN9;E7EP94;B4E388;B4E1S9;B4DVU9;B4DNV4;C9JCM4;E7EP11;B2R6X5;B3KSM6;P17066;Q53FC7;B3KTT5;Q5SP16;B4DNX1;B4E1T6;P48741;B4DHP5 1 20.3722 19.70376 20.21916 19.89714 19.99175 20.05457
24
+ A8K5T7;Q9Y2Z0;A8K7W3;Q9Y2Z0-2;B4DYC6 1 -11.04554 -8.394851 -12.22395 -12.15968 -9.030668 -9.055989
25
+ Q59EM9;Q66K58;P0CG48;A8K674;Q96H31;Q96MH4;Q96C32;Q9UFQ0;P0CG47;Q5PY61;Q5U5U6;B2RDW1;P62979;Q5RKT7;B4DV12;Q5UGI3;P62987;Q3MIH3;Q49A90;Q8WYN9 1 25.01933 25.02817 25.25324 24.37498 24.61352 24.12123
26
+ Q3ZCU9;A8K690;P31948;B4DM70 1 -15.79622 -12.4429 -8.251936 -14.61531 -6.618255 -11.69185
27
+ Q05D08;Q9UQ80;Q6PIN5;A8K6Y1 1 19.58187 19.67385 19.48418 -9.563393 -9.759739 -13.90931
28
+ Q14240-2;Q14240;A8K7F6;P60842;E7EQG2;Q9NZE6;B4DNH2;A8K088;Q96B07;Q59F68;B4DJX6;B4DKP9 1 20.29019 -3.275673 18.7028 -9.760659 -11.02793 -8.931159
29
+ Q59HD4;A8K7X6;Q68Y55;B4DLC0;Q6IPF4;Q15366;Q32Q82;B4DXP5;B4DRD7;P57721;P57721-4;A8MX33;E9PFP8;Q5MJP6;P57721-5;P57721-3;P57721-2 1 22.9206 23.02955 22.65014 21.91368 21.96141 22.22335
30
+ Q9UBL6;B7Z1M3;Q9HCH3;B7Z370;Q96A23-2;Q86YQ8;Q9UBL6-2;O95741;Q96A23;Q8IYJ1;A8K8A4;Q96FN4;O75131;B2RD40;Q719H8;B3KWK1;Q7Z6C8;Q86VY2;Q4G168 1 -7.090923 -13.03055 17.60074 -15.48375 -7.483465 -9.849869
31
+ Q13561-2;Q53H88;Q13561-3;Q13561;B3KTX4;A8K8J9 1 -13.29258 -11.61868 -16.22564 -11.85453 -13.5876 -8.071517
32
+ A8K9C4;P68104;Q53G85;Q53GE9;Q53HM9;Q53HQ7;Q53HR5;Q5VTE0;Q6IPN6;Q6IPS9;Q6IPT9;E7EUM7;Q6IQ15;B4DNE0;Q96RE1;Q53GA1;Q9NZS6;B4DV42;Q53G89;Q9H2I7;Q16577;Q53HR1;Q8IUB0;Q504Z0;Q6P4C9;Q96CD8;Q6P082;Q8TBL1;Q96C29;B4E2C5;Q05639;Q59GP5;Q14222;Q5JR01;A9X7H1;A6PW80;Q96EB3;E7EPH7;Q6NSH7;Q2F837;Q6NS35 1 25.19363 25.12912 24.41125 24.75903 24.928 24.59087
33
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34
+ A8KAY2;Q75N90;E7EP57;Q6ZNB8;B3KU56 1 -14.53446 -13.40562 -9.063076 -17.21276 -9.328329 -8.495333
35
+ Q9H2G2;Q9H2G2-2;REV__Q9P2R3-2;REV__Q9P2R3;REV__B3KPZ0;Q5M775;B4DZC9;A8MV89;B4E2A4;Q5M775-4;REV__Q5H9P4;Q5M775-2;Q5M775-3;Q5M775-5 1 19.92454 -8.690648 -6.982073 -12.38774 -12.12938 -12.40572
36
+ A8MVA2 1 -10.62001 -14.80463 -5.787057 -11.14217 -9.217167 -13.77398
37
+ C9JS35;Q92890-1;B4E3I3;Q541A5;Q92890;A8MW31;C9J6N9;B7Z9N3;A6NJ11;C9IZG3;C9JNP9 1 19.71 19.57119 19.18175 18.66716 18.48562 18.95311
38
+ A8MXP9;P43243;Q68D11;D6REM6;D6R991 1 -10.82731 -4.6525 -5.913542 -11.42858 -14.86205 -13.279
39
+ C9JE52;A8MZ76;Q2TNB3;Q6FHK9;Q86SZ7;Q9UL46 1 21.74755 21.54628 21.21804 20.50048 20.27537 20.84805
40
+ E7EX29;D0PNI1;P63104;B0AZS6;B7Z465;E7EX24;B7Z2E6;Q2F831;E7ESK7 1 19.81649 19.99811 19.79994 18.96002 18.55981 19.11802
41
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42
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43
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44
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45
+ E9PAV3;B2R4P8;Q13765;B4DDI8 1 19.63336 19.85194 19.99189 19.41607 19.86116 -11.03913
46
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47
+ B2R4R9;P62857 1 21.36335 21.36608 21.48094 21.57768 20.64262 21.08868
48
+ B2R4U3;O00762;Q5TZN3;E1P5N7;A6NP33 1 19.57873 19.47781 18.81994 17.99722 17.64934 -9.015995
49
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50
+ B2R9K8;P40227;Q59ET3;B4DPJ8;A1JUI8;A6NCD2;B4DN39;Q92526;B4DYB0;B4DX20 1 20.17597 19.99272 19.95603 27.8846 27.92388 27.62659
51
+ B2R9U2;Q02790 1 -9.570673 -6.285736 -13.28069 -15.74234 -14.50727 -8.327213
52
+ B2RBR9;Q14974;B7Z752;B7ZAV6;B7Z5M1 1 18.6568 18.27653 -14.11772 17.96002 17.45282 -8.417989
53
+ P10809;B3GQS7;B7Z597;B7Z5E7;B7Z4F6;E7ESH4;Q53SE2;E7EXB4;B7Z532;C9JL25;B7Z712;C9JCQ4;C9JL19;C9J0S9;Q53QD5 1 23.93454 23.96402 23.99136 23.44468 23.2764 23.46376
54
+ B3KM68;Q9Y6E2;E7ETZ4;B7Z4K8;B5MCH7;B5MCE7;Q05D83;B4DLZ8;Q53FN7;B4DWF7;Q7L1Q6;E9PRN2;Q7L1Q6-2;Q75MG1;D3DN77 1 19.31358 19.20125 18.97396 -10.97263 -12.16192 -8.993392
55
+ B3KNA8;Q07352;B4E1N3;B4DG15 1 -10.32378 -6.598993 -9.45362 -9.234979 -9.904229 -11.74547
56
+ B3KUH0;Q8WUX9;E5RJI3;B3KRZ9;E5RIU9;B4DKJ6 1 17.05801 17.9016 -8.524639 -8.500674 -3.22365 -6.724072
57
+ B3KW39;Q5H9R6;Q8WXH5 1 -11.1052 -5.320193 -13.60777 -17.3987 -9.64648 -16.14916
58
+ E9PDP1;B3KXM2;Q07161;P36873-2;P62136;P36873;Q9UPN1;E9PMD7;P62140;B4DJ75;B7ZB67;B4E163;E7ETD8;C9JP48;C9J9S3;A6NNR3 1 19.56744 19.48564 19.48156 18.37105 18.27362 18.7264
59
+ P04350;B4DE77;B4DJ43;B4DFH6;E7EM46 1 -7.801593 18.33136 19.15247 -12.86542 -12.8622 -7.263447
60
+ P32119;B4DF70;A6NIW5 1 -12.16686 -14.48203 -12.85298 -9.178046 -6.847968 -9.206059
61
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62
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+ Q13748;Q1ZYQ1;Q6PEY2;Q13748-2;B4DQK4;Q9UQM3 1 -10.66357 -14.06973 -12.08348 -14.28111 -5.237717 17.14907
175
+ Q13885;Q9BVA1;B2R6L0;O43209;B7Z4N1;Q9UGA2 1 -13.49121 -6.262399 -11.33813 -8.947213 -14.87637 -8.820883
176
+ Q14966-5 1 -7.021094 -14.92009 -13.04827 -12.08927 -7.937469 -11.1881
177
+ Q15365;Q53SS8 1 24.66622 24.74242 24.65589 23.77062 23.85158 23.54109
178
+ Q2NKY5 1 -15.55575 -10.25709 -14.05433 -8.462026 -13.69572 16.70819
179
+ Q9UMY4;Q3SYF1;Q9UMY4-2;A6NMW4 1 -7.442906 -11.63373 -6.078456 -19.74594 -13.79196 -10.40766
180
+ Q53GA7;Q9BQE3;B7Z1K5;E9PGK3;Q8N532 1 -11.74152 -11.2261 -11.21979 -9.335281 -6.95872 -15.17143
181
+ Q53HV2;Q99832;Q6IBT3;B7Z4T9;B8ZZC9;B7Z4Z7;B7Z7I4;B7Z1C9;A8MWI8 1 20.17524 20.24853 19.75053 27.4538 27.50325 27.39116
182
+ Q549M8;Q5RLJ0;Q9Y224 1 19.77843 19.70592 18.89552 -10.58809 18.03859 -8.44814
183
+ Q562R1 1 -8.519845 -10.30984 -18.02548 -6.304536 -10.44245 -12.38124
184
+ Q5RHS7 1 -12.1832 -12.45635 -17.51425 -7.780077 -8.588738 18.39933
185
+ Q5T6W5;P61978-2;Q6IBN1;P61978;P61978-3;B4DUQ1;Q5EC54;B4DFF1;Q5T6W2;Q5T6W1;B3KU16 1 20.83977 21.10687 20.64086 19.81011 19.92268 20.32202
186
+ Q5T749 1 20.20884 20.02445 20.65421 19.93919 19.96888 19.5098
187
+ Q6FG99;P05386;Q7Z612;Q6ICQ4 1 20.68603 20.81096 20.92796 20.37592 20.44556 20.28275
188
+ Q6GPH4-6 1 -15.89455 -12.66758 -8.491282 -12.51258 -13.26758 -11.67764
189
+ Q8IVF2;Q8IVF2-3 1 -12.25156 -7.448378 -17.52637 -9.166928 -5.064223 -2.999552
190
+ Q8NBJ5 1 -7.16766 -15.19173 -9.879982 -12.1978 -10.33225 21.02553
191
+ Q96C19;Q59EU6;Q9BUP0;Q5JYW8;C9JTI6;E9PFH3;B4DEE0;Q7Z2R5;Q53SA2 1 -10.63977 18.64776 18.75818 -15.16592 -12.90091 -8.669762
192
+ Q96FQ6 1 20.54519 20.61648 19.14143 19.61153 17.51044 17.52076
193
+ Q99471;Q9C084 1 -8.978248 -18.35719 -10.29207 -11.89493 18.06081 -9.915236
194
+ Q9BUF5;B4DP54;B3KS31;B4E386 1 -9.339276 -15.59846 -14.69548 14.72179 -7.716224 -8.1283
195
+ Q9BZK4 1 -9.736339 -9.588387 -9.981355 -13.86738 -12.08974 -11.07565
196
+ Q9C000;Q9C000-4;Q9C000-2;Q9C000-3 1 -11.13027 -7.488196 -9.515059 -1.631392 -8.864885 -13.01796
197
+ Q9HB15 1 -9.450394 -6.710937 -9.582086 -7.694815 -12.83965 -13.21885
198
+ Q9Y3D6 1 -9.938221 -8.330604 -8.094868 17.66581 -8.104318 -12.47573
199
+ Q9Y490;Q5TCU6 1 22.33066 22.39676 22.3996 20.73422 21.23403 21.39571
data/spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt ADDED
@@ -0,0 +1,134 @@
1
+ protid protlen 0 0 0 1 1 1
2
+ A8K2X8 1 21.44294 21.35676 21.02439 27.51676 27.83744 27.34908
3
+ B2R9K8 1 20.17597 19.99272 19.95603 27.8846 27.92388 27.62659
4
+ B5BTY7 1 21.85148 22.03671 21.9407 27.39942 27.44932 27.54694
5
+ O14737 1 21.03059 20.54548 21.56123 28.76696 28.86304 28.60145
6
+ P17987 1 17.85392 17.0281 18.56309 27.4677 27.4964 27.33048
7
+ Q59H77 1 19.61184 19.67721 19.23673 27.72175 27.93568 27.5947
8
+ P50990 1 22.38743 22.56686 22.1832 27.88052 28.13256 27.85863
9
+ P50991 1 18.2702 19.35316 18.61924 27.32071 27.30583 27.11088
10
+ Q53HV2 1 20.17524 20.24853 19.75053 27.4538 27.50325 27.39116
11
+ P16104 1 17.04511 21.57658 16.06153 21.6756 18.18093 21.91554
12
+ P04406 1 20.84445 20.82648 20.52258 20.91634 21.22588 20.78532
13
+ A5JHP3 1 21.5695 21.77989 16.98853 21.44081 21.40561 20.8966
14
+ A5YM50 1 22.25381 22.27523 22.3938 20.48886 20.20729 20.32608
15
+ A6NE09 1 19.60259 20.11426 19.26591 19.04354 18.54808 17.21706
16
+ P30044 1 19.97519 20.10917 19.06863 18.47908 18.01149 18.66837
17
+ A6NHL2 1 16.27894 16.07361 16.8989 17.68499 15.52398 16.64005
18
+ A8K0T9 1 17.5 19.27394 18.9881 18.06098 17.16758 16.77324
19
+ A8K220 1 22.1986 22.38929 22.38087 21.16944 21.32592 21.29418
20
+ A8K3K1 1 17.65141 18.28707 16.90648 15.55354 15.72711 17.30632
21
+ A8K4I2 1 20.76418 20.74993 21.21561 21.25678 21.20574 20.81245
22
+ Q99615 1 17.26984 18.26467 17.81942 17.05523 17.88267 16.65556
23
+ B4DSZ4 1 19.52338 19.43561 19.70301 18.72341 19.21295 19.45617
24
+ A8K4Z4 1 17.82607 17.72419 15.61066 15.81553 17.74059 17.51518
25
+ Q59EJ3 1 20.3722 19.70376 20.21916 19.89714 19.99175 20.05457
26
+ Q59EM9 1 25.01933 25.02817 25.25324 24.37498 24.61352 24.12123
27
+ Q3ZCU9 1 16.68366 17.22239 16.99913 16.93082 16.60097 17.33755
28
+ Q05D08 1 19.58187 19.67385 19.48418 17.04255 17.31607 16.87639
29
+ Q14240-2 1 20.29019 16.87264 18.7028 17.21878 17.3111 17.43529
30
+ Q59HD4 1 22.9206 23.02955 22.65014 21.91368 21.96141 22.22335
31
+ A8K9C4 1 25.19363 25.12912 24.41125 24.75903 24.928 24.59087
32
+ A8KAY2 1 17.3623 17.65194 17.38799 16.58807 18.03223 17.94092
33
+ C9JS35 1 19.71 19.57119 19.18175 18.66716 18.48562 18.95311
34
+ C9JE52 1 21.74755 21.54628 21.21804 20.50048 20.27537 20.84805
35
+ E7EX29 1 19.81649 19.99811 19.79994 18.96002 18.55981 19.11802
36
+ B2R4P2 1 21.84219 21.74086 20.95865 21.18707 17.35854 20.667
37
+ E9PAV3 1 19.63336 19.85194 19.99189 19.41607 19.86116 17.59601
38
+ B2R4R0 1 18.54582 20.73513 20.94528 20.9234 21.9374 20.9102
39
+ B2R4R9 1 21.36335 21.36608 21.48094 21.57768 20.64262 21.08868
40
+ B2R4U3 1 19.57873 19.47781 18.81994 17.99722 17.64934 17.69965
41
+ B2R679 1 23.11618 22.90564 22.8795 22.50913 22.308 22.55194
42
+ B2R9U2 1 16.70504 17.30696 16.39207 17.22315 17.21392 16.94009
43
+ B2RBR9 1 18.6568 18.27653 17.93161 17.96002 17.45282 18.32935
44
+ P10809 1 23.93454 23.96402 23.99136 23.44468 23.2764 23.46376
45
+ B3KM68 1 19.31358 19.20125 18.97396 16.25668 18.25362 16.57732
46
+ B3KUH0 1 17.05801 17.9016 19.00256 17.38616 15.89326 18.06615
47
+ E9PDP1 1 19.56744 19.48564 19.48156 18.37105 18.27362 18.7264
48
+ P04350 1 16.85094 18.33136 19.15247 16.94814 17.74995 16.56077
49
+ P32119 1 17.0827 16.93012 17.40475 17.76032 17.44621 18.0944
50
+ Q15417 1 19.49717 19.00306 18.5068 16.23989 18.66171 19.17767
51
+ P08238 1 21.50896 21.49892 21.6747 20.74041 19.85345 20.78987
52
+ D3DPU2 1 21.6832 21.56025 21.57261 21.13871 20.94027 21.01004
53
+ P27348 1 19.05931 17.18165 16.87782 17.10118 16.91788 18.07608
54
+ E9PCF5 1 21.01536 20.88487 20.59596 20.02188 20.60991 19.93848
55
+ Q14103 1 20.51768 20.62819 20.17207 19.77349 19.95844 20.11032
56
+ P25685 1 16.4296 15.51336 16.76997 18.82448 16.52999 17.56193
57
+ Q15785 1 19.30108 19.34886 19.13508 17.85515 17.24573 16.80598
58
+ B4DZF2 1 17.18549 17.53374 18.33988 16.23582 16.9198 17.20416
59
+ B5BU38 1 21.04059 20.88502 20.86439 18.36158 18.94135 16.53514
60
+ E7EQR4 1 18.95923 18.9798 18.53069 17.41753 16.41974 17.7951
61
+ E9PAN3 1 19.20557 19.4868 20.23911 18.23193 19.54538 19.36602
62
+ P22626 1 20.31274 20.01522 18.98151 19.64375 20.24098 19.74498
63
+ C7DJS2 1 17.94159 18.26781 17.71091 16.34532 17.00877 17.29584
64
+ P18085 1 22.84364 22.81016 22.56813 22.2741 21.73719 22.17618
65
+ Q53F37 1 17.79371 17.75215 17.37138 16.84039 16.93211 17.59234
66
+ D6W4Z6 1 20.38669 20.38943 20.23421 19.6097 19.409 20.2207
67
+ P15924 1 17.31456 17.38259 16.95984 18.03004 17.45421 16.70534
68
+ E7ETK2 1 18.29894 17.60824 17.5474 16.52044 16.97056 16.52645
69
+ Q8TAT6-2 1 19.63839 20.18386 18.57186 18.21062 17.97885 16.70952
70
+ Q9H0U4 1 23.89208 23.98198 23.74273 22.67282 22.63962 22.37263
71
+ E9KL23 1 20.19039 18.37422 17.38497 19.48016 16.45898 17.42385
72
+ E9KL35 1 22.7494 22.82188 23.23513 22.19403 22.20735 22.10246
73
+ E9KL39 1 23.27056 23.22121 23.03547 22.45749 21.99016 22.59855
74
+ E9PDH9 1 19.58989 19.63041 18.8317 16.97905 18.34508 16.89386
75
+ Q8WUD1 1 19.60047 19.71431 19.1277 17.10974 19.05658 18.01028
76
+ E9PK25 1 22.4381 22.38922 22.36666 21.75087 21.28308 21.29435
77
+ O43175 1 21.11108 20.84751 20.54425 19.98607 19.97533 19.86478
78
+ O60493 1 20.12943 20.30775 20.00498 19.04705 17.07916 16.51069
79
+ O60664 1 22.81284 22.78905 22.8987 22.01376 22.08443 21.56941
80
+ P04632 1 22.87076 22.89759 23.22585 21.78788 21.66635 21.91232
81
+ P04792 1 23.466 23.29852 22.92664 22.68541 22.72837 22.47338
82
+ P05198 1 19.6046 19.77038 20.09171 19.89141 19.54542 19.34953
83
+ P05387 1 21.68166 21.4206 21.29558 20.65211 20.97526 20.30162
84
+ P06733 1 20.06894 19.9805 20.20275 17.23294 19.39897 19.33723
85
+ P07355-2 1 25.34996 25.25158 25.17976 24.09184 23.9968 24.0441
86
+ P07384 1 21.46508 21.429 21.70771 19.9959 19.90806 19.46408
87
+ P07437 1 24.5093 24.59024 24.54646 22.91379 22.79198 23.11634
88
+ P07737 1 20.42634 20.55515 16.73716 19.72442 19.87533 19.66007
89
+ P07900-2 1 17.32102 15.5011 17.60533 16.36718 18.14835 17.08387
90
+ P08758 1 19.69729 19.32854 19.04817 18.29212 18.16315 19.23916
91
+ P09211 1 22.56888 22.45493 22.36209 22.41568 22.29765 21.92401
92
+ P09382 1 25.12017 25.13739 24.96354 24.19024 23.97044 24.05961
93
+ P09651 1 19.90721 19.9045 19.93934 19.30425 19.05261 19.30828
94
+ P11142 1 23.61358 23.56023 24.01171 23.54097 23.31769 23.14404
95
+ P11586 1 19.62578 20.54501 20.32608 17.81965 19.10991 16.76862
96
+ P13639 1 23.80902 23.84 23.60162 22.4743 22.20774 22.27481
97
+ P14618 1 22.23248 22.28729 21.86359 21.69562 21.39037 21.54581
98
+ P18206 1 21.10534 21.0001 19.93531 18.44273 19.34953 19.23079
99
+ P20290 1 19.05515 18.77481 18.83201 17.28506 17.59213 18.37954
100
+ P25398 1 23.54981 23.68752 23.9228 23.2254 23.59309 23.01667
101
+ Q9BUQ0 1 19.67533 20.05669 20.02797 19.48599 18.95356 19.06321
102
+ P30050 1 19.5282 19.22771 19.76158 19.58602 19.40674 19.05608
103
+ P31151 1 21.41101 20.94049 17.67464 17.65567 16.86133 17.67002
104
+ P46060 1 17.41218 16.31357 17.86077 18.2444 18.51837 17.7381
105
+ P48643 1 18.24529 16.44629 16.80848 17.40421 18.3968 16.80939
106
+ P51148 1 22.42401 22.49931 22.80075 21.62582 21.73723 21.4171
107
+ P51149 1 21.89807 21.86948 21.64777 20.35681 20.17121 20.69702
108
+ P61026 1 21.11388 22.00717 16.40936 20.01209 20.61746 20.56104
109
+ P61088 1 21.85935 21.72226 21.87376 20.92832 20.85681 20.85711
110
+ P61106 1 16.84908 17.8136 17.00607 17.29525 17.0999 16.80307
111
+ P61204 1 21.42992 21.4289 21.03113 21.60603 21.18041 21.39603
112
+ P61289-2 1 22.46214 22.42846 22.45651 21.61553 21.28444 21.46523
113
+ P62258 1 15.90053 16.69171 17.89677 16.81378 15.69759 17.2101
114
+ Q01995 1 21.99186 21.96116 22.44831 21.29905 21.51831 21.04414
115
+ Q02413 1 19.08613 19.28297 18.48821 17.01407 18.01257 16.26142
116
+ Q06323 1 23.0555 23.03174 23.0523 22.30563 22.26959 22.29955
117
+ Q07812-2 1 20.52726 20.44799 20.19484 19.19359 18.97259 19.80985
118
+ Q09666 1 22.77412 22.6297 21.90705 22.6742 23.10792 22.4803
119
+ Q13748 1 17.92476 16.06442 16.0866 16.33296 16.85818 17.14907
120
+ Q13885 1 16.22638 16.66555 17.55659 17.64022 17.3861 16.95564
121
+ Q15365 1 24.66622 24.74242 24.65589 23.77062 23.85158 23.54109
122
+ Q9UMY4 1 17.29476 17.33109 15.93148 16.89334 17.65937 16.41726
123
+ Q53GA7 1 16.60637 16.00322 17.03156 17.37824 17.56524 19.2664
124
+ Q549M8 1 19.77843 19.70592 18.89552 17.05412 18.03859 17.81947
125
+ Q562R1 1 15.61821 17.93727 17.60435 16.29778 17.38981 16.14947
126
+ Q5T6W5 1 20.83977 21.10687 20.64086 19.81011 19.92268 20.32202
127
+ Q5T749 1 20.20884 20.02445 20.65421 19.93919 19.96888 19.5098
128
+ Q6FG99 1 20.68603 20.81096 20.92796 20.37592 20.44556 20.28275
129
+ Q6GPH4-6 1 17.45312 17.14393 16.4793 17.29402 17.28194 16.86516
130
+ Q96C19 1 15.74879 18.64776 18.75818 16.76085 17.58502 17.33129
131
+ Q96FQ6 1 20.54519 20.61648 19.14143 19.61153 17.51044 17.52076
132
+ Q9BUF5 1 18.12246 16.98663 17.94654 14.72179 18.71585 16.6628
133
+ Q9Y3D6 1 16.61321 16.02214 17.00952 17.66581 17.96566 16.83891
134
+ Q9Y490 1 22.33066 22.39676 22.3996 20.73422 21.23403 21.39571
data/spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt_qspecgp ADDED
@@ -0,0 +1,134 @@
1
+ Protein S0 S0 S0 S1 S1 S1 S0 S1 S21 S0 S0 S0 S0 S0 S0 S0 S0 S0 BayesFactor FoldChange RBstat FDR FLAG
2
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.002 1.00000
3
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.005 1.00000
4
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.001 1.00000
5
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.008 1.00000
6
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.005 1.00000
7
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
8
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.007 1.00000
9
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.005 1.00000
10
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.008 1.00000
11
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.006 1.00000
12
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.007 1.00000
13
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.010 1.00000
14
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.008 1.00000
15
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
16
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.006 1.00000
17
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.003 1.00000
18
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.003 1.00000
19
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
20
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.001 1.00000
21
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
22
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.002 1.00000
23
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.005 1.00000
24
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.001 1.00000
25
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
26
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.002 1.00000
27
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.001 1.00000
28
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.004 1.00000
29
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.001 1.00000
30
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.002 1.00000
31
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.004 1.00000
32
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.001 1.00000
33
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.002 1.00000
34
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.002 1.00000
35
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.001 1.00000
36
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.006 1.00000
37
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.001 1.00000
38
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
39
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
40
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.002 1.00000
41
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
42
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.009 1.00000
43
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
44
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.006 1.00000
45
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.007 1.00000
46
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
47
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
48
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.006 1.00000
49
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
50
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.001 1.00000
51
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.003 1.00000
52
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.002 1.00000
53
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.000 0.010 0.000 1.00000
54
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data/spec/testfiles/ms/quant/remove_rest_of_proteins.rb ADDED
@@ -0,0 +1,13 @@
1
+ #!/usr/bin/env ruby
2
+
3
+ file = ARGV.shift
4
+
5
+ base = file.chomp(File.extname(file))
6
+
7
+ File.open(base + '.oneprot.tsv','w') do |out|
8
+ IO.foreach(file) do |line|
9
+ data = line.chomp.split("\t")
10
+ data[0] = data[0].split(';')[0]
11
+ out.puts data.join("\t")
12
+ end
13
+ end
data/spec/testfiles/ms/quant/unlog_transform.rb ADDED
@@ -0,0 +1,13 @@
1
+ #!/usr/bin/env ruby
2
+
3
+ file = ARGV.shift
4
+
5
+ base = file.chomp(File.extname(file))
6
+
7
+ File.open(base + '.oneprot.tsv','w') do |out|
8
+ IO.foreach(file) do |line|
9
+ data = line.chomp.split("\t")
10
+
11
+ out.puts data.join("\t")
12
+ end
13
+ end
data/spec/testfiles/plms1/output.key ADDED
Binary file