mspire 0.5.0 → 0.6.1

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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
+ A8KAH7;P13861;Q9BUB1 1 -12.12438 -16.2057 -10.1214 -15.34898 -9.445698 -12.16657
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
+ Q13148-2;Q13148;B4DRW3;B1AKP7 1 -9.201861 -8.547015 -12.34555 -4.826214 -13.71331 -14.84832
42
+ P10599;B1ALW1;O60744 1 -10.34632 -10.56697 -11.52899 -7.476205 -12.8407 -10.40727
43
+ B2R4M6;P06702 1 -12.68759 -14.11326 -8.289717 -8.96431 -9.109454 -6.145557
44
+ B2R4P2;Q06830;Q13162;E9PEN3 1 21.84219 21.74086 20.95865 21.18707 -9.354398 20.667
45
+ E9PAV3;B2R4P8;Q13765;B4DDI8 1 19.63336 19.85194 19.99189 19.41607 19.86116 -11.03913
46
+ B2R4R0;P62805;Q0VAS5;Q6B823 1 -9.551398 20.73513 20.94528 20.9234 21.9374 20.9102
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
+ B2R679;Q5SQT9;Q6FID4;Q9NR31;Q8NG23;B4DQ19;D6RDB2;Q5SQT8;E9PBN0;Q5SQU0;D6RAA2 1 23.11618 22.90564 22.8795 22.50913 22.308 22.55194
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
+ Q15417;Q6FHA7;B4DFK6;B4DP09;E7ENQ7;E9PDU6;Q9BWY6 1 19.49717 19.00306 18.5068 -14.06474 18.66171 19.17767
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