Repository 'kinamine_y_for_peptide_shaker'
hg clone https://toolshed.g2.bx.psu.edu/repos/jfb/kinamine_y_for_peptide_shaker

Changeset 0:e21ef020d1a6 (2019-01-11)
Next changeset 1:791e87f39276 (2019-09-17)
Commit message:
Uploaded
added:
KM Y PS/._Kinamine_PS.xml
KM Y PS/.shed.yml
KM Y PS/JavaApplication4.jar
KM Y PS/Kinamine_PS.xml
KM Y PS/test-data/output_SubBackFreq.csv
KM Y PS/test-data/output_Substrates.csv
KM Y PS/test-data/psm.tabular
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+name: kinamine7
+categories: [Computational chemistry]
+owner: jfb
+description: Kinamine 7_to_7 extract substrates
+long_description: This tool is intended for use with a mass spec file.name: kinamine
+homepage_url: https://pubs.acs.org/doi/abs/10.1021/ja507164a
+remote_repository_url: https://github.umn.edu/blank121/KinaMine/tree/Galaxy-7-7
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+<tool id="kinamine_shaker" name="Kinamine_for_Peptide_Shaker" version="0.3.0">
+    <description>Extracts phosphorylated motifs from Peptide Shaker PSM file</description>
+    <requirements>
+       <requirement type="package">openjdk</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        mkdir -p outputs &&
+        ## KimaMine relies on the file name extension for the fasta file
+        ln -s '$reference' reference.fasta &&
+        java -Djava.awt.headless=true -jar '$__tool_directory__/JavaApplication4.jar' '$psm_phos' reference.fasta outputs 0.5 output
+    ]]></command>
+    <inputs>
+        <param format="tabular" name="psm_phos" type="data" label="PSM Phosphorylation Report"/>
+        <param format="fasta" name="reference" type="data" label="Protein FASTA reference"/>
+        <param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
+    </inputs>      
+    <outputs>
+        <data format="csv" name="Substrates" from_work_dir="outputs/output_Substrates.csv" label="${outGroup}_Substrates.csv"/>
+        <data format="csv" name="SBF" from_work_dir="outputs/output_SubBackFreq.csv" label="${outGroup}_SubstrateBackgroundFrequency.csv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="psm_phos" ftype="txt" value="PSM phos.csv"/>
+            <param name="reference" ftype="fasta" value="reference.fasta"/>
+            <param name="SBF" ftype="csv" value="SBF.csv"/>
+            <output name="Substrates" ftype="csv" file="output_Substrates.csv"/>
+            <output name="SBF" ftype="csv" file="output_SubBackFreq.csv"/>
+        </test>
+    </tests>
+
+    
+    <help><![CDATA[
+Kinamine takes a Distinct Peptide Report and extracts from it all peptides containing a phospho(Y), along with the 7 amino acids N- and C- terminal to the pY in that peptide (assuming they were discovered at a threshold above the given FDR value).  This file is the *Substrates* file
+Additionally, all discovered peptides are assumed to have come from a protein.  For every phospho(Y) peptide, KinaMine takes the associated protein accession number, searches the FASTA file for that accession number and returns the amino acid percent composition of the protein(s) which that peptide came from.  This file is the *Substrate Background Frequency* file
+This tool is intended to be used in conjunction with Negative Motif Finder and Kinatest, the three together creating a GalaxyP version of the KINATEST-ID workbook.
+
+===========
+
+Inputs
+
+PSM Phosphorylation Report: This is the file that Peptide Shaker can creates after a search is run using SearchGUI
+
+===========
+
+**Intended Purpose**
+This tool is intended for Academic use.  
+This tool is intended as part of a KALIP-KINATEST pipeline.  
+Briefly, KALIP involved treating cell lysate first with trypsin, second with phosphotase, and finally with a given kinase, then running that cell lysate on a Mass Spec to discover what peptides were present.  
+KinaMine then extracts only the phospho-Y peptides and the proteins they came from.  Negative Motif finder finds all pY-containing peptides that could have been discovered but weren't.  Kinatest then uses all this data to discover candidate substrates which will be specific for the given kinase and no others.  From the discovered substrates, a biosensor can be made.
+
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1021/ja507164a</citation>
+    </citations>
+</tool>
+
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b'@@ -0,0 +1,36 @@\n+Amino Acids,Q92979,O00148,Q8N5Y8,Q00839,O14548,Q9H0D6,Q9Y277,Q8NDV3,P15259,P51114,P19623,O00160,P62241,Q9UKV3,P61158,Q9Y285,A6NHL2,P10809,Q9Y281,P62249,P27695,Q9UGN4,Q06124,O95573,Q8NBQ5,P62253,Q9TQE0,P13051,Q9Y295,P26599,P63104,P62258,P26358,P29401,P31942,Q9BQ48,P31943,P31946,P07858,P08708,Q86SX6,P31948,P31947,P54646,P18754,O60678,P16333,Q9BYD2,P62263,P31949,P25098,Q9Y224,P29692,Q14807,Q5JQS6,P21964,Q6PI48,Q9Y230,Q9Y5Z4,O14744,P61106,P07437,Q92769,P26196,Q07666,Q9NR30,P38159,Q9NQR4,O00116,Q9BWF3,P59044,P61353,Q8N257,P29218,P07203,P09622,P04179,P28340,Q9H8W4,Q06323,P11908,Q9UN86,Q10472,Q10471,O00139,Q9UL46,P51571,P51570,Q8NC51,Q13748,Q6S8J3,P08754,Q9H4M9,A6NHR9,P06576,A3KMH1,Q15018,Q9Y3Q3,Q58FF3,P00390,Q96A33,Q9NUU7,P57053,Q8NBJ5,Q8WWY3,P25205,P62879,Q9Y5V0,P62873,P25685,P51991,P23284,Q15029,Q9Y676,P49411,Q8TB72,P36578,Q9UKM9,P16989,P14324,O96011,Q8WX92,P62888,P61313,Q13094,O14950,Q6GTX8,Q9UMR2,P53701,O00567,P13693,Q9NR09,P35241,P62899,Q5T0F9,Q15283,P23246,O43264,P51531,Q58FG0,O00571,O95185,P51532,O14979,O75083,Q99733,Q96ST3,P14550,Q58FF8,Q9H4A4,Q15052,P28702,Q16143,Q58FF7,Q58FF6,Q15056,P06733,P26583,P31930,O00505,Q9Y624,O00507,Q5R372,P37235,Q6UUV9,Q9NWU5,P61981,P60891,ALDOA_RABIT,P31939,P49458,P55072,O43242,P06748,Q96A65,O60814,Q9NV31,Q99798,P60660,P55084,Q92922,O14910,Q92918,P51965,Q9Y5S9,P17844,Q99543,Q00610,O14920,P62854,Q9BQ04,Q86UX7,Q92905,Q13905,Q9HCC0,P50402,Q9UKK9,Q16181,Q6DRA6,Q14204,Q14203,Q14687,Q14444,Q16629,Q13356,Q9BYX7,P18085,Q9UPN3,Q96GX9,Q01130,O75391,Q9C0C9,O75390,P07195,Q9Y2G9,P79483,Q9NTK5,Q16630,Q15785,P24752,P38919,Q13126,Q14697,P13639,P62805,P62807,P46781,Q86VP6,P11216,P68104,P22102,Q13131,Q16881,P46778,P36969,O75368,P68363,Q6UXN9,Q9Y6Q5,Q9NY65,P31040,Q15560,P22314,Q93008,Q16891,Q9BQE3,P32119,P35626,P62826,P68133,Q9UNM6,P37802,Q29974,P68366,Q13151,Q14240,P43487,P61978,P43246,P55060,O15042,P78347,P54136,Q16666,P78344,O75347,P13667,P10398,Q04837,Q13162,Q8IZD4,Q14019,Q9Y4H4,Q9NZT2,P11021,P63096,P00338,Q96RP9,Q7L2H7,Q8N6M0,O15067,Q9BUR5,P98179,Q7KZ85,Q96PK6,Q15363,Q9BUQ8,P48741,P02788,P02787,P02786,Q15366,Q9H7D0,Q15126,Q08170,P21281,P37840,Q9NY33,Q9NXR7,P28906,P55263,P23458,P60842,P54578,Q96L92,Q8IWS0,Q6P1J9,P07108,Q9H324,P62195,P41252,Q53FD0,P46940,O94868,Q13765,P31689,P29144,O75533,P10768,P19105,P19338,Q86VH4,Q5JXB2,O43933,P29350,Q15717,P55209,P30101,Q8WXI9,Q8NBX0,O15270,Q32P51,P07339,Q13547,Q8IYT4,P34931,A3KN83,P34932,P16298,O43707,Q92540,Q04446,P08670,Q07955,Q92785,P53041,P06493,P04075,Q13310,O75746,O95758,Q96IX5,Q9P258,Q5MCW4,P63244,Q9H361,P00505,O60488,P62158,Q14651,Q9UKY7,P35606,Q13564,P14927,P31483,Q86XP3,P46736,Q05516,O60256,P63010,Q7Z388,O60496,Q9BUJ2,Q96IV0,O15460,P55884,P13804,O75964,P12955,A5A3E0,P45880,P28065,P78527,P32322,Q00059,P63267,P63261,TRFE_HUMAN,P61088,Q96AE4,Q9Y6E2,P17174,Q92598,A4D263,Q9HAP6,P47813,Q14671,E9PAV3,Q06830,P62191,P28074,Q8TDN6,Q9H6Z4,Q9Y4B4,P00519,P63272,P24941,Q9NZN3,O15226,Q9NZN4,Q9HCS7,Q9BZ11,P08238,P43686,O15228,Q7KZF4,P06899,P67809,O14672,Q92619,Q9UBB6,O00267,Q8NEY8,Q96M27,Q96JM2,P60174,Q9UJS0,Q9GIY3,Q9Y2X3,Q9ULW0,Q92614,P27348,P52565,O95202,P48047,Q92608,Q9UI08,Q9Y399,Q9NRX4,Q9P107,P15144,Q92841,Q30134,O15523,Q9UI12,P50395,Q9UI15,Q92835,Q13813,Q12965,GSTP1_HUMAN,P15104,Q9Y2Z0,P18615,P63220,P62136,P0C7P4,P05556,P07737,P04229,P49354,Q5JS13,Q9NRZ9,Q99460,Q7L576,Q9NQ79,Q6UB35,P20700,P62140,Q9UFN0,Q9ULZ3,Q30154,O95478,P0CG47,Q8WUA2,P49189,Q10567,O00462,Q13838,P52758,P0CG48,P41212,P40121,P84103,Q30167,P62318,P62312,Q10570,Q9Y2T7,Q96SB3,O00231,P53618,O00232,P19784,P53611,Q8IY18,P16035,Q8TAA3,P05141,P07320,P53621,Q12768,Q12765,Q6IA86,O00483,O60506,O00487,Q9NQ29,P42768,P62333,P61244,Q5VWZ2,Q9BZK7,P61247,P26038,P04264,P08865,P08621,Q562R1,Q13625,Q5QNW6,Q9H853,Q7Z5R6,P0CG39,P0CG38,O76094,P18669,Q9HBI0,Q96LR5,P61011,Q9Y383,Q9Y2W2,Q9Y2W1,P04632,P07900,P23396,P16615,P14678,Q9UHF7,P62750,P62993,Q96RU3,P48444,P62995,Q9GZR7,Q04917,P07910,P49773,Q9UQ88,Q69YN4,Q9HDC9,Q99880,Q96S55,Q99877,P12270,Q15154,P46013,Q15393,Q99879,Q15397,P26641,P50552,P26640,P12236,P12235,'..b',1,1,1,3,2,1,1,1,1,1,1,4,1,4,1,1,1,1,4,2,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,2,1,1,1,1,1,4,2,2,4,1,2,1,2,1,3,1,1,1,1,1,1,1,5,2,8,1,1,2,1,1,2,1,1,2,1,4,1,1,1,1,1,1,1,1,1,1,2,1,2,1,1,1,1,1,3,2,1,1,1,1,6,2,1,1,1,1,1,1,1,4,1,3,1,1,3,4,3,2,1,3,2,1,1,1,2,1,1,1,2,3,1,4,2,1,1,1,1,1,1,4,1,2,1,1,2,6,4,1,1,1,1,6,3,2,1,1,2,1,1,2,8,1,1,4,1,2,1,1,1,1,1,2,1,1,1,8,1,1,3,2,1,3,2,1,1,1,4,1,1,1,4,3,1,2,1,1,2,1,1,1,1,5,1,2,1,3,2,1,1,1,2,1,1,1,1,1,3,1,1,4,1,1,1,1,2,1,1,4,1,2,2,1,1,1,1,4,1,1,1,1,2,1,2,1,1,1,1,2,2,1,2,1,1,2,1,1,1,2,2,2,1,1,1,1,2,6,1,5,1,1,1,2,1,1,2,4,1,1,1,3,1,1,5,1,1,1,2,1,2,1,2,1,1,8\n+Total AAs,244,267,323,806,114,874,284,1235,253,536,302,1098,208,1328,418,477,406,158,149,146,318,150,460,720,300,170,266,304,367,557,170,233,1280,631,139,92,449,244,339,135,157,519,216,552,452,469,313,267,151,105,689,244,262,597,115,221,645,418,184,576,215,444,458,483,404,715,196,276,658,173,891,136,126,336,98,461,176,1107,249,233,321,449,105,265,686,239,173,422,387,418,376,354,534,762,529,1872,415,173,399,440,480,388,126,622,491,853,240,76,332,240,356,216,962,258,452,1008,427,290,342,353,245,580,115,145,533,172,209,453,268,594,138,4857,604,121,123,849,669,672,1572,334,646,597,1613,244,466,386,1273,325,381,650,622,537,134,597,505,228,341,209,480,521,250,2070,72,193,593,126,247,251,360,591,82,806,356,259,473,126,184,780,151,452,1105,233,821,176,173,535,568,1639,697,115,359,663,334,1094,525,254,219,436,164,4646,1271,1144,694,226,527,375,180,5938,204,209,227,1292,466,334,1309,266,278,478,309,162,411,239,52,858,103,126,194,403,843,441,433,574,461,160,170,114,335,313,425,383,519,272,1018,2554,757,449,142,688,216,377,378,220,266,433,305,408,200,440,868,915,620,274,588,729,869,129,645,186,148,271,515,142,160,657,654,302,241,770,242,192,1338,180,157,726,339,201,108,367,666,698,760,322,350,192,494,511,126,707,376,328,327,1154,347,483,232,331,531,123,590,398,1262,275,1657,515,215,331,1249,144,282,171,710,518,153,961,624,353,323,505,593,429,562,320,412,482,466,641,732,148,525,521,1145,702,466,201,207,499,240,418,660,571,457,58,522,527,317,631,387,670,149,629,110,877,537,140,214,819,247,550,283,880,723,412,390,612,533,873,284,103,429,1075,283,209,4097,346,214,333,375,698,152,653,201,392,860,438,137,144,1127,925,199,367,160,353,499,1467,1149,117,264,175,705,407,855,309,724,387,619,910,126,324,447,1152,731,1083,348,418,2566,167,676,266,529,783,1581,245,160,294,213,336,390,296,124,944,967,652,266,291,465,400,199,976,2452,1108,209,373,333,350,83,286,283,801,140,266,312,537,129,922,447,628,275,586,327,247,135,266,260,229,492,424,919,879,443,137,685,452,333,124,266,120,80,1443,364,815,423,953,436,350,331,1101,220,250,298,174,1233,1159,346,756,81,410,310,354,502,389,83,221,514,264,577,644,295,341,376,1134,134,241,172,1038,1075,610,254,70,201,455,389,641,955,268,854,259,997,289,1285,156,176,612,423,188,804,246,250,126,439,1147,289,126,281,126,726,530,2896,399,126,648,487,380,297,298,298,1033,756,332,479,144,248,450,234,268,144,795,353,260,319,394,718,242,261,295,391,260,126,531,305,535,586,280,521,173,898,1394,148,469,467,649,928,2490,136,377,106,2511,228,417,475,509,303,321,724,472,586,671,377,156,483,2620,651,526,439,2079,213,215,221,235,226,1265,934,149,454,1714,128,343,513,821,358,257,147,390,187,505,239,278,1531,289,266,365,432,453,271,439,206,272,221,335,115,326,266,274,333,131,287,299,532,440,318,337,404,531,126,166,96,451,176,273,435,102,753,191,747,356,524,181,450,126,301,740,452,392,459,425,176,286,447,197,153,728,490,462,296,248,1382,1985,352,304,167,286,448,215,1045,786,904,247,375,790,208,196,585,300,493,274,1246,913,1152,193,516,133,327,126,266,452,266,215,252,432,211,1104,207,217,803,401,337,63,456,253,93,1655,361,303,473,292,839,346,261,691,194,543,863,248,193,244,169,266,266,215,267,207,696,449,700,2286,392,826,341,196,709,167,300,625,967,547,2282,182,399,923,792,542,948,1014,226,272,830,414,528,144,526,106,639,374,151,67,247,612,210,159,463,211,2335,587,148,410,1047,215,126,1486,454,1508,104,219,180,254,876,353,644,151,291,193,278,643,181,200,416\n'
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diff -r 000000000000 -r e21ef020d1a6 KM Y PS/test-data/output_Substrates.csv
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+++ b/KM Y PS/test-data/output_Substrates.csv Fri Jan 11 11:06:14 2019 -0500
b
b'@@ -0,0 +1,1010 @@\n+Substrates,Species,Reference,-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7,,,,,,,,,,,Phosphosite\n+,,O00160; Q12965,,,,H,Q,V,E,Y,L,G,L,K,,,,,,,HQVEYLGLK,RVKHQVEYLGLKENI,\n+,,Q9Y6E2,,,,,,,N,Y,A,Q,V,F,N,K,,,,,NYAQVFNK,DHETIRNYAQVFNKL,\n+,,P00519,G,G,Q,Y,G,E,V,Y,E,G,V,W,K,K,,,,,GGQYGEVYEGVWKK,GGQYGEVYEGVWKKY,\n+,,A4D263,,,,,,,A,Y,E,D,V,P,W,D,K,,,,AYEDVPWDK,KSSTQKAYEDVPWDK,\n+,,Q9Y2L1,,,,A,S,L,T,Y,A,E,A,Q,L,R,,,,,ASLTYAEAQLR,NSKASLTYAEAQLRI,\n+,,P60842,,,,,D,Q,I,Y,D,I,F,Q,K,,,,,,DQIYDIFQK,RGFKDQIYDIFQKLN,\n+,,Q02543,K,S,S,G,E,I,V,Y,C,G,Q,V,F,E,K,,,,KSSGEIVYCGQVFEK,KSSGEIVYCGQVFEK,\n+,,O00232,,,,,,A,I,Y,D,T,P,C,I,Q,A,,,,AIYDTPCIQA,CKHYRAIYDTPCIQA,\n+,,Q14687,,V,D,T,S,V,H,Y,N,I,P,E,L,Q,S,,,,VDTSVHYNIPELQS,KVDTSVHYNIPELQS,\n+,,Q8WUM4,,T,P,S,N,E,L,Y,K,P,L,R,,,,,,,TPSNELYKPLR,MATFISVQLKKTS,\n+,,P26640,L,H,E,E,G,I,I,Y,R,,,,,,,,,,LHEEGIIYR,LHEEGIIYRSTRLVN,\n+,,P31939,,,,,N,G,N,Y,C,V,L,Q,M,D,Q,,,,NGNYCVLQMDQ,SKKKNGNYCVLQMDQ,\n+,,P14649; P60660,,,,,,I,L,Y,S,Q,C,G,D,V,M,,,,ILYSQCGDVM,VGDGKILYSQCGDVM,TGDGKILYSQCGDVM,\n+,,O14548,L,T,S,D,S,T,V,Y,D,Y,A,G,K,,,,,,LTSDSTVYDYAGK,LTSDSTVYDYAGKNK,\n+,,Q07864,G,S,T,L,E,E,V,Y,G,S,V,A,K,,,,,,GSTLEEVYGSVAK,GSTLEEVYGSVAKVA,\n+,,Q9UKY7,,L,Q,L,D,N,Q,Y,A,V,L,E,N,Q,K,,,,LQLDNQYAVLENQK,MQISSEKEEDDNE,\n+,,P49773,S,D,G,G,Q,S,V,Y,H,V,H,L,H,V,L,,,,SDGGQSVYHVHLHVL,SDGGQSVYHVHLHVL,\n+,,P52272,N,E,C,G,H,V,L,Y,A,D,I,K,,,,,,,NECGHVLYADIK,NECGHVLYADIKMEN,\n+,,P10768,,,,,,S,G,Y,H,Q,S,A,S,E,H,,,,SGYHQSASEH,NFISKSGYHQSASEH,\n+,,Q86XP3,,,,,K,S,E,Y,T,Q,P,T,P,I,Q,,,,KSEYTQPTPIQ,HQIRKSEYTQPTPIQ,\n+,,Q9P107,,,,,,,D,Y,Y,Q,P,L,A,A,K,,,,DYYQPLAAK,VAQQKRDYYQPLAAK,\n+,,P61088; Q5JXB2,,,,,,,I,Y,H,P,N,V,D,K,,,,,IYHPNVDK,VRFMTKIYHPNVDKL,\n+,,Q86UX7,,,,L,T,Q,L,Y,E,Q,A,R,,,,,,,LTQLYEQAR,PVRLTQLYEQARWDL,\n+,,P23284,,,,,,,H,Y,G,P,G,W,V,S,M,,,,HYGPGWVSM,ENFKLKHYGPGWVSM,\n+,,Q8WUA2,,N,T,N,Q,D,I,Y,R,,,,,,,,,,NTNQDIYR,KNTNQDIYREMGFGH,\n+,,O14920,,,,,,V,I,Y,T,Q,L,S,K,,,,,,VIYTQLSK,EKKVRVIYTQLSKTV,\n+,,GSTP1_HUMAN; P09211;P09211;,,,,A,S,C,L,Y,G,Q,L,P,K,,,,,,ASCLYGQLPK,SLKASCLYGQLPKFQ,\n+,,P62241,,Q,W,Y,E,S,H,Y,A,L,P,L,G,R,,,,,QWYESHYALPLGR,RQWYESHYALPLGRK,\n+,,Q15393,,,,,,,D,Y,I,V,V,G,S,D,S,,,,DYIVVGSDS,MAEEMVEA,\n+,,P60842,,G,F,K,D,Q,I,Y,D,I,F,Q,K,,,,,,GFKDQIYDIFQK,RGFKDQIYDIFQKLN,\n+,,P22314,,,,,A,E,N,Y,D,I,P,S,A,D,R,,,,AENYDIPSADR,SNLRAENYDIPSADR,\n+,,A3KN83; Q9Y2G9,,,,,,V,V,Y,A,S,A,T,G,A,S,,,,VVYASATGAS,LPKARVVYASATGAS,LPLARVVYASATGAS,\n+,,P23396,,E,L,A,E,D,G,Y,S,G,V,E,V,R,,,,,ELAEDGYSGVEVR,RELAEDGYSGVEVRV,\n+,,Q5JQS6,,,,S,E,T,E,Y,A,L,L,R,,,,,,,SETEYALLR,RERSETEYALLRTSV,\n+,,P07437,,,,,I,S,V,Y,Y,N,E,A,T,G,G,,,,ISVYYNEATGG,QLDRISVYYNEATGG,\n+,,Q9NQ79,,,,,S,S,P,Y,Y,A,L,R,,,,,,,SSPYYALR,VDERSSPYYALRDRQ,\n+,,Q9Y230,T,T,E,M,E,T,I,Y,D,L,G,T,K,,,,,,TTEMETIYDLGTK,TTEMETIYDLGTKMI,\n+,,P16885,,,,,,,H,Y,C,A,I,A,D,A,K,,,,HYCAIADAK,DQKWTRHYCAIADAK,\n+,,P38159; Q96E39,,,,,,D,S,Y,G,G,P,P,R,,,,,,DSYGGPPR,MVEADRPGK,LSRGRDSYGGPPRRE,\n+,,P41252,,S,D,T,P,L,I,Y,K,,,,,,,,,,SDTPLIYK,RSDTPLIYKAVPSWF,\n+,,P30086,S,G,T,V,L,S,D,Y,V,G,S,G,P,P,K,,,,SGTVLSDYVGSGPPK,SGTVLSDYVGSGPPK,\n+,,Q9NYK5,,D,A,H,A,L,I,Y,K,,,,,,,,,,DAHALIYK,KDAHALIYKDLPFET,\n+,,O43615,D,Q,D,E,L,N,P,Y,A,A,W,R,,,,,,,DQDELNPYAAWR,DQDELNPYAAWRLLD,\n+,,P62318,V,A,Q,L,E,Q,V,Y,I,R,,,,,,,,,VAQLEQVYIR,VAQLEQVYIRGSKIR,\n+,,P09651; Q32P51;Q32P51;,,,,,,,D,Y,F,E,Q,Y,G,K,,,,,DYFEQYGK,EEHHLRDYFEQYGKI,\n+,,Q07955,,E,A,G,D,V,C,Y,A,D,V,Y,R,,,,,,EAGDVCYADVYR,REAGDVCYADVYRDG,\n+,,Q9Y230,,,,,G,T,S,Y,Q,S,P,H,G,I,P,,,,GTSYQSPHGIP,TRIRGTSYQSPHGIP,\n+,,Q15717,,,,D,A,N,L,Y,I,S,G,L,P,R,,,,,DANLYISGLPR,VIKDANLYISGLPRT,\n+,,O14950; P19105,,,,G,N,F,N,Y,I,E,F,T,R,,,,,,GNFNYIEFTR,DKKGNFNYIEFTRIL,\n+,,P55263,,,,,A,G,H,Y,A,A,S,I,I,I,R,,,,AGHYAASIIIR,ECIRAGHYAASIIIR,\n+,,Q04837,,S,G,D,S,E,V,Y,Q,L,G,D,V,S,Q,,,,SGDSEVYQLGDVSQ,RSGDSEVYQLGDVSQ,\n+,,Q15814,,,,,,,L,Y,G,N,P,N,T,L,R,,,,LYGNPNTLR,SNCTVRLYGNPNTLR,\n+,,P62995,I,Y,M,G,R,P,T,Y,G,S,S,R,,,,,,,IYMGRPTYGSSR,IYMGRPTYGSSRRRD,\n+,,Q13813,,,,,E,E,L,Y,Q,N,L,T,R,,,,,,EELYQNLTR,YVTKEELYQNLTREQ,\n+,,Q7L5N7,,,K,H,L,D,E,Y,A,S,I,A,S,S,S,,,,KHLDEYASIASSS,VRKHLDEYASIASSS,\n+,,P14866,N,D,Q,D,T,W,D,Y,T,N,P,N,L,S,G,,,,NDQDTWDYTNPNLSG,NDQDTWDYTN'..b'RV,\n+,,Q9UHF7,G,D,D,T,P,V,G,Y,S,V,P,I,K,P,L,,,,GDDTPVGYSVPIKPL,GDDTPVGYSVPIKPL,\n+,,Q8NFH5,,,A,S,T,S,D,Y,Q,V,I,S,D,R,,,,,ASTSDYQVISDR,YKASTSDYQVISDRQ,\n+,,Q96A65,K,F,L,D,T,S,H,Y,S,T,A,G,S,S,S,,,,KFLDTSHYSTAGSSS,KFLDTSHYSTAGSSS,\n+,,Q02790,I,V,Y,L,K,P,S,Y,A,F,G,S,V,G,K,,,,IVYLKPSYAFGSVGK,IVYLKPSYAFGSVGK,\n+,,Q14240,,G,F,K,D,Q,I,Y,E,I,F,Q,K,,,,,,GFKDQIYEIFQK,RGFKDQIYEIFQKLN,\n+,,O00231,,T,T,A,N,A,I,Y,C,P,P,K,,,,,,,TTANAIYCPPK,RTTANAIYCPPKLQA,\n+,,P61247,,,,,,T,S,Y,A,Q,H,Q,Q,V,R,,,,TSYAQHQQVR,NQIRKTSYAQHQQVR,\n+,,Q02790,H,I,T,C,K,P,E,Y,A,Y,G,S,A,G,S,,,,HITCKPEYAYGSAGS,HITCKPEYAYGSAGS,\n+,,P09622,L,L,N,N,S,H,Y,Y,H,M,A,H,G,K,,,,,LLNNSHYYHMAHGK,LLNNSHYYHMAHGKD,\n+,,Q00325,,I,Q,T,Q,P,G,Y,A,N,T,L,R,,,,,,IQTQPGYANTLR,RIQTQPGYANTLRDA,\n+,,P62805,,R,I,S,G,L,I,Y,E,E,T,R,,,,,,,RISGLIYEETR,KRISGLIYEETRGVL,\n+,,P62191; P62195; Q8NB90;P62195;Q8NB90;,,,,G,V,L,L,Y,G,P,P,G,T,G,K,,,,GVLLYGPPGTGK,MEEEFIRNQEQ,QPKGVLLYGPPGTGK,APRGVLLYGPPGTGK,\n+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b
diff -r 000000000000 -r e21ef020d1a6 KM Y PS/test-data/psm.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/KM Y PS/test-data/psm.tabular Fri Jan 11 11:06:14 2019 -0500
[
b'@@ -0,0 +1,4351 @@\n+\tProtein(s)\tSequence\tVariable Modifications\tFixed Modifications\tSpectrum File\tSpectrum Title\tSpectrum Scan Number\tRT\tm/z\tMeasured Charge\tIdentification Charge\tTheoretical Mass\tIsotope Number\tPrecursor m/z Error [ppm]\tLocalization Confidence\tProbabilistic PTM score\tD-score\tConfident Phosphosites\t#Confident Phosphosites\tAmbiguous Phosphosites\t#Ambiguous Phosphosites\tConfidence [%]\tValidation\n+1\tP30740\tLGVQDLFNSSK\t\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 1.21 min, Period: 1, Cycle(s): 42979 (Experiment 1)\t42979\t72.404\t604.32019\t2+\t2+\t1206.6244519773002\t0\t1.1377169445543516\t\t\t\t\t\t\t\t100.0\tConfident\n+2\tP15259, P18669, Q8N0Y7\tHYGGLTGLNK\t\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 0.64 min, Period: 1, Cycle(s): 15926 (Experiment 1)\t15926\t38.245\t530.282898\t2+\t2+\t1058.5508931142201\t0\t0.32996752546837377\t\t\t\t\t\t\t\t99.73045822102425\tConfident\n+3\tP49327\tAGLYGLPR\tPhosphorylation of Y(4)\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 0.97 min, Period: 1, Cycle(s): 31918 (Experiment 1)\t31918\t57.964\t464.230042\t2+\t2+\t925.4422677895602\t1\t-0.09872263809433697\tPhosphorylation of Y (4: Very Confident)\tPhosphorylation of Y (4: 100.0)\tPhosphorylation of Y (4: 99.65034965034964)\tY4\t1\t\t0\t99.73614775725594\tConfident\n+4\tQ9NZT2\tGTGTVGRAQNYQK\tPhosphorylation of Y(11)\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 0.75 min, Period: 1, Cycle(s): 21349 (Experiment 1)\t21349\t45.224\t730.334473\t2+\t2+\t1458.6616560225305\t0\t-4.972324537127415\tPhosphorylation of Y (11: Very Confident)\tPhosphorylation of Y (11: 100.0)\tPhosphorylation of Y (11: 100.0)\tY11\t1\t\t0\t100.0\tDoubtful\n+5\tP68104, Q05639, Q5VTE0\tIGGIGTVPVGR\t\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 0.87 min, Period: 1, Cycle(s): 26949 (Experiment 1)\t26949\t52.168\t513.309326\t2+\t2+\t1024.60292868708\t0\t1.1400344498829633\t\t\t\t\t\t\t\t100.0\tConfident\n+6\tP07900\tIMKDILEK\t\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 0.74 min, Period: 1, Cycle(s): 20653 (Experiment 1)\t20653\t44.304\t495.28952\t2+\t2+\t988.5627036678802\t0\t1.8003628530197229\t\t\t\t\t\t\t\t100.0\tConfident\n+7\tP49368\tIPGGIIEDSCVLR\t\tCarbamidomethylation of C(10)\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 1.10 min, Period: 1, Cycle(s): 38940 (Experiment 1)\t38940\t66.281\t714.878845\t2+\t2+\t1427.7442498401501\t0\t-0.7782947530783138\t\t\t\t\t\t\t\t97.55434782608695\tConfident\n+8\tO75937\tLLLDQEQK\t\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 0.77 min, Period: 1, Cycle(s): 21774 (Experiment 1)\t21774\t45.918\t493.779602\t2+\t2+\t985.5444107514504\t0\t0.2433423567884188\t\t\t\t\t\t\t\t99.73474801061008\tConfident\n+9\tO43390\tSTAYEDYYYHPPPR\tPhosphorylation of Y(4)\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 0.85 min, Period: 1, Cycle(s): 25835 (Experiment 1)\t25835\t50.883\t613.586731\t3+\t3+\t1837.7348805324402\t0\t1.8921930883410392\tPhosphorylation of Y (4: Random)\tPhosphorylation of Y (8: 0.0, 9: 0.0)\tPhosphorylation of Y (8: 0.0)\t\t0\tY4-{Y4 Y7 Y8 Y9}\t1\t100.0\tConfident\n+10\tP46781\tLFEGNALLR\t\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 1.07 min, Period: 1, Cycle(s): 37446 (Experiment 1)\t37446\t64.463\t516.795837\t'..b'dent\n+4341\tP20290\tVQASLAANTFTITGHAETK\t\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 0.95 min, Period: 1, Cycle(s): 31265 (Experiment 1)\t31265\t57.195\t654.009827\t3+\t3+\t1959.0061545081005\t0\t0.7630326762984392\t\t\t\t\t\t\t\t100.0\tConfident\n+4342\tP53621\tTLDLPIYVTR\tPhosphorylation of Y(7)\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 1.31 min, Period: 1, Cycle(s): 45860 (Experiment 1)\t45860\t78.479\t635.827393\t2+\t2+\t1269.63700441448\t0\t2.5389438460307914\tPhosphorylation of Y (7: Very Confident)\tPhosphorylation of Y (7: 100.0)\tPhosphorylation of Y (7: 99.03069466882067)\tY7\t1\t\t0\t99.7289972899729\tConfident\n+4343\tP31948\tEGLQNMEAR\t\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 0.68 min, Period: 1, Cycle(s): 17669 (Experiment 1)\t17669\t40.518\t524.248535\t2+\t2+\t1046.4814932250601\t0\t0.9764856237191194\t\t\t\t\t\t\t\t99.45945945945947\tConfident\n+4344\tP13796\tVYALPEDLVEVNPK\tPhosphorylation of Y(2)\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 1.27 min, Period: 1, Cycle(s): 44840 (Experiment 1)\t44840\t76.211\t833.912842\t2+\t2+\t1664.8062545675507\t1\t0.9129121847609198\tPhosphorylation of Y (2: Very Confident)\tPhosphorylation of Y (2: 100.0)\tPhosphorylation of Y (2: 100.0)\tY2\t1\t\t0\t100.0\tConfident\n+4345\tP61978\tDYDDMSPR\t\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 0.68 min, Period: 1, Cycle(s): 18030 (Experiment 1)\t18030\t41.017\t499.698334\t2+\t2+\t997.3811104774502\t0\t1.0051964028315887\t\t\t\t\t\t\t\t100.0\tConfident\n+4346\tP31930\tADLTEYLSTHYK\tPhosphorylation of Y(11)\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 1.03 min, Period: 1, Cycle(s): 35096 (Experiment 1)\t35096\t61.632\t507.561005\t3+\t3+\t1519.6595903338603\t0\t1.0476687264289857\tPhosphorylation of Y (11: Doubtfull)\tPhosphorylation of Y (11: 5.275914931706089)\tPhosphorylation of Y (6: 98.08027923211169)\t\t0\tY11-{Y6 Y11}\t1\t99.25925925925925\tConfident\n+4347\tP53396\tEILIPVFK\t\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 1.30 min, Period: 1, Cycle(s): 45554 (Experiment 1)\t45554\t77.784\t479.802368\t2+\t2+\t957.5899043918903\t0\t0.29040557666356864\t\t\t\t\t\t\t\t96.22641509433963\tConfident\n+4348\tP25789\tVEIATLTR\t\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 0.84 min, Period: 1, Cycle(s): 25563 (Experiment 1)\t25563\t50.57\t451.768829\t2+\t2+\t901.5232813840503\t0\t-0.195141440164142\t\t\t\t\t\t\t\t99.7289972899729\tConfident\n+4349\tQ9H6Z4\tDTGQLYAALHHR\tPhosphorylation of Y(6)\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 0.86 min, Period: 1, Cycle(s): 26291 (Experiment 1)\t26291\t51.409\t731.333557\t2+\t2+\t1460.6561767192704\t0\t-2.471952724010381\tPhosphorylation of Y (6: Very Confident)\tPhosphorylation of Y (6: 100.0)\tPhosphorylation of Y (6: 100.0)\tY6\t1\t\t0\t100.0\tConfident\n+4350\tP06899, P23527, P33778, Q16778, Q6DN03, Q6DRA6, Q8N257\tESYSIYVYK\tPhosphorylation of Y(6)\t\tProteinPilot formatted MGF of data 42.mgf\tFile: llparker_perez512_20180218_16704_ABL_PME_TR3_PLUS, Sample: Sample001 (sample number 1), Elution: 1.03 min, Period: 1, Cycle(s): 35269 (Experiment 1)\t35269\t61.833\t616.267639\t2+\t2+\t1230.5209716027305\t0\t-0.2000237312796789\tPhosphorylation of Y (6: Random)\tPhosphorylation of Y (6: 0.0, 8: 0.0)\tPhosphorylation of Y (6: 26.201045899998782)\t\t0\tY6-{Y3 Y6 Y8}\t1\t99.72972972972973\tConfident\n'