changeset 0:eac197ac2fb2 draft

Uploaded

Binary file transposy/._NMF.xml has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/transposy/.shed.yml	Tue Feb 27 11:29:18 2018 -0500
@@ -0,0 +1,8 @@
+categories: [Computational chemistry]
+description: Transposy transposes a data frame
+homepage_url: https://pubs.acs.org/doi/abs/10.1021/ja507164a
+long_description: This tool is only intended to perform a small but necessary data cleanup step during the KinaMine-KinaTest process
+
+name: transposy.R
+owner: blank121
+remote_repository_url: https://github.umn.edu/blank121/Transposy

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/transposy/NMF.xml	Tue Feb 27 11:29:18 2018 -0500
@@ -0,0 +1,47 @@
+<tool id="kinamine_java" name="Negative-Motif-Finder 7_to_7" version="1.0.0">
+    <description>discover unphosphorylated substrates</description>
+    <requirements>
+       <requirement type="package">R</requirement>
+    </requirements>
+    <command><![CDATA[
+		ln -s '$FASTA' input1.tabular && 
+        ln -s '$positives' input2.csv &&
+		ln -s '$SBF' input3.csv &&
+        Rscript '$__tool_directory__/NMF.R'
+    ]]></command>
+    <inputs>
+		<param format="csv" name="SBF" type="data" label="Substrate Background Frequency"/>
+        <param format="tabular" name="FASTA" type="data" label="Human Proteome Reference"/>
+        <param format="csv" name="positives" type="data" label="Positive/Phosphorylated Substrate List"/>
+    </inputs>      
+    <outputs>
+        <data format="csv" name="Negatives" from_work_dir="output1.csv" label="Negative Motifs.csv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="FASTA" ftype="csv" value="reference.csv"/>
+            <param name="positives" ftype="csv" value="substrates.csv"/>
+            <param name="SBF" ftype="csv" value="SBF.csv"/>
+			<output name="Negatives" file="negatives.csv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Using the output from KinaMine, plus the Uniprot file that was used with KinaMine, this program finds all Y-centered motifs which *could* have been present as positive motifs but were not seen by the Mass Spec
+This tool is intended to be used in conjunction with KinaMine 7-7 and Kinatest.R, the three together creating a GalaxyP version of the KINATEST-ID workbook.
+===========
+Inputs
+===========
+**Substrate Background Frequency**
+**Positive/Phosphorylated Substrate List**
+These two come directly from the KinaMine output
+
+**Human Proteome Reference**
+This should be a tabularized version of a FASTA taken from the Reviewed Human Uniprot database, consisting of all human proteins plus a list of common Mass Spectrometry contaminants.
+This file should be created by using the same FASTA file used for KinaMine and running FASTA to Tabular on it using GalaxyP
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1021/ja507164a</citation>
+    </citations>
+</tool>
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/transposy/test-data/outputy.csv	Tue Feb 27 11:29:18 2018 -0500
@@ -0,0 +1,332 @@
+"Amino Acids","A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y","Properties","Hydrophobic","Polar","Small","Negative","Postive","Amide","Large Aliphatic","Small Aliphatic","Aromatic","Hydroxy","X","Number of Y","Number of pY","Total AAs"
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/transposy/test-data/transposy.csv	Tue Feb 27 11:29:18 2018 -0500
@@ -0,0 +1,36 @@
+Amino Acids,sp|Q14204|DYHC1_HUMAN,sp|Q08170|SRSF4_HUMAN,sp|Q13813|SPTN1_HUMAN,sp|E9PAV3|NACAM_HUMAN,sp|P51659|DHB4_HUMAN,sp|P26599|PTBP1_HUMAN,sp|Q9NR30|DDX21_HUMAN,sp|Q9NVA2|SEP11_HUMAN,sp|P14927|QCR7_HUMAN,sp|P51531|SMCA2_HUMAN,sp|Q9BQE3|TBA1C_HUMAN,sp|Q92608|DOCK2_HUMAN,sp|P42684|ABL2_HUMAN,sp|Q99426|TBCB_HUMAN,sp|Q9NWQ8|PHAG1_HUMAN,sp|P48643|TCPE_HUMAN,sp|Q92841|DDX17_HUMAN,sp|Q9GIY3|2B1E_HUMAN,sp|O00487|PSDE_HUMAN,sp|P08238|HS90B_HUMAN,sp|P60174|TPIS_HUMAN,sp|P31939|PUR9_HUMAN,sp|P31689|DNJA1_HUMAN,sp|P23193|TCEA1_HUMAN,sp|P62750|RL23A_HUMAN,sp|Q96QV6|H2A1A_HUMAN,sp|P11940|PABP1_HUMAN,sp|P62807|H2B1C_HUMAN,sp|P62312|LSM6_HUMAN,sp|P20618|PSB1_HUMAN,sp|Q15056|IF4H_HUMAN,sp|O00567|NOP56_HUMAN,sp|Q8TCJ2|STT3B_HUMAN,sp|P63220|RS21_HUMAN,sp|P52272|HNRPM_HUMAN,sp|Q07955|SRSF1_HUMAN,sp|Q9BTM1|H2AJ_HUMAN,sp|P50914|RL14_HUMAN,sp|P22234|PUR6_HUMAN,sp|P57053|H2BFS_HUMAN,sp|P62701|RS4X_HUMAN,sp|P10809|CH60_HUMAN,sp|P55884|EIF3B_HUMAN,sp|P23284|PPIB_HUMAN,sp|Q4VC31|CCD58_HUMAN,sp|Q86UX7|URP2_HUMAN,sp|Q5JNZ5|RS26L_HUMAN,sp|O75390|CISY_HUMAN,sp|P30101|PDIA3_HUMAN,sp|Q07020|RL18_HUMAN,sp|Q99798|ACON_HUMAN,sp|Q9Y6E2|BZW2_HUMAN,sp|P48047|ATPO_HUMAN,sp|P07948|LYN_HUMAN,sp|Q9Y5Z4|HEBP2_HUMAN,sp|Q9Y6Q5|AP1M2_HUMAN,sp|P0DP23|CALM1_HUMAN,sp|Q14141|SEPT6_HUMAN,sp|Q93077|H2A1C_HUMAN,sp|P60842|IF4A1_HUMAN,sp|P62917|RL8_HUMAN,sp|P63010|AP2B1_HUMAN,sp|Q8NBX0|SCPDL_HUMAN,sp|Q9P0V9|SEP10_HUMAN,sp|Q8WXX5|DNJC9_HUMAN,sp|P22314|UBA1_HUMAN,sp|P10696|PPBN_HUMAN,sp|P62979|RS27A_HUMAN,sp|P22626|ROA2_HUMAN,sp|Q5VTE0|EF1A3_HUMAN,sp|P00558|PGK1_HUMAN,sp|Q71U36|TBA1A_HUMAN,sp|P63244|RACK1_HUMAN,sp|Q13200|PSMD2_HUMAN,sp|P07737|PROF1_HUMAN,sp|Q9Y5V0|ZN706_HUMAN,sp|P07858|CATB_HUMAN,sp|P26038|MOES_HUMAN,sp|Q12906|ILF3_HUMAN,sp|Q8TAQ2|SMRC2_HUMAN,sp|P83881|RL36A_HUMAN,sp|P32119|PRDX2_HUMAN,sp|Q16778|H2B2E_HUMAN,sp|Q02790|FKBP4_HUMAN,sp|P78527|PRKDC_HUMAN,sp|P05141|ADT2_HUMAN,sp|P11310|ACADM_HUMAN,sp|Q10567|AP1B1_HUMAN,sp|P54136|SYRC_HUMAN,sp|P49458|SRP09_HUMAN,sp|P46781|RS9_HUMAN,sp|Q969H8|MYDGF_HUMAN,sp|O60814|H2B1K_HUMAN,sp|P62906|RL10A_HUMAN,sp|Q6FI13|H2A2A_HUMAN,sp|P31942|HNRH3_HUMAN,sp|Q6P2Q9|PRP8_HUMAN,sp|P18124|RL7_HUMAN,sp|P19105|ML12A_HUMAN,sp|Q99878|H2A1J_HUMAN,sp|P23528|COF1_HUMAN,sp|Q07666|KHDR1_HUMAN,sp|Q96IX5|USMG5_HUMAN,sp|P62318|SMD3_HUMAN,sp|P60660|MYL6_HUMAN,sp|Q9Y617|SERC_HUMAN,sp|P60709|ACTB_HUMAN,sp|P30086|PEBP1_HUMAN,sp|P51532|SMCA4_HUMAN,sp|Q13263|TIF1B_HUMAN,sp|P17980|PRS6A_HUMAN,sp|P38159|RBMX_HUMAN,sp|P23396|RS3_HUMAN,sp|P38919|IF4A3_HUMAN,sp|Q13162|PRDX4_HUMAN,sp|P26639|SYTC_HUMAN,sp|Q13242|SRSF9_HUMAN,sp|P53621|COPA_HUMAN,sp|P55060|XPO2_HUMAN,sp|Q92922|SMRC1_HUMAN,sp|Q15393|SF3B3_HUMAN,sp|Q9UKY7|CDV3_HUMAN,sp|Q9UBQ7|GRHPR_HUMAN,sp|O75347|TBCA_HUMAN,sp|P78347|GTF2I_HUMAN,sp|P12004|PCNA_HUMAN,sp|Q12931|TRAP1_HUMAN,sp|Q9UDY4|DNJB4_HUMAN,sp|P62987|RL40_HUMAN,sp|Q16881|TRXR1_HUMAN,sp|Q9BZZ5|API5_HUMAN,sp|Q6DN03|H2B2C_HUMAN,sp|Q01130|SRSF2_HUMAN,sp|Q9P258|RCC2_HUMAN,sp|P19338|NUCL_HUMAN,sp|P14866|HNRPL_HUMAN,sp|O14910|LIN7A_HUMAN,sp|P18669|PGAM1_HUMAN,sp|Q92499|DDX1_HUMAN,sp|Q9H361|PABP3_HUMAN,sp|O00571|DDX3X_HUMAN,sp|Q13595|TRA2A_HUMAN,sp|P45880|VDAC2_HUMAN,sp|P68363|TBA1B_HUMAN,sp|Q14240|IF4A2_HUMAN,sp|Q9NUP9|LIN7C_HUMAN,sp|P09651|ROA1_HUMAN,sp|P11142|HSP7C_HUMAN,sp|P61978|HNRPK_HUMAN,sp|Q9UKM9|RALY_HUMAN,sp|P0DMV8|HS71A_HUMAN,sp|Q6UXN9|WDR82_HUMAN,sp|P23246|SFPQ_HUMAN,sp|P47756|CAPZB_HUMAN,sp|Q96AE4|FUBP1_HUMAN,sp|P08754|GNAI3_HUMAN,sp|Q8TEM1|PO210_HUMAN,sp|Q15181|IPYR_HUMAN,sp|A6NHR9|SMHD1_HUMAN,sp|P27348|1433T_HUMAN,sp|O43390|HNRPR_HUMAN,sp|P35579|MYH9_HUMAN,sp|P07900|HS90A_HUMAN,sp|P14625|ENPL_HUMAN,sp|O00483|NDUA4_HUMAN,sp|P63096|GNAI1_HUMAN,sp|P06733|ENOA_HUMAN,sp|P0DP25|CALM3_HUMAN,sp|P61313|RL15_HUMAN,sp|P68104|EF1A1_HUMAN,sp|Q99880|H2B1L_HUMAN,sp|Q9Y2W1|TR150_HUMAN,sp|Q5Y7A7|2B1D_HUMAN,sp|P46782|RS5_HUMAN,sp|P26641|EF1G_HUMAN,sp|P62277|RS13_HUMAN,sp|Q9BXY0|MAK16_HUMAN,sp|Q13151|ROA0_HUMAN,sp|Q9BUR5|MIC26_HUMAN,sp|Q8NB90|SPAT5_HUMAN,sp|Q7L5N7|PCAT2_HUMAN,sp|Q16531|DDB1_HUMAN,sp|P61604|CH10_HUMAN,sp|P06576|ATPB_HUMAN,sp|Q16629|SRSF7_HUMAN,sp|P58876|H2B1D_HUMAN,sp|P62851|RS25_HUMAN,sp|P55209|NP1L1_HUMAN,sp|Q9HAP6|LIN7B_HUMAN,sp|P55072|TERA_HUMAN,sp|Q9NSD9|SYFB_HUMAN,sp|Q96GX9|MTNB_HUMAN,sp|Q13765|NACA_HUMAN,sp|P55084|ECHB_HUMAN,sp|P08621|RU17_HUMAN,sp|P04229|2B11_HUMAN,sp|Q9HCS7|SYF1_HUMAN,sp|Q9Y2X3|NOP58_HUMAN,sp|P62195|PRS8_HUMAN,sp|P62140|PP1B_HUMAN,sp|P04899|GNAI2_HUMAN,sp|P84103|SRSF3_HUMAN,sp|O95573|ACSL3_HUMAN,sp|P33991|MCM4_HUMAN,sp|P61244|MAX_HUMAN,sp|O75368|SH3L1_HUMAN,sp|P61981|1433G_HUMAN,sp|Q15717|ELAV1_HUMAN,sp|O15042|SR140_HUMAN,sp|P04075|ALDOA_HUMAN,sp|P62258|1433E_HUMAN,sp|Q93079|H2B1H_HUMAN,sp|Q96KK5|H2A1H_HUMAN,sp|Q15785|TOM34_HUMAN,sp|P29401|TKT_HUMAN,sp|O94905|ERLN2_HUMAN,sp|P12956|XRCC6_HUMAN,sp|Q5JQS6|GSAML_HUMAN,sp|O14617|AP3D1_HUMAN,sp|Q9H3P7|GCP60_HUMAN,sp|Q13547|HDAC1_HUMAN,sp|P36578|RL4_HUMAN,sp|P06899|H2B1J_HUMAN,sp|P00390|GSHR_HUMAN,sp|P62191|PRS4_HUMAN,sp|Q5QNW6|H2B2F_HUMAN,sp|P63261|ACTG_HUMAN,sp|Q9UL46|PSME2_HUMAN,sp|P00505|AATM_HUMAN,sp|P55795|HNRH2_HUMAN,sp|P25685|DNJB1_HUMAN,sp|P23526|SAH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+Large Aliphatic,16.46577701,4.251012146,14.52265372,9.047160731,14.67391304,15.44256121,11.87739464,13.28671329,15.31531532,13.58490566,12.91759465,16.39344262,11.33671743,10.24590164,11.11111111,17.00554529,11.24828532,11.27819549,14.51612903,15.19337017,12.23776224,14.69594595,13.09823678,11.96013289,14.1025641,18.32061069,9.748427673,9.523809524,16.25,14.93775934,7.661290323,15.31986532,15.73849879,12.04819277,11.09589041,5.241935484,17.05426357,6.976744186,15.76470588,9.523809524,17.11026616,15.88132635,11.3022113,12.03703704,13.19444444,16.64167916,7.826086957,16.30901288,12.87128713,12.76595745,16.28205128,15.99045346,15.49295775,14.6484375,10.24390244,15.8392435,11.40939597,14.28571429,16.92307692,17.24137931,10.50583658,18.35645678,14.91841492,14.0969163,11.53846154,13.89413989,13.72180451,13.46153846,5.382436261,12.12121212,13.66906475,13.08203991,14.82649842,16.62995595,12.14285714,6.578947368,10.61946903,13.51819757,9.060402685,10.29654036,8.490566038,13.63636364,10.31746032,13.07189542,17.65988372,14.09395973,13.06413302,17.80821918,17.72727273,10.46511628,17.5257732,8.092485549,9.523809524,16.12903226,16.15384615,7.514450867,16.44539615,16.53225806,11.69590643,17.1875,13.85542169,8.803611738,13.79310345,14.28571429,11.25827815,15.40540541,14.66666667,11.76470588,12.62902247,10.65868263,16.85649203,3.836317136,14.81481481,17.03163017,18.08118081,14.2461964,7.692307692,15.93137255,20.49433574,10.04524887,15.52999178,4.651162791,17.98780488,15.74074074,12.1242485,16.47509579,16.90340909,13.05637982,17.96875,14.48382126,17.55725191,8.808290155,2.714932127,11.11111111,6.338028169,8.998302207,12.87553648,15.35433071,13.91891892,9.508716323,11.78247734,3.546099291,12.24489796,13.08203991,17.44471744,13.19796954,4.301075269,13.62229102,13.82289417,11.11111111,14.3525741,14.05750799,6.223479491,16.96750903,9.161490683,14.97175141,15.68627451,11.41868512,16.35910224,15.91836735,8.68878357,15.56122449,15.30054645,13.69863014,17.28395062,14.97175141,14.51612903,11.40939597,11.2745098,12.12121212,10.31746032,4.293193717,11.27819549,15.19607843,10.29748284,18.54304636,13.33333333,5.245901639,14.64646465,18.14109742,16.36029412,17.28070175,12.74509804,15.87901701,5.042016807,9.523809524,12.8,12.02046036,14.00966184,15.8808933,18.50594228,11.98347107,9.76744186,13.71308017,6.636155606,12.40601504,14.26900585,15.6899811,17.73399015,17.12538226,14.36619718,5.487804878,16.66666667,16.22247972,10.625,9.649122807,13.76518219,12.57668712,10.68999028,14.83516484,15.68627451,9.523809524,17.1875,13.26860841,14.92776886,15.33923304,16.25615764,8.888888889,16.13183001,10.03787879,11.2033195,13.1147541,10.31746032,13.79310345,16.59090909,9.523809524,14.93333333,16.73640167,13.48837209,8.017817372,11.76470588,16.2037037,12.21498371,8.163265306,12.78538813,17.30496454,14.89141675,18.64035088,11.96969697,11.25827815,8.823529412,13.45755694,14.8018648,20.96069869,13.69863014,13.87755102,10.31746032,11.65413534,9.427609428,12.84046693,14.71698113,17.86283892,16.84665227,8.536585366,14.1509434,17.87878788,13.59223301,7.826086957,15.1459854,16.30434783,9.523809524,14.3525741,13.16725979,11.27819549,9.375,3.720930233,11.88118812,15.05376344,17.42243437,6.686046512,11.62790698,15.58935361,12.74509804,10.34482759,3.349282297,18.37349398,16.63652803,18.57142857,11.40939597,12.56281407,13.81578947,14.36464088,14.18181818,15.06849315,16.2086818,13.77952756,11.11111111,13.62637363,13.55263158,16.92307692,11.26126126,13.5678392,12.20338983,14.11483254,18.63354037,11.27819549,10.97560976,9.523809524,15.36643026,15.02145923,17.39130435,17.54385965,13.94230769,9.090909091,16.8358209,3.968253968,11.44278607,12.5,21.02189781,15.6626506,16.27906977,19.15351506,14.42307692,8.240534521,15.53398058,13.00813008,17.99485861,13.29113924,11.45251397,10.34482759,9.010152284,10.31746032,14.75409836,18.57585139,17.29957806,11.66666667,12.04620462,13.07420495,13.82113821,11.27819549,8.571428571
+Small Aliphatic,18.76883341,13.56275304,18.2038835,24.54282964,27.44565217,24.10546139,20.30651341,16.55011655,14.41441441,15.97484277,23.60801782,15.24590164,22.75803723,24.18032787,17.82407407,23.10536044,22.77091907,22.93233083,23.87096774,15.74585635,30.41958042,26.35135135,20.1511335,15.94684385,21.15384615,26.71755725,23.74213836,23.01587302,21.25,23.23651452,23.79032258,20.03367003,21.42857143,26.5060241,31.23287671,25,28.68217054,32.09302326,21.41176471,23.01587302,20.53231939,29.66841187,20.27027027,27.77777778,17.36111111,19.04047976,23.47826087,22.74678112,20.79207921,20.74468085,22.94871795,18.61575179,24.88262911,17.96875,19.51219512,19.38534279,19.46308725,16.58986175,30,18.96551724,31.51750973,19.53041622,24.00932401,15.19823789,20.76923077,22.02268431,27.2556391,15.38461538,32.01133144,27.48917749,28.77697842,23.72505543,20.18927445,23.23788546,27.85714286,19.73684211,21.82890855,15.7712305,26.84563758,20.92257002,16.98113208,25.25252525,22.22222222,20.69716776,17.12693798,29.19463087,26.12826603,21.28556375,18.48484848,19.76744186,20.6185567,30.05780347,23.80952381,18.89400922,30,32.08092486,15.20342612,18.5483871,13.4502924,28.90625,21.68674699,24.15349887,22.4137931,26.19047619,23.8410596,25.67567568,21.06666667,20.85561497,18.15421979,25.86826347,20.50113895,22.25063939,27.16049383,19.22141119,19.92619926,17.28907331,21.26696833,20.4248366,16.16889804,20.63348416,22.02136401,28.68217054,25,16.66666667,19.33867735,20.68965517,19.17613636,18.39762611,14.0625,26.04006163,18.51145038,18.13471503,15.38461538,28.16091954,26.33802817,25.29711375,24.03433476,21.65354331,22.2972973,24.08874802,21.75226586,17.0212766,23.80952381,23.50332594,19.41031941,26.39593909,32.52688172,23.06501548,19.65442765,28.43137255,24.49297972,18.21086262,23.76237624,16.24548736,28.88198758,18.36158192,24.74827769,20.41522491,17.70573566,17.55102041,24.80252765,16.73469388,14.20765027,16.18929016,16.04938272,19.20903955,26.26728111,19.46308725,21.56862745,27.48917749,22.22222222,14.86910995,22.93233083,23.03921569,20.36613272,19.86754967,12.33333333,39.3442623,20.70707071,21.83650616,22.24264706,20.35087719,33.33333333,29.30056711,16.80672269,22.22222222,24,14.83375959,26.57004831,22.45657568,19.35483871,21.07438017,23.72093023,25.94936709,16.93363844,22.93233083,18.24561404,20.2268431,21.42857143,17.43119266,18.5915493,15.24390244,19.72222222,18.77172654,13.125,23.68421053,18.62348178,22.6993865,12.73080661,25.82417582,18.82352941,23.01587302,29.6875,20.71197411,24.71910112,22.41887906,15.43513957,10.37037037,16.9991327,20.45454545,18.67219917,24.59016393,23.01587302,27.39463602,19.09090909,23.01587302,20.8,19.24686192,25.11627907,26.05790646,20.29411765,24.76851852,21.17263844,20.40816327,32.87671233,20.42553191,18.61427094,15.35087719,22.27272727,27.81456954,21.89542484,16.563147,22.96037296,15.72052402,21.46118721,19.59183673,22.22222222,22.55639098,22.8956229,23.92996109,17.61006289,19.93620415,22.2462203,19.51219512,21.06918239,16.66666667,32.03883495,24.34782609,26.64233577,16.07142857,22.22222222,24.49297972,23.84341637,22.55639098,21.25,16.27906977,22.77227723,20.43010753,13.72315036,13.95348837,14.53488372,21.29277567,19.11764706,17.24137931,14.83253589,23.4939759,28.02893309,22.38095238,19.46308725,21.6080402,23.02631579,21.27071823,22.90909091,25.34246575,24.89048188,21.06299213,20.63492063,23.07692308,22.23684211,30,22.07207207,20.60301508,24.06779661,21.05263158,16.97722567,22.93233083,18.29268293,22.22222222,18.20330969,15.66523605,20.86956522,20.61403509,17.78846154,17.61363636,19.10447761,34.39153439,14.92537313,14.28571429,15.91240876,17.26907631,29.45736434,18.57962697,12.5,26.72605791,29.12621359,13.41463415,18.50899743,17.72151899,23.74301676,17.93103448,25.50761421,22.22222222,30.91334895,16.09907121,19.54992968,19.28571429,25.57755776,23.67491166,17.07317073,22.55639098,23.80952381
+Aromatic,8.243650452,4.048582996,6.715210356,1.684311838,8.288043478,6.403013183,5.874840358,7.459207459,12.61261261,5.471698113,9.576837416,9.726775956,6.768189509,9.836065574,4.398148148,3.696857671,7.818930041,11.27819549,5.806451613,7.458563536,7.342657343,7.094594595,6.04534005,4.318936877,5.128205128,3.053435115,7.547169811,5.555555556,8.75,9.128630705,8.870967742,5.555555556,14.04358354,7.228915663,4.383561644,9.274193548,3.100775194,6.046511628,7.764705882,5.555555556,7.224334601,3.141361257,9.705159705,10.18518519,5.555555556,8.845577211,5.217391304,8.798283262,10.0990099,5.85106383,6.794871795,9.546539379,4.694835681,10.3515625,9.756097561,10.40189125,6.711409396,7.142857143,3.076923077,7.142857143,5.447470817,6.723585912,10.72261072,7.929515419,7.307692308,8.695652174,7.518796992,7.051282051,11.898017,6.70995671,5.755395683,9.534368071,8.517350158,6.27753304,7.857142857,3.947368421,11.79941003,6.585788562,6.599552573,5.518945634,7.547169811,10.60606061,5.555555556,8.496732026,8.793604651,12.41610738,9.026128266,6.322444679,8.636363636,8.139534884,6.701030928,10.98265896,5.555555556,6.451612903,3.076923077,11.84971098,11.43468951,9.274193548,9.941520468,3.125,7.228915663,6.997742664,13.79310345,3.968253968,7.947019868,8.918918919,8.533333333,9.625668449,5.221615058,4.431137725,4.783599089,8.695652174,5.761316872,7.299270073,10.33210332,10.65006916,13.12217195,8.905228758,9.47476828,5.972850679,8.463434675,4.651162791,5.182926829,3.703703704,7.915831663,6.130268199,7.8125,9.495548961,3.90625,7.550077042,7.824427481,7.25388601,5.882352941,7.279693487,5.070422535,8.658743633,3.862660944,8.267716535,7.972972973,7.606973059,9.365558912,9.929078014,9.863945578,9.534368071,7.862407862,4.060913706,11.55913978,6.346749226,7.127429806,5.555555556,6.55226209,11.50159744,5.091937765,6.859205776,6.055900621,9.88700565,7.154213037,10.38062284,7.780548628,7.755102041,9.952606635,4.744897959,7.37704918,7.97011208,13.58024691,9.88700565,7.142857143,6.711409396,10.29411765,6.70995671,5.555555556,7.329842932,10.90225564,5.882352941,13.50114416,6.622516556,8,10.16393443,12.62626263,5.375139978,8.823529412,7.807017544,7.843137255,5.482041588,7.983193277,5.555555556,4,8.184143223,4.347826087,5.831265509,8.149405772,8.26446281,2.325581395,7.594936709,5.034324943,10.52631579,10.40935673,5.103969754,4.187192118,10.39755352,9.577464789,7.317073171,9.027777778,5.677867903,4.375,10.52631579,7.692307692,9.202453988,6.219630709,6.593406593,7.450980392,5.555555556,3.125,6.472491909,7.223113965,8.554572271,8.702791461,5.925925926,5.290546401,8.143939394,10.37344398,5.152224824,5.555555556,6.32183908,4.545454545,5.555555556,8.533333333,7.949790795,9.302325581,11.35857461,8.823529412,7.407407407,8.794788274,10.20408163,7.762557078,15.03546099,11.06514995,6.578947368,9.242424242,3.311258278,4.901960784,7.453416149,7.342657343,3.930131004,6.849315068,7.755102041,5.555555556,11.27819549,10.77441077,7.587548638,7.547169811,7.177033493,4.967602592,6.707317073,8.805031447,10.60606061,5.825242718,5.217391304,5.656934307,5.434782609,5.555555556,6.55226209,4.982206406,10.90225564,7.5,8.372093023,8.118811881,6.451612903,6.92124105,6.104651163,9.88372093,9.505703422,8.333333333,6.206896552,7.655502392,6.325301205,5.786618445,10,6.711409396,11.05527638,9.868421053,8.839779006,5.090909091,7.534246575,7.009159697,8.858267717,5.555555556,7.692307692,11.18421053,3.076923077,9.684684685,8.040201005,9.152542373,10.52631579,6.211180124,12.40601504,10.36585366,5.555555556,10.40189125,5.150214592,6.086956522,9.649122807,7.692307692,11.36363636,9.611940299,11.11111111,5.970149254,12.5,3.941605839,6.425702811,3.100775194,7.890961263,10.57692308,11.35857461,10.67961165,9.756097561,5.655526992,9.493670886,3.351955307,6.206896552,2.664974619,5.555555556,4.683840749,10.21671827,8.298171589,6.904761905,9.570957096,11.30742049,7.723577236,11.65413534,10
+Hydroxy,10.99870857,25.70850202,9.66828479,23.43599615,11.54891304,13.1826742,12.77139208,11.18881119,3.603603604,10.50314465,11.58129176,11.8579235,15.73604061,12.70491803,18.98148148,9.611829945,12.07133059,15.03759398,9.35483871,11.32596685,10.48951049,11.99324324,6.297229219,15.28239203,7.051282051,9.160305344,10.8490566,17.46031746,8.75,14.10788382,11.69354839,13.63636364,12.95399516,9.638554217,6.301369863,14.11290323,8.527131783,6.511627907,12.23529412,16.66666667,10.2661597,10.29668412,10.56511057,9.722222222,11.11111111,10.64467766,8.695652174,12.66094421,9.900990099,12.23404255,10.8974359,10.50119332,15.96244131,10.7421875,14.63414634,13.71158392,10.73825503,11.75115207,6.923076923,11.8226601,7.392996109,11.09925293,13.51981352,12.55506608,8.461538462,11.24763705,12.40601504,10.8974359,10.4815864,11.03896104,9.832134293,11.30820399,19.24290221,10.46255507,15,9.210526316,12.38938053,8.145580589,12.52796421,12.19110379,8.490566038,10.1010101,17.46031746,10.02178649,12.35465116,9.731543624,8.551068884,11.80189673,8.939393939,9.302325581,6.18556701,15.02890173,16.66666667,9.677419355,6.923076923,8.092485549,10.23554604,5.241935484,11.11111111,7.8125,11.44578313,10.60948081,17.24137931,7.936507937,8.609271523,10,13.6,12.8342246,11.05039466,14.01197605,8.883826879,18.67007673,9.465020576,12.16545012,11.0701107,9.128630705,10.40723982,10.62091503,11.32852729,10.40723982,11.91454396,14.34108527,11.58536585,2.777777778,12.3246493,14.17624521,12.35795455,10.97922849,9.375,10.93990755,11.45038168,16.58031088,24.88687783,12.45210728,10.42253521,10.18675722,11.58798283,8.267716535,10,12.36133122,14.95468278,21.9858156,18.36734694,11.52993348,10.56511057,9.644670051,14.51612903,12.69349845,12.0950324,13.39869281,11.70046802,15.97444089,8.486562942,12.27436823,7.919254658,12.14689266,15.63328034,8.30449827,11.52119701,13.06122449,7.898894155,8.163265306,11.61202186,12.95143213,7.407407407,11.01694915,10.13824885,10.73825503,8.333333333,11.25541126,18.25396825,20.52356021,15.03759398,10.78431373,11.67048055,11.25827815,11,12.13114754,12.12121212,11.7581187,12.5,13.59649123,8.823529412,11.15311909,21.8487395,18.25396825,8.8,7.928388747,11.11111111,8.933002481,10.3565365,9.917355372,16.74418605,13.5021097,7.551487414,14.66165414,9.473684211,10.77504726,8.128078818,8.562691131,12.11267606,14.63414634,12.36111111,13.78910776,16.875,8.771929825,11.74089069,13.49693252,14.09135083,11.53846154,9.411764706,17.46031746,7.03125,11.97411003,11.87800963,11.20943953,11.65845649,17.77777778,12.40242845,9.090909091,9.751037344,8.899297424,16.66666667,12.64367816,10.68181818,17.46031746,13.6,7.531380753,10.46511628,12.91759465,10.29411765,8.796296296,11.07491857,13.26530612,11.41552511,14.18439716,14.68459152,11.84210526,13.33333333,12.58278146,13.39869281,12.21532091,9.906759907,13.10043668,11.87214612,11.83673469,17.46031746,15.03759398,7.407407407,15.75875486,11.82389937,8.931419458,15.1187905,15.85365854,9.748427673,8.181818182,8.737864078,6.956521739,10.40145985,10.63664596,18.25396825,11.70046802,9.964412811,14.66165414,8.125,7.441860465,11.28712871,12.90322581,11.09785203,23.54651163,11.04651163,9.505703422,12.25490196,9.655172414,10.04784689,11.44578313,11.93490054,9.047619048,10.73825503,11.05527638,7.894736842,9.668508287,10.54545455,7.534246575,12.5049781,11.61417323,18.25396825,10.65934066,13.15789474,6.923076923,12.83783784,8.542713568,12.88135593,10.52631579,12.42236025,15.78947368,15.24390244,18.25396825,12.52955083,14.59227468,12.17391304,11.84210526,9.134615385,11.93181818,8.895522388,9.788359788,8.955223881,7.142857143,13.13868613,6.024096386,7.751937984,10.40172166,11.53846154,11.80400891,10.67961165,12.19512195,8.740359897,10.75949367,11.17318436,8.965517241,12.69035533,16.66666667,11.47540984,7.430340557,11.39240506,12.26190476,14.52145215,16.96113074,12.60162602,14.66165414,11.9047619
+X,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Number of Y,128,14,41,10,19,10,12,11,7,41,19,71,33,14,10,6,29,10,8,24,5,18,11,5,5,3,19,5,5,11,6,12,40,2,5,15,3,2,7,5,5,7,19,4,1,18,3,18,19,5,23,12,5,24,8,16,2,10,3,12,6,29,15,12,10,30,17,6,22,12,4,19,6,26,5,1,17,13,41,26,4,7,5,16,118,14,15,27,22,4,4,6,5,6,3,23,104,11,4,3,6,22,5,3,4,13,15,10,41,10,10,27,6,13,10,26,17,39,29,27,38,5,4,4,24,7,22,11,3,24,14,4,9,13,8,28,4,8,19,20,24,22,10,19,12,4,19,15,17,10,15,11,14,10,23,15,49,10,56,11,40,34,25,24,4,13,11,2,10,12,5,28,9,5,14,6,11,15,13,18,10,35,3,13,11,5,3,10,5,13,21,11,2,12,13,9,38,14,7,12,12,4,29,22,4,5,14,10,19,13,12,5,3,13,17,14,21,5,29,22,28,9,5,13,11,5,15,8,12,25,9,15,25,3,10,46,40,16,25,1,8,11,21,3,7,11,5,9,21,9,31,17,9,4,12,13,4,3,13,30,5,15,4,10,6,7,25,4,18,14,4,11,9,6,6,8,16,12,2,5,4,9,3,8,55,13,5,28,28,3,16,5,7,18,13,13,14,5,17,13,7,8,10,8,69,22,1,3,9,7,3,48,8,24,5,10,11,7,3,6,11,5,11,12,29,23,26,12,11,10,24
+Number of pY,2,1,1,1,1,4,3,1,1,1,7,1,5,1,3,1,2,2,2,8,1,2,2,2,1,1,1,3,1,1,1,1,1,1,2,4,1,1,1,2,1,2,2,1,1,1,1,1,2,1,1,1,1,2,1,1,2,1,1,4,1,1,2,1,1,1,1,1,4,4,1,7,2,1,2,1,1,2,2,1,2,1,3,4,2,1,2,1,1,1,1,1,3,1,1,1,1,1,1,1,4,1,1,2,1,1,5,2,1,1,1,4,1,2,1,1,3,1,2,1,2,2,1,2,1,1,1,1,1,2,2,3,2,1,1,2,1,1,1,1,1,1,1,7,4,1,5,3,1,1,1,1,2,2,1,1,1,1,1,2,3,1,7,3,1,1,4,2,3,4,3,1,1,1,2,1,1,2,1,1,1,1,1,2,1,3,1,2,1,2,1,1,1,1,1,1,1,2,1,2,1,1,1,3,1,1,1,2,2,3,2,3,1,1,1,1,1,1,1,1,2,2,3,1,1,3,5,1,2,1,1,1,2,1,1,1,1,1,1,1,1,1,5,3,2,2,3,1,1,1,1,4,2,3,1,2,5,1,3,2,3,1,1,1,1,1,1,1,2,1,1,1,2,2,1,3,2,4,2,3,1,1,1,1,3,1,3,1,3,1,1,2,2,2,1,1,1,3,1,1,1,1,1,1,2,1,1,1,9,1,1,1,1,1,1,1,2,2,1,2,1,3,1,2,1,1,1,1,1,1,1
+Total AAs,4646,494,2472,2078,736,531,783,429,111,1590,449,1830,1182,244,432,541,729,266,310,724,286,592,397,301,156,131,636,126,80,241,248,594,826,83,730,248,129,215,425,126,263,573,814,216,144,667,115,466,505,188,780,419,213,512,205,423,149,434,130,406,257,937,429,454,260,1058,532,156,353,462,417,451,317,908,140,76,339,577,894,1214,106,198,126,459,4128,298,421,949,660,86,194,173,126,217,130,346,2335,248,171,128,166,443,58,126,151,370,375,187,1647,835,439,391,243,411,271,723,221,1224,971,1105,1217,258,328,108,998,261,704,337,128,649,524,193,221,522,710,589,233,254,740,631,662,282,294,451,407,197,372,646,463,306,641,313,707,277,644,354,1887,289,2005,245,633,1960,732,803,81,354,434,149,204,462,126,955,266,204,437,151,300,305,198,893,544,1140,102,529,238,126,125,391,207,806,589,242,215,474,437,266,855,529,406,327,355,164,720,863,160,114,247,326,1029,364,255,126,128,309,623,339,609,135,1153,528,482,427,126,522,440,126,375,239,430,449,340,432,614,98,219,705,967,456,660,151,306,483,858,229,219,245,126,266,297,514,795,627,463,164,318,330,103,115,548,1288,126,641,281,266,160,215,505,93,838,344,172,263,204,145,209,332,553,210,149,199,152,362,275,146,2511,508,126,910,760,130,444,199,295,418,483,266,328,126,423,466,115,228,208,176,1675,378,201,56,685,249,129,1394,104,449,103,246,389,158,358,145,788,126,427,323,711,840,606,283,246,266,420

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/transposy/transposy.R	Tue Feb 27 11:29:18 2018 -0500
@@ -0,0 +1,10 @@
+#transpose a csv file, DO NOTHING ELSE
+
+inputy<-read.csv(file = "transposy.csv", header = FALSE, stringsAsFactors = FALSE)
+outputy<-"outputy.csv"
+
+inputy<-as.data.frame(inputy)
+
+transposy<-t(inputy)
+
+write.table(x=transposy,file = outputy,row.names = FALSE,col.names = FALSE,sep=",")