Repository 'kinamine7_7'
hg clone https://toolshed.g2.bx.psu.edu/repos/jfb/kinamine7_7

Changeset 3:98246fd9617a (2018-02-23)
Previous changeset 2:454de52dd5a8 (2018-02-20) Next changeset 4:24c09eccd392 (2018-02-28)
Commit message:
Uploaded
added:
zippable Kinamine-JJ/._Kinamine.xml
zippable Kinamine-JJ/.shed.yml
zippable Kinamine-JJ/KinaMine.jar
zippable Kinamine-JJ/Kinamine.xml
zippable Kinamine-JJ/test-data/FDRreport.txt
zippable Kinamine-JJ/test-data/output_SubBackFreq.csv
zippable Kinamine-JJ/test-data/output_Substrates.csv
zippable Kinamine-JJ/test-data/outputoutput_Substrate Background Frequency.csv
zippable Kinamine-JJ/test-data/outputoutput_Substrates.csv
zippable Kinamine-JJ/test-data/reference.fasta
removed:
zippable Kinamine/._Kinamine.xml
zippable Kinamine/.shed.yml
zippable Kinamine/KinaMine.jar
zippable Kinamine/Kinamine.xml
zippable Kinamine/test-data/FDRreport.txt
zippable Kinamine/test-data/reference.fasta
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diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine-JJ/._Kinamine.xml
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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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diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine-JJ/KinaMine.jar
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diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine-JJ/Kinamine.xml
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+<tool id="kinamine_java" name="Kinamine_7_to_7" version="0.5.0">
+    <description>Extracts phosphorylated motifs</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__/KinaMine.jar' '$FDRreport' reference.fasta outputs $fdr output
+    ]]></command>
+    <inputs>
+        <param format="tabular" name="FDRreport" type="data" label="Distinct Peptide Report"/>
+        <param format="fasta" name="reference" type="data" label="Protein FASTA reference"/>
+        <param name="fdr" type="integer" value="1" min="1"  max="100"  label="FDR"/>
+        <param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
+    </inputs>      
+    <outputs>
+        <data format="csv" name="Substrates" from_work_dir="outputs/output_Substrates.csv" label="${outGroup}_Substrates.csv"/>
+        <data format="csv" name="SBF" from_work_dir="outputs/output_SubBackFreq.csv" label="${outGroup}_SubstrateBackgroundFrequency.csv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="FDRreport" ftype="txt" value="FDRreport.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
+===========
+**Distinct Peptide Report**
+This is a the Distinct Peptide Summary of a Protein Pilot search (though the summary must be exported as a .txt file in this case).  The Distinct Peptide Summary is one of the tabs in .xlsx file created by Protein Pilot, it can be exported to a .txt file by normal excel functions
+
+**FASTA reference**
+This should be a FASTA taken from the Reviewed Human Uniprot database, consisting of all human proteins plus a list of common Mass Spectrometry contaminants
+
+**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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diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine-JJ/test-data/FDRreport.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/zippable Kinamine-JJ/test-data/FDRreport.txt Fri Feb 23 11:55:02 2018 -0500
b
b'@@ -0,0 +1,234606 @@\n+Peptide Locus\tBest N (Peptide)\tAll N\tAccessions\tNames\tStart Position\tBest Conf (Peptide)\tBest Hypoth Conf\tSequence\tModifications\tProtein Modifications\tCleavages\tdMass\tObs MW\tObs m/z\tTheor MW\tTheor m/z\tTheor z\tRedundant Acqs\tBest Spectrum\tScore\tFeature Prob\tAcq Time\tIntensity (Peptide)\tIntensity at Acq\tApex Time (Peptide)\tElution Peak Width (Peptide)\tSum MS2 Counts\tf Seq Signal\tf Seq Fam Signal\tMax Peptide in Seq Fam\tSpecific\tUsed for Quant\tQuant Annotation\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+1.001\t1\t1; 80\tsp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5; Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1\t26\t94\t93.98\tSLIINTFYSNK\tPhospho(Y)@8\tPhospho(Y)@33\tcleaved M-S@N-term\t0.00271863\t1378.656128\t690.3353\t1378.653442\t690.3339844\t2\t2\t1.1.1.27095.1\t9\t0.0192\t43.26708\t298797.5\t\t\t\t\t0.3359\t0.2799\tTRUE\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+1.002\t1\t1; 80\tsp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5; Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1\t26\t94\t50.59\tSLIINTFYSNK\tPhospho(S)@9\tPhospho(S)@34\tcleaved M-S@N-term\t0.000643439\t1378.654053\t690.3343\t1378.653442\t690.3339844\t2\t2\t2.1.1.27261.1\t8\t0.5415\t43.08825\t291851.6\t\t\t\t\t0.3281\t0.2734\tFALSE\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+1.003\t1\t1; 80\tsp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5; Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1\t26\t94\t17.97\tSLIINTFYSNK\tPhospho(T)@6\tPhospho(T)@31\tcleaved M-S@N-term\t0.00271863\t1378.656128\t690.3353\t1378.653442\t690.3339844\t2\t1\t1.1.1.27095.1\t7\t0.5395\t43.26708\t298797.5\t\t\t\t\t0.3359\t0.2799\tTRUE\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+3.001\t1\t1; 29\tsp|P08238|HS90B_HUMAN; sp|P14625|ENPL_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Endoplasmin OS=Homo sapiens GN=HSP90B1 PE=1 SV=1\t42\t98.8\t98.81\tELISNASDALDK\t\t\t\t0.00128149\t1274.636719\t638.3256\t1274.635376\t638.3250122\t2\t5\t1.1.1.17949.1\t10\t1\t30.55683\t266479.1\t\t\t\t\t1\t1\tTRUE\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+4.001\t1\t1; 80\tsp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5; Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1\t56\t99\t99\tYESLTDPSK\t\t\t\t2.03E-03\t1038.489014\t520.2518\t1038.486938\t520.2507324\t2\t2\t1.1.1.9743.1\t9\t1\t19.15072\t321876.8\t\t\t\t\t0.5247\t0.5247\tFALSE\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+5.001\t1\t1; 80\tsp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5; Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1\t56\t99\t99\tYESLTDPSK\tPhospho(Y)@1\tPhospho(Y)@56\t\t-6.54E-05\t1118.453247\t560.2339\t1118.453247\t560.2339478\t2\t5\t2.1.1.9333.1\t10\t0.0486\t18.38703\t945565.4\t\t\t\t\t1.5414\t1.5414\tFALSE\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+6.001\t1\t1\tsp|P08238|HS90B_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4\t73\t99\t99\tIDIIPNPQER\t\t\t\t0.00138263\t1193.641846\t597.8282\t1193.640381\t597.8275146\t2\t2\t1.1.1.21087.1\t8\t1\t34.93665\t426070.5\t\t\t\t\t1\t1\tTRUE\t1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+7.001\t1\t1; 80\tsp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5; Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapi'..b'\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n+\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n'
b
diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine-JJ/test-data/output_SubBackFreq.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/zippable Kinamine-JJ/test-data/output_SubBackFreq.csv Fri Feb 23 11:55:02 2018 -0500
b
b'@@ -0,0 +1,36 @@\n+Amino Acids,sp|P84085|ARF5_HUMAN,sp|E9PAV3|NACAM_HUMAN,tr|B0QY89|B0QY89_HUMAN,tr|E9PM92|E9PM92_HUMAN,sp|P26599|PTBP1_HUMAN,tr|H0YL12|H0YL12_HUMAN,tr|Q5T6W2|Q5T6W2_HUMAN,tr|K7EJ44|K7EJ44_HUMAN,tr|Q5JR95|Q5JR95_HUMAN,tr|B2R5W2|B2R5W2_HUMAN,tr|D6RFH2|D6RFH2_HUMAN,sp|P62834|RAP1A_HUMAN,sp|O60664-3|PLIN3_HUMAN,sp|Q9NWQ8|PHAG1_HUMAN,sp|P35241-5|RADI_HUMAN,sp|O43776|SYNC_HUMAN,tr|A0A0G2JIW1|A0A0G2JIW1_HUMAN,sp|Q92841|DDX17_HUMAN,sp|Q16543|CDC37_HUMAN,sp|Q96RU3|FNBP1_HUMAN,tr|F8VV59|F8VV59_HUMAN,sp|O60664-4|PLIN3_HUMAN,tr|C9K052|C9K052_HUMAN,sp|P31689|DNJA1_HUMAN,sp|P62330|ARF6_HUMAN,tr|A0A0A0MR02|A0A0A0MR02_HUMAN,tr|E9PQZ1|E9PQZ1_HUMAN,tr|A0A0A0MRR7|A0A0A0MRR7_HUMAN,sp|P61978-3|HNRPK_HUMAN,sp|P25398|RS12_HUMAN,tr|A0A087X1X7|A0A087X1X7_HUMAN,sp|A6NHR9-2|SMHD1_HUMAN,tr|E7ETZ0|E7ETZ0_HUMAN,sp|P61978-2|HNRPK_HUMAN,sp|P14868-2|SYDC_HUMAN,sp|P15531|NDKA_HUMAN,tr|E9PLL6|E9PLL6_HUMAN,sp|P0C7P4|UCRIL_HUMAN,sp|P48960-3|CD97_HUMAN,tr|E5RI46|E5RI46_HUMAN,sp|A6NHR9-3|SMHD1_HUMAN,sp|P20042|IF2B_HUMAN,sp|P62899-3|RL31_HUMAN,sp|P60660-2|MYL6_HUMAN,sp|Q92688-2|AN32B_HUMAN,sp|P61224|RAP1B_HUMAN,tr|H7C4P1|H7C4P1_HUMAN,tr|F5GYB5|F5GYB5_HUMAN,sp|P51570-2|GALK1_HUMAN,sp|Q86VP6-2|CAND1_HUMAN,tr|D6RIW1|D6RIW1_HUMAN,tr|B8A6G2|B8A6G2_HUMAN,tr|E9PPH5|E9PPH5_HUMAN,tr|H3BM89|H3BM89_HUMAN,tr|X1WI28|X1WI28_HUMAN,sp|Q86UX7|URP2_HUMAN,tr|A0A0A0MT58|A0A0A0MT58_HUMAN,sp|Q9BTT0|AN32E_HUMAN,tr|I3NI03|I3NI03_HUMAN,sp|P78527-2|PRKDC_HUMAN,tr|E9PMW7|E9PMW7_HUMAN,sp|P55327-3|TPD52_HUMAN,sp|Q99832-2|TCPH_HUMAN,tr|J3QQM1|J3QQM1_HUMAN,sp|P55327-4|TPD52_HUMAN,sp|P55327-2|TPD52_HUMAN,tr|E7EMB3|E7EMB3_HUMAN,sp|Q15233|NONO_HUMAN,sp|P61019|RAB2A_HUMAN,tr|E9PFL9|E9PFL9_HUMAN,sp|Q9BXP5-5|SRRT_HUMAN,tr|A0A0G2JJV3|A0A0G2JJV3_HUMAN,sp|P55327-6|TPD52_HUMAN,sp|P55327-5|TPD52_HUMAN,sp|Q6UUV9|CRTC1_HUMAN,sp|P62917|RL8_HUMAN,sp|Q01081|U2AF1_HUMAN,tr|E7EQV3|E7EQV3_HUMAN,sp|P62195-2|PRS8_HUMAN,tr|A0A0D9SFB3|A0A0D9SFB3_HUMAN,sp|P22626|ROA2_HUMAN,sp|Q06323-2|PSME1_HUMAN,tr|A0A087WV23|A0A087WV23_HUMAN,tr|H0YNJ9|H0YNJ9_HUMAN,sp|P55327-7|TPD52_HUMAN,sp|Q5VTE0|EF1A3_HUMAN,sp|P14866-2|HNRPL_HUMAN,sp|P51991-2|ROA3_HUMAN,tr|E9PIZ1|E9PIZ1_HUMAN,tr|E9PL71|E9PL71_HUMAN,sp|Q9BXS5-2|AP1M1_HUMAN,tr|E9PGX9|E9PGX9_HUMAN,sp|P00338-3|LDHA_HUMAN,sp|Q06323-3|PSME1_HUMAN,tr|H0Y8E6|H0Y8E6_HUMAN,sp|P30626-3|SORCN_HUMAN,tr|S6FRS6|S6FRS6_HUMAN,sp|P55209-3|NP1L1_HUMAN,sp|P33316-2|DUT_HUMAN,sp|Q14019|COTL1_HUMAN,sp|A8MYV0|DCD2C_HUMAN,sp|O00410|IPO5_HUMAN,tr|H0Y6E7|H0Y6E7_HUMAN,tr|E9PKZ0|E9PKZ0_HUMAN,sp|O14979-3|HNRDL_HUMAN,tr|Q5T7C4|Q5T7C4_HUMAN,tr|I3L3D5|I3L3D5_HUMAN,tr|E7EX05|E7EX05_HUMAN,sp|Q16778|H2B2E_HUMAN,sp|Q02790|FKBP4_HUMAN,sp|P42331-4|RHG25_HUMAN,sp|P01112|RASH_HUMAN,tr|A0A0C4DGL3|A0A0C4DGL3_HUMAN,sp|Q10567|AP1B1_HUMAN,tr|F8WE65|F8WE65_HUMAN,tr|Q53FA3|Q53FA3_HUMAN,sp|Q12906-4|ILF3_HUMAN,sp|P42331-2|RHG25_HUMAN,sp|Q5JQS6-2|GSAML_HUMAN,tr|H3BNV9|H3BNV9_HUMAN,sp|O43491|E41L2_HUMAN,tr|F8W0W4|F8W0W4_HUMAN,sp|P28065-2|PSB9_HUMAN,sp|O60814|H2B1K_HUMAN,tr|K7ENB4|K7ENB4_HUMAN,sp|Q8TAA3|PSA7L_HUMAN,sp|P31942|HNRH3_HUMAN,tr|A0A087WYD1|A0A087WYD1_HUMAN,sp|Q9NUU7|DD19A_HUMAN,sp|P13073|COX41_HUMAN,sp|Q99878|H2A1J_HUMAN,sp|P62847-3|RS24_HUMAN,tr|E5RH77|E5RH77_HUMAN,sp|Q07666|KHDR1_HUMAN,sp|P42331-6|RHG25_HUMAN,tr|D6R9Z1|D6R9Z1_HUMAN,sp|Q8WU68|U2AF4_HUMAN,tr|R4GNH3|R4GNH3_HUMAN,tr|E7ETK0|E7ETK0_HUMAN,sp|P25787|PSA2_HUMAN,tr|A0A087WX09|A0A087WX09_HUMAN,tr|H3BUE4|H3BUE4_HUMAN,tr|A0A087WZQ7|A0A087WZQ7_HUMAN,sp|Q6UUV9-3|CRTC1_HUMAN,sp|P49902-2|5NTC_HUMAN,tr|B1ANR0|B1ANR0_HUMAN,sp|Q96QK1|VPS35_HUMAN,sp|P39019|RS19_HUMAN,sp|Q9Y5S9-2|RBM8A_HUMAN,tr|H0YEU2|H0YEU2_HUMAN,tr|H7BZ72|H7BZ72_HUMAN,tr|E9PRZ9|E9PRZ9_HUMAN,sp|Q8TAA3-5|PSA7L_HUMAN,sp|Q15427|SF3B4_HUMAN,tr|J3QLH6|J3QLH6_HUMAN,tr|H0YMM5|H0YMM5_HUMAN,sp|Q96L21|RL10L_HUMAN,tr|B7Z4S1|B7Z4S1_HUMAN,sp|P38159-2|RBMX_HUMAN,tr|E7ESZ1|E7ESZ1_HUMAN,sp|Q01844|EWS_HUMAN,tr|H0YB39|H0YB39_HUMAN,tr|B8ZZP4|B8ZZP4_HUMAN,sp|Q99873-3|ANM1_HUMAN,sp|P12004|PCNA_HUMAN,sp|Q9H115-2|SNAB_HUMAN,tr|J3KRP2|J3KRP2_HUMAN,sp|Q01130|SRSF2_HUMAN,tr|H0YB34|H0YB34_HUMAN,sp|P14866|HNRPL_HUMAN,sp'..b'49,208,288,445,178,426,362,627,129,693,367,520,214,353,233,516,331,48,153,445,239,283,503,2498,767,420,558,710,4646,248,494,749,43,738,169,337,366,135,285,152,137,383,557,871,165,181,766,253,108,286,116,191,409,148,528,338,196,127,220,254,171,269,1640,139,241,416,228,826,226,130,235,216,188,166,339,414,252,1906,636,488,128,814,535,148,129,548,531,509,114,115,274,594,172,501,904,122,388,655,146,207,382,130,712,280,231,919,180,1058,532,238,756,942,187,64,71,76,652,652,188,284,149,347,379,90,1679,222,242,663,4128,1170,126,86,272,404,173,202,804,944,286,396,247,798,872,690,58,151,370,150,126,127,283,434,153,187,529,413,366,739,134,126,175,243,551,616,535,763,942,339,99,527,300,522,264,712,196,117,1217,252,742,258,378,127,661,543,262,147,550,191,140,128,345,710,276,259,204,330,147,525,493,662,276,589,710,769,324,189,284,124,240,140,510,647,531,679,707,644,2005,245,201,466,747,732,803,417,458,120,333,835,462,955,622,278,437,690,627,97,122,1140,529,37,291,298,196,391,284,288,341,569,500,589,184,305,325,132,750,93,155,1223,292,140,728,753,390,203,391,482,66,631,309,153,155,309,303,265,121,121,318,790,528,179,271,340,449,1304,459,458,429,393,370,98,452,879,110,274,607,143,793,795,1018,132,638,146,263,350,561,548,201,429,262,126,63,178,170,327,573,274,84,543,93,527,209,221,379,232,332,210,650,389,135,966,148,180,130,306,75,224,295,556,464,408,382,103,179,188,154,137,592,380,176,115,756,967,493,101,166,427,709,435,399,332,606,148,151,157,620,286,199,152,2472,159,71,113,48,583,449,229,361,731,679,177,373,292,253,270,277,56,286,592,261,198,301,131,215,83,320,636,434,126,255,261,449,928,167,1014,130,297,331,702,246,722,215,179,1270,875,525,48,219,573,71,476,951,336,287,585,505,880,193,913,248,241,306,1018,224,256,217,286,131,193,507,295,370,186,137,615,702,937,697,251,935,295,140,577,894,482,600,362,106,257,351,127,285,156,593,479,268,298,332,174,194,308,181,811,130,197,447,264,292,333,187,221,131,911,261,210,471,76,130,400,133,178,612,644,372,487,508,130,132,198,280,159,2452,523,160,105,873,2541,331,193,248,522,227,415,237,90,186,457,254,291,531,392,856,484,451,597,296,198,646,162,350,149,1306,641,456,272,1887,1086,244,465,673,531,248,195,187,794,223,434,209,204,248,74,265,180,893,153,644,321,876,249,126,165,876,509,452,207,98,641,133,215,150,349,106,179,1739,993,296,82,355,339,853,736,364,169,309,129,175,201,504,100,263,427,361,324,499,197,440,242,181,361,474,945,748,326,363,253,654,614,1143,705,583,212,254,432,136,142,155,353,126,677,1572,514,121,197,129,194,138,237,808,317,215,193,294,371,51,646,145,259,125,204,570,309,268,761,145,324,174,645,910,444,418,259,162,562,479,147,165,143,742,126,661,359,289,423,547,527,2477,210,126,125,134,1675,669,804,378,167,194,551,410,195,449,447,117,417,246,854,85,624,232,440,251,725,246,166,151,613,235,514,699,647,160,334,1590,150,115,533,204,335,368,130,166,366,289,363,165,150,731,388,724,454,230,158,210,300,66,347,80,1388,341,213,208,103,209,67,134,614,134,140,248,129,173,474,764,425,303,231,126,733,66,597,526,659,98,267,381,189,531,188,264,235,274,524,467,208,466,103,1230,526,350,153,939,414,731,198,100,417,307,451,186,448,453,385,363,88,1145,195,612,568,174,87,108,252,194,584,299,139,149,257,166,118,578,283,174,248,375,519,1348,155,835,439,299,391,220,110,706,412,1115,360,723,255,692,588,125,168,53,971,267,782,457,752,523,83,233,479,380,472,188,115,104,253,126,204,64,233,469,475,338,177,348,467,197,472,183,463,249,187,336,351,131,852,196,285,106,361,98,355,170,102,288,39,137,452,248,189,163,470,134,368,102,408,806,506,393,113,176,353,231,1382,135,82,318,155,915,445,356,474,121,406,274,432,641,114,243,201,326,75,108,660,293,539,397,714,464,623,267,696,533,195,375,431,167,1091,386,98,181,650,301,858,385,219,367,245,335,466,423,297,139,618,181,164,1085,418,530,480,184,712,760,586,170,527,250,53,935,505,159,204,170,247,527,207,199,184,345,318,586,1862,298,760,325,592,199,483,145,519,2457,591,952,706,393,194,212,188,56,249,519,1394,104,445,70,1104,168,158,485,126,152,67,1092,323,170,468,101,410,370,88,\n'
b
diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine-JJ/test-data/output_Substrates.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/zippable Kinamine-JJ/test-data/output_Substrates.csv Fri Feb 23 11:55:02 2018 -0500
b
b'@@ -0,0 +1,1254 @@\n+Substrates,Species,Reference,-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7, , , ,Phosphite\n+,,sp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN,,,,D,Q,T,E,Y,L,E,E,R,,,,,,,DQTEYLEER,LKEDQTEYLEERRVK,LKEDQTEYLEERRIK,\n+,,tr|H0YKK0|H0YKK0_HUMAN; sp|P09661|RU2A_HUMAN,,,,,S,L,T,Y,L,S,I,L,R,,,,,,SLTYLSILR,ASLKSLTYLSILRNP,\n+,,sp|P27695|APEX1_HUMAN,,,,,,L,D,Y,F,L,L,S,H,,,,,,LDYFLLSH,NVGWRLDYFLLSHSL,\n+,,tr|A0A0D9SGF6|A0A0D9SGF6_HUMAN; tr|A0A0D9SF54|A0A0D9SF54_HUMAN; sp|Q13813|SPTN1_HUMAN; sp|Q13813-3|SPTN1_HUMAN; sp|Q13813-2|SPTN1_HUMAN,E,L,P,T,A,F,D,Y,V,E,F,T,R,,,,,,ELPTAFDYVEFTR,ELPTAFDYVEFTRSL,\n+,,sp|O00299|CLIC1_HUMAN,D,E,E,I,E,L,A,Y,E,Q,V,A,K,,,,,,DEEIELAYEQVAK,DEEIELAYEQVAKAL,\n+,,tr|H7C2W9|H7C2W9_HUMAN; tr|C9JU56|C9JU56_HUMAN; tr|B7Z4E3|B7Z4E3_HUMAN; tr|B7Z4C8|B7Z4C8_HUMAN; sp|P62899|RL31_HUMAN; sp|P62899-3|RL31_HUMAN; sp|P62899-2|RL31_HUMAN,,,,,,,L,Y,T,L,V,T,Y,V,P,,,,LYTLVTYVP,EDSPNKLYTLVTYVP,\n+,,tr|H3BLZ8|H3BLZ8_HUMAN; sp|Q92841|DDX17_HUMAN; sp|Q92841-3|DDX17_HUMAN; sp|Q92841-2|DDX17_HUMAN; sp|Q92841-1|DDX17_HUMAN,,,,,,N,F,Y,V,E,H,P,E,V,A,,,,NFYVEHPEVA,PKFEKNFYVEHPEVA,\n+,,sp|O43390|HNRPR_HUMAN; sp|O43390-4|HNRPR_HUMAN; sp|O43390-2|HNRPR_HUMAN; sp|O60506|HNRPQ_HUMAN; sp|O60506-2|HNRPQ_HUMAN; sp|O60506-4|HNRPQ_HUMAN; sp|O60506-3|HNRPQ_HUMAN; tr|B7Z645|B7Z645_HUMAN,,,,,,T,G,Y,T,L,D,V,T,T,G,,,,TGYTLDVTTG,ALLERTGYTLDVTTG,\n+,,sp|Q96G03|PGM2_HUMAN; sp|Q96G03-2|PGM2_HUMAN,,,,,,,V,Y,W,D,N,G,A,Q,I,,,,VYWDNGAQI,QDNGYKVYWDNGAQI,\n+,,sp|Q9Y2X3|NOP58_HUMAN,,,,,,,,Y,G,L,I,Y,H,A,S,,,,YGLIYHAS,SRRDTPKYGLIYHAS,\n+,,tr|A0A087WVQ6|A0A087WVQ6_HUMAN; sp|Q00610|CLH1_HUMAN; sp|Q00610-2|CLH1_HUMAN,,,,,,,,Y,N,N,V,S,N,F,G,,,,YNNVSNFG,YDAAKLLYNNVSNFG,\n+,,tr|G8JLB6|G8JLB6_HUMAN; tr|E9PCY7|E9PCY7_HUMAN; sp|P31943|HNRH1_HUMAN; tr|H0YBD7|H0YBD7_HUMAN; tr|H0YB39|H0YB39_HUMAN,G,Y,G,G,Y,D,D,Y,N,G,Y,N,D,G,Y,,,,GYGGYDDYNGYNDGY,GYGGYDDYNGYNDGY,\n+,,sp|P31939|PUR9_HUMAN; sp|P31939-2|PUR9_HUMAN,,,,,N,G,N,Y,C,V,L,Q,M,D,Q,,,,NGNYCVLQMDQ,SKKKNGNYCVLQMDQ,\n+,,tr|J3KND3|J3KND3_HUMAN; tr|G8JLA2|G8JLA2_HUMAN; tr|G3V1V0|G3V1V0_HUMAN; tr|F8W1R7|F8W1R7_HUMAN; tr|F8VPF3|F8VPF3_HUMAN; tr|B7Z6Z4|B7Z6Z4_HUMAN; sp|P60660|MYL6_HUMAN; sp|P60660-2|MYL6_HUMAN,,,,,,I,L,Y,S,Q,C,G,D,V,M,,,,ILYSQCGDVM,TGDGKILYSQCGDVM,AGDGKILYSQCGDVM,\n+,,sp|P04899|GNAI2_HUMAN; sp|P04899-6|GNAI2_HUMAN; sp|P04899-5|GNAI2_HUMAN; sp|P04899-4|GNAI2_HUMAN; sp|P04899-3|GNAI2_HUMAN; sp|P04899-2|GNAI2_HUMAN,,,I,A,Q,S,D,Y,I,P,T,Q,Q,D,V,,,,IAQSDYIPTQQDV,ERIAQSDYIPTQQDV,\n+,,tr|K7EQA9|K7EQA9_HUMAN; tr|K7EIU0|K7EIU0_HUMAN; sp|Q16543|CDC37_HUMAN,G,L,D,P,V,E,V,Y,E,S,L,P,E,E,L,,,,GLDPVEVYESLPEEL,GLDPVEVYESLPEEL,\n+,,sp|P40939|ECHA_HUMAN; tr|H0YFD6|H0YFD6_HUMAN,,,D,G,P,G,F,Y,T,T,R,,,,,,,,DGPGFYTTR,VKDGPGFYTTRCLAP,\n+,,sp|P09211|GSTP1_HUMAN; tr|A8MX94|A8MX94_HUMAN,,,L,A,S,P,E,Y,V,N,L,P,I,N,G,,,,LASPEYVNLPING,AFLASPEYVNLPING,\n+,,tr|G8JLB6|G8JLB6_HUMAN; tr|E9PCY7|E9PCY7_HUMAN; sp|P31943|HNRH1_HUMAN; tr|H0YBD7|H0YBD7_HUMAN; tr|H0YB39|H0YB39_HUMAN,G,Y,D,D,Y,N,G,Y,N,D,G,Y,G,F,G,,,,GYDDYNGYNDGYGFG,GYDDYNGYNDGYGFG,\n+,,sp|P25205|MCM3_HUMAN; sp|P25205-2|MCM3_HUMAN,,V,Q,V,V,G,T,Y,R,,,,,,,,,,VQVVGTYR,RVQVVGTYRCLPGKK,\n+,,sp|Q9UKY7|CDV3_HUMAN; tr|D6R9V8|D6R9V8_HUMAN,,L,Q,L,D,N,Q,Y,A,V,L,E,N,Q,K,,,,LQLDNQYAVLENQK,KLQLDNQYAVLENQK,\n+,,tr|B0QY89|B0QY89_HUMAN; sp|Q9Y262|EIF3L_HUMAN; sp|Q9Y262-2|EIF3L_HUMAN,,Q,Y,E,Q,Q,T,Y,Q,V,I,P,E,V,I,,,,QYEQQTYQVIPEVI,RQYEQQTYQVIPEVI,\n+,,sp|P12235|ADT1_HUMAN; sp|P05141|ADT2_HUMAN; tr|V9GYG0|V9GYG0_HUMAN,,,,,,,Q,Y,K,G,I,I,D,C,V,,,,QYKGIIDCV,QISAEKQYKGIIDCV,QITADKQYKGIIDCV,\n+,,sp|P31948|STIP1_HUMAN; sp|P31948-3|STIP1_HUMAN; sp|P31948-2|STIP1_HUMAN,,,E,A,A,D,G,Y,Q,R,,,,,,,,,EAADGYQR,CKEAADGYQRCMMAQ,\n+,,sp|P53396|ACLY_HUMAN; sp|P53396-2|ACLY_HUMAN,,,,,D,G,V,Y,V,L,D,L,A,A,K,,,,DGVYVLDLAAK,VVTKDGVYVLDLAAK,\n+,,sp|P78527|PRKDC_HUMAN; sp|P78527-2|PRKDC_HUMAN,V,G,A,Y,M,L,M,Y,K,,,,,,,,,,VGAYMLMYK,VGAYMLMYKGANRTE,\n+,,sp|Q9H1E3|NUCKS_HUMAN,,,,K,V,V,D,Y,S,Q,F,Q,E,S,D,,,,KVVDYSQFQESD,RNRKVVDYSQFQESD,\n+,,sp|P09211|GSTP1_HUMAN; tr|A8MX94|A8MX94_HUMAN,,,,A,S,C,L,Y,G,Q,L,P,K,,,,,,ASCLYGQLPK,SLKASCLYGQLPK'..b'YNA,LQKLGAVYDVSHYNA,\n+,,tr|B0YJC4|B0YJC4_HUMAN; sp|P08670|VIME_HUMAN,,,,,,S,L,Y,A,S,S,P,G,G,V,,,,SLYASSPGGV,PSTSRSLYASSPGGV,\n+,,sp|P62805|H4_HUMAN,,,,D,A,V,T,Y,T,E,H,A,K,,,,,,DAVTYTEHAK,VIRDAVTYTEHAKRK,\n+,,sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN,,I,E,P,I,D,E,Y,C,V,Q,Q,L,K,,,,,IEPIDEYCVQQLK,MIEPIDEYCVQQLKE,\n+,,sp|P50991|TCPD_HUMAN; sp|P50991-2|TCPD_HUMAN,,,,,,,A,Y,I,L,N,L,V,K,,,,,AYILNLVK,VLREERAYILNLVKQ,\n+,,sp|P61978-3|HNRPK_HUMAN; sp|P61978|HNRPK_HUMAN; sp|P61978-2|HNRPK_HUMAN; tr|Q5T6W2|Q5T6W2_HUMAN,,,,,,,A,Y,E,P,Q,G,G,S,G,,,,AYEPQGGSG,PSEWQMAYEPQGGSG,\n+,,sp|Q7KZF4|SND1_HUMAN,,S,E,A,V,V,E,Y,V,F,S,G,S,R,,,,,SEAVVEYVFSGSR,RSEAVVEYVFSGSRL,\n+,,tr|G3V4C1|G3V4C1_HUMAN; tr|B2R5W2|B2R5W2_HUMAN; sp|P07910-4|HNRPC_HUMAN; sp|P07910-2|HNRPC_HUMAN; tr|G3V4W0|G3V4W0_HUMAN; tr|B4DY08|B4DY08_HUMAN; tr|G3V251|G3V251_HUMAN; tr|G3V5X6|G3V5X6_HUMAN; tr|G3V3K6|G3V3K6_HUMAN,G,S,S,F,D,L,D,Y,D,F,Q,R,,,,,,,GSSFDLDYDFQR,GSSFDLDYDFQRDYY,GSSFDLDYDFQR,\n+,,sp|P08238|HS90B_HUMAN,,D,N,S,T,M,G,Y,M,M,A,K,,,,,,,DNSTMGYMMAK,RDNSTMGYMMAKKHL,\n+,,sp|Q06830|PRDX1_HUMAN,,,T,I,A,Q,D,Y,G,V,L,K,,,,,,,TIAQDYGVLK,KRTIAQDYGVLKADE,\n+,,sp|P23193|TCEA1_HUMAN; sp|P23193-2|TCEA1_HUMAN; tr|B7Z4S1|B7Z4S1_HUMAN; tr|A0A0A0MT58|A0A0A0MT58_HUMAN; sp|Q15560|TCEA2_HUMAN; sp|Q15560-2|TCEA2_HUMAN,,,,,N,C,T,Y,T,Q,V,Q,T,R,,,,,NCTYTQVQTR,CKKKNCTYTQVQTRS,CRKKNCTYTQVQTRS,\n+,,tr|K7EQ48|K7EQ48_HUMAN; tr|A0A0A0MTS2|A0A0A0MTS2_HUMAN; sp|P06744|G6PI_HUMAN; sp|P06744-2|G6PI_HUMAN,,,,,,V,W,Y,V,S,N,I,D,G,T,,,,VWYVSNIDGT,SGGPRVWYVSNIDGT,\n+,,sp|P23246|SFPQ_HUMAN; tr|H0Y9K7|H0Y9K7_HUMAN; sp|P23246-2|SFPQ_HUMAN,H,G,T,F,E,Y,E,Y,S,Q,R,,,,,,,,HGTFEYEYSQR,HGTFEYEYSQRWKSL,\n+,,tr|G3V0E5|G3V0E5_HUMAN; sp|P02786|TFR1_HUMAN,,,,,A,F,T,Y,I,N,L,D,K,,,,,,AFTYINLDK,LHLKAFTYINLDKAV,\n+,,tr|G3V0E5|G3V0E5_HUMAN; sp|P02786|TFR1_HUMAN,,,,N,E,N,S,Y,V,P,R,,,,,,,,NENSYVPR,KLLNENSYVPREAGS,\n+,,tr|Q5T123|Q5T123_HUMAN; tr|A0A087WV23|A0A087WV23_HUMAN; sp|Q9H299|SH3L3_HUMAN,,,,,,,V,Y,S,T,S,V,T,G,S,,,,VYSTSVTGS,MSGLRVYSTSVTGS,SMSGLRVYSTSVTGS,\n+,,sp|O43776|SYNC_HUMAN,,E,P,F,P,T,I,Y,V,D,S,Q,K,,,,,,EPFPTIYVDSQK,KEPFPTIYVDSQKEN,\n+,,sp|P04406|G3P_HUMAN; sp|P04406-2|G3P_HUMAN,,,,,,,,Y,D,N,E,F,G,Y,S,,,,YDNEFGYS,FVKLISWYDNEFGYS,\n+,,sp|P11142|HSP7C_HUMAN; tr|E9PKE3|E9PKE3_HUMAN; tr|Q53FA3|Q53FA3_HUMAN; sp|P34931|HS71L_HUMAN; sp|P11021|GRP78_HUMAN,P,T,A,A,A,I,A,Y,G,L,D,K,,,,,,,PTAAAIAYGLDK,PTAAAIAYGLDKKVG,PTAAAIAYGLDKGGQ,PTAAAIAYGLDKREG,\n+,,sp|P50990-2|TCPQ_HUMAN; sp|P50990|TCPQ_HUMAN,,,,,,,L,Y,A,V,H,Q,E,G,N,,,,LYAVHQEGN,NEVISKLYAVHQEGN,\n+,,sp|P62273|RS29_HUMAN; sp|P62273-2|RS29_HUMAN,,,,,,,,Y,G,L,N,M,C,R,,,,,YGLNMCR,RHGLIRKYGLNMCRQ,\n+,,sp|P46977|STT3A_HUMAN; sp|P46977-2|STT3A_HUMAN,,,,E,N,D,Y,Y,T,P,T,G,E,F,R,,,,ENDYYTPTGEFR,HIKENDYYTPTGEFR,\n+,,sp|P22626|ROA2_HUMAN; sp|P22626-2|ROA2_HUMAN,,,,,,,Y,Y,E,Q,W,G,K,,,,,,YYEQWGK,EESLRNYYEQWGKLT,\n+,,sp|P19338|NUCL_HUMAN,,,,S,I,S,L,Y,Y,T,G,E,K,,,,,,SISLYYTGEK,DGRSISLYYTGEKGQ,\n+,,sp|P63010|AP2B1_HUMAN; sp|P63010-3|AP2B1_HUMAN; sp|P63010-2|AP2B1_HUMAN; tr|A0A087X253|A0A087X253_HUMAN; sp|Q10567|AP1B1_HUMAN; sp|Q10567-4|AP1B1_HUMAN; sp|Q10567-3|AP1B1_HUMAN; sp|Q10567-2|AP1B1_HUMAN,V,E,G,Q,D,M,L,Y,Q,S,L,K,,,,,,,VEGQDMLYQSLK,VEGQDMLYQSLKLTN,\n+,,tr|U3KQK0|U3KQK0_HUMAN; sp|Q99880|H2B1L_HUMAN; sp|Q99879|H2B1M_HUMAN; sp|Q99877|H2B1N_HUMAN; sp|Q93079|H2B1H_HUMAN; sp|Q5QNW6|H2B2F_HUMAN; sp|Q5QNW6-2|H2B2F_HUMAN; sp|P62807|H2B1C_HUMAN; sp|P58876|H2B1D_HUMAN; sp|O60814|H2B1K_HUMAN; sp|P57053|H2BFS_HUMAN,E,S,Y,S,V,Y,V,Y,K,,,,,,,,,,ESYSVYVYK,ESYSVYVYKVLKQVH,\n+,,tr|H0YB22|H0YB22_HUMAN; tr|E5RH77|E5RH77_HUMAN; sp|P62263|RS14_HUMAN,D,R,D,E,S,S,P,Y,A,A,M,L,A,A,Q,,,,DRDESSPYAAMLAAQ,DRDESSPYAAMLAAQ,\n+,,tr|B0QY89|B0QY89_HUMAN; sp|Q9Y262|EIF3L_HUMAN; sp|Q9Y262-2|EIF3L_HUMAN; tr|B0QY90|B0QY90_HUMAN,Y,D,N,V,H,P,N,Y,H,K,,,,,,,,,YDNVHPNYHK,YDNVHPNYHKEPFLQ,\n+,,tr|G3V4C1|G3V4C1_HUMAN; tr|B2R5W2|B2R5W2_HUMAN; sp|P07910-4|HNRPC_HUMAN; sp|P07910-2|HNRPC_HUMAN; tr|G3V4W0|G3V4W0_HUMAN; tr|B4DY08|B4DY08_HUMAN; tr|G3V251|G3V251_HUMAN; tr|G3V5X6|G3V5X6_HUMAN; tr|G3V3K6|G3V3K6_HUMAN,,,,,,V,Q,Y,V,N,E,R,,,,,,,VQYVNER,KGFAFVQYVNERNAR,\n'
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diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine-JJ/test-data/outputoutput_Substrate Background Frequency.csv
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Binary file zippable Kinamine-JJ/test-data/outputoutput_Substrate Background Frequency.csv has changed
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diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine-JJ/test-data/outputoutput_Substrates.csv
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Binary file zippable Kinamine-JJ/test-data/outputoutput_Substrates.csv has changed
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diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine-JJ/test-data/reference.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/zippable Kinamine-JJ/test-data/reference.fasta Fri Feb 23 11:55:02 2018 -0500
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b'@@ -0,0 +1,183132 @@\n+>sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB PE=1 SV=3\n+MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN\n+>sp|P31946-2|1433B_HUMAN Isoform Short of 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB\n+MDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN\n+>sp|P62258|1433E_HUMAN 14-3-3 protein epsilon OS=Homo sapiens GN=YWHAE PE=1 SV=1\n+MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGEEQNKEALQDVEDENQ\n+>sp|P62258-2|1433E_HUMAN Isoform SV of 14-3-3 protein epsilon OS=Homo sapiens GN=YWHAE\n+MVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGEEQNKEALQDVEDENQ\n+>sp|Q04917|1433F_HUMAN 14-3-3 protein eta OS=Homo sapiens GN=YWHAH PE=1 SV=4\n+MGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADGNEKKLEKVKAYREKIEKELETVCNDVLSLLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEEAGEGN\n+>sp|P61981|1433G_HUMAN 14-3-3 protein gamma OS=Homo sapiens GN=YWHAG PE=1 SV=2\n+MVDREQLVQKARLAEQAERYDDMAAAMKNVTELNEPLSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTSADGNEKKIEMVRAYREKIEKELEAVCQDVLSLLDNYLIKNCSETQYESKVFYLKMKGDYYRYLAEVATGEKRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALNYSVFYYEIQNAPEQACHLAKTAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDDDGGEGNN\n+>sp|P31947|1433S_HUMAN 14-3-3 protein sigma OS=Homo sapiens GN=SFN PE=1 SV=1\n+MERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEGSEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEEGGEAPQEPQS\n+>sp|P31947-2|1433S_HUMAN Isoform 2 of 14-3-3 protein sigma OS=Homo sapiens GN=SFN\n+MERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEGSEEKGPEVREYRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEEGGEAPQEPQS\n+>sp|P27348|1433T_HUMAN 14-3-3 protein theta OS=Homo sapiens GN=YWHAQ PE=1 SV=1\n+MEKTELIQKAKLAEQAERYDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDTSDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEECDAAEGAEN\n+>sp|P63104|1433Z_HUMAN 14-3-3 protein zeta/delta OS=Homo sapiens GN=YWHAZ PE=1 SV=1\n+MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTEGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGEN\n+>sp|P63104-2|1433Z_HUMAN Isoform 2 of 14-3-3 protein zeta/delta OS=Homo sapiens GN=YWHAZ\n+MSQPCRKLWRHNYETSSCIEFLKSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGEN\n+>sp|P30443|1A01_HUMAN HLA class I histocompatibility antigen, A-1 alpha chain OS=Homo sapiens GN=HLA-A PE=1 SV=1\n+MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWELSSQPTIPIVGIIAGLVLLGAVIT'..b'KELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGQAGAAASESLFIS\n+>sp|LYSC_CHICK|\n+MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL\n+>sp|MYG_HORSE|\n+MGLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG\n+>sp|OVAL_CHICK|\n+MGSIGAASMEFCFDVFKELKVHHANENIFYCPIAIMSALAMVYLGAKDSTRTQINKVVRFDKLPGFGDSIEAQCGTSVNVHSSLRDILNQITKPNDVYSFSLASRLYAEERYPILPEYLQCVKELYRGGLEPINFQTAADQARELINSWVESQTNGIIRNVLQPSSVDSQTAMVLVNAIVFKGLWEKAFKDEDTQAMPFRVTEQESKPVQMMYQIGLFRVASMASEKMKILELPFASGTMSMLVLLPDEVSGLEQLESIINFEKLTEWTSSNVMEERKIKVYLPRMKMEEKYNLTSVLMAMGITDVFSSSANLSGISSAESLKISQAVHAAHAEINEAGREVVGSAEAGVDAASVSEEFRADHPFLFCIKHIATNAVLFFGRCVSP\n+>sp|BGAL_ECOLI|\n+MTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVTVSLWQGETQVASGTAPFGGEIIDERGGYADRVTLRLNVENPKLWSAEIPNLYRAVVELHTADGTLIEAEACDVGFREVRIENGLLLLNGKPLLIRGVNRHEHHPLHGQVMDEQTMVQDILLMKQNNFNAVRCSHYPNHPLWYTLCDRYGLYVVDEANIETHGMVPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSLGNESGHGANHDALYRWIKSVDPSRPVQYEGGGADTTATDIICPMYARVDEDQPFPAVPKWSIKKWLSLPGETRPLILCEYAHAMGNSLGGFAKYWQAFRQYPRLQGGFVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDRQFCMNGLVFADRTPHPALTEAKHQQQFFQFRLSGQTIEVTSEYLFRHSDNELLHWMVALDGKPLASGEVPLDVAPQGKQLIELPELPQPESAGQLWLTVRVVQPNATAWSEAGHISAWQQWRLAENLSVTLPAASHAIPHLTTSEMDFCIELGNKRWQFNRQSGFLSQMWIGDKKQLLTPLRDQFTRAPLDNDIGVSEATRIDPNAWVERWKAAGHYQAEAALLQCTADTLADAVLITTAHAWQHQGKTLFISRKTYRIDGSGQMAITVDVEVASDTPHPARIGLNCQLAQVAERVNWLGLGPQENYPDRLTAACFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQFNISRYSQQQLMETSHRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEFQLSAGRYHYQLVWCQK\n+>sp|DHE3_BOVIN|\n+MYRYLGEALLLSRAGPAALGSASADSAALLGWARGQPAAAPQPGLVPPARRHYSEAAADREDDPNFFKMVEGFFDRGASIVEDKLVEDLKTRETEEQKRNRVRSILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCITVGESDGSIWNPDGIDPKELEDFKLQHGTILGFPKAKIYEGSILEVDCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLNNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNEAGVTFT\n+>sp|GFP_AEQVI|\n+MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK\n+>sp|SRPP_HEVBR|\n+MAEEVEEERLKYLDFVRAAGVYAVDSFSTLYLYAKDISGPLKPGVDTIENVVKTVVTPVYYIPLEAVKFVDKTVDVSVTSLDGVVPPVIKQVSAQTYSVAQDAPRIVLDVASSVFNTGVQEGAKALYANLEPKAEQYAVITWRALNKLPLVPQVANVVVPTAVYFSEKYNDVVRGTTEQGYRVSSYLPLLPTEKITKVFGDEAS\n+>sp|REF_HEVBR|\n+MAEDEDNQQGQGEGLKYLGFVQDAATYAVTTFSNVYLFAKDKSGPLQPGVDIIEGPVKNVAVPLYNRFSYIPNGALKFVDSTVVASVTIIDRSLPPIVKDASIQVVSAIRAAPEAARSLASSLPGQTKILAKVFYGEN\n+>sp|PLMP_GRIFR|\n+MFSSVMVALVSLAVAVSANPGLSLKVSGPEAVDGVNNLKVVTTITNTGDETLKLLNDPRGALHTMPTDTFAITNESGETPSFIGVKVKYVPSMAAKSTGENVFAVIAPGQSVNVEHDLSAAYNFTSSGAGTYALEALNVFNYIDPETNEPVEIWADAEAHTTAVSGKLAVVRATPTLTRPVTYNGCSSSEQSALAAAASAAQSYVAESLSYLQTHTAATPRYTTWFGSYISSRHSTVLQHYTDMNSNDFSSYSFDCTCTAAGTFAYVYPNRFGTVYLCGAFWKAPTTGTDSQAGTLVHESSHFTRNGGTKDYAYGQAAAKSLATMDPDKAVMNADNHEYFSENNPAQS\n+>KKA1_ECOLX\n+MSHIQRETSCSRPRLNSNLDADLYGYKWARDNVGQSGATIYRLYGKPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGKTAFQVLEEYPDSGENIVDALAVFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDASDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGIADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF\n'
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diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine/._Kinamine.xml
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Binary file zippable Kinamine/._Kinamine.xml has changed
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diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine/.shed.yml
--- a/zippable Kinamine/.shed.yml Tue Feb 20 14:58:51 2018 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,6 +0,0 @@
-categories: [Computational chemistry]
-description: Kinamine 7_to_7 extract substrates
-homepage_url: https://pubs.acs.org/doi/abs/10.1021/ja507164a
-long_description: This tool is intended for use with a mass spec file.name: kinamine
-owner: blank121
-remote_repository_url: https://github.umn.edu/blank121/KinaMine/tree/Galaxy-7-7
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diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine/KinaMine.jar
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Binary file zippable Kinamine/KinaMine.jar has changed
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diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine/Kinamine.xml
--- a/zippable Kinamine/Kinamine.xml Tue Feb 20 14:58:51 2018 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,49 +0,0 @@
-<tool id="kinamine_java" name="Kinamine_7_to_7" version="0.5.0">
-    <description>Extracts phosphorylated motifs</description>
-    <requirements>
-       <requirement type="package" version="8.0.1440.1">Java</requirement>
-    </requirements>
-    <command><![CDATA[
-        mkdir -p output &&
-        java -Djava.awt.headless=true -cp '$__tool_directory__/Kinamine.jar' kinamine.KinaMine $FDRreport $reference output $fdr
-    ]]></command>
-    <inputs>
-        <param format="txt" name="FDRreport" type="data" label="Distinct Peptide Report"/>
-        <param format="fasta" name="reference" type="data" label="FASTA reference genome"/>
-        <param name="fdr" type="integer" value"1" min="1"  max="100"  label="FDR"/>
-        <param name="outGroup" type="text" value"kinase" label="Kinase Name"/>
-    </inputs>      
-    <outputs>
-        <data format="csv" name="Substrates" from_work_dir="output_Substrates.csv" label="${outGroup}_Substrates.csv"/>
-        <data format="csv" name="SBF" from_work_dir="output2_Substrate Background Frequency.csv" label="$[outGroup]_Substrate Background Frequency"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="FDRreport" ftype="txt" value="FDRreport.csv"/>
-            <param name="reference" ftype="fasta" value="reference.fasta"/>
-            <param name="SBF" ftype="csv" value="SBF.csv"/>
-            <output name="SDtable" file="SDtable.csv"/>
-            <output name="EPM" file="EPM.csv"/>
-            <output name="Characterization" file="Characterization.csv"/>
-        </test>
-    </tests>
-
-    
-    <help><![CDATA[
-This takes a Distinct Peptide Report and extracts from it all phospho-motifs that were discovered at a threshold above a given FDR value.  This tool is intended to be used in conjunction with Negative Motif Finder and Kinatest.R, the three together creating a GalaxyP version of the KINATEST-ID workbook.
-
-===========
-Inputs
-===========
-**Distinct Peptide Report**
-This is... ask Minervo
-
-**FASTA reference**
-This should be a FASTA taken from the Reviewed Human Uniprot database, consisting of all human proteins plus a list of common Mass Spectrometry contaminants
-
-    ]]></help>
-    <citations>
-        <citation type="doi">10.1021/ja507164a</citation>
-    </citations>
-</tool>
-
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diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine/test-data/FDRreport.txt
--- a/zippable Kinamine/test-data/FDRreport.txt Tue Feb 20 14:58:51 2018 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,234606 +0,0 @@\n-Peptide Locus\tBest N (Peptide)\tAll N\tAccessions\tNames\tStart Position\tBest Conf (Peptide)\tBest Hypoth Conf\tSequence\tModifications\tProtein Modifications\tCleavages\tdMass\tObs MW\tObs m/z\tTheor MW\tTheor m/z\tTheor z\tRedundant Acqs\tBest Spectrum\tScore\tFeature Prob\tAcq Time\tIntensity (Peptide)\tIntensity at Acq\tApex Time (Peptide)\tElution Peak Width (Peptide)\tSum MS2 Counts\tf Seq Signal\tf Seq Fam Signal\tMax Peptide in Seq Fam\tSpecific\tUsed for Quant\tQuant Annotation\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-1.001\t1\t1; 80\tsp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5; Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1\t26\t94\t93.98\tSLIINTFYSNK\tPhospho(Y)@8\tPhospho(Y)@33\tcleaved M-S@N-term\t0.00271863\t1378.656128\t690.3353\t1378.653442\t690.3339844\t2\t2\t1.1.1.27095.1\t9\t0.0192\t43.26708\t298797.5\t\t\t\t\t0.3359\t0.2799\tTRUE\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-1.002\t1\t1; 80\tsp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5; Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1\t26\t94\t50.59\tSLIINTFYSNK\tPhospho(S)@9\tPhospho(S)@34\tcleaved M-S@N-term\t0.000643439\t1378.654053\t690.3343\t1378.653442\t690.3339844\t2\t2\t2.1.1.27261.1\t8\t0.5415\t43.08825\t291851.6\t\t\t\t\t0.3281\t0.2734\tFALSE\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-1.003\t1\t1; 80\tsp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5; Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1\t26\t94\t17.97\tSLIINTFYSNK\tPhospho(T)@6\tPhospho(T)@31\tcleaved M-S@N-term\t0.00271863\t1378.656128\t690.3353\t1378.653442\t690.3339844\t2\t1\t1.1.1.27095.1\t7\t0.5395\t43.26708\t298797.5\t\t\t\t\t0.3359\t0.2799\tTRUE\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-3.001\t1\t1; 29\tsp|P08238|HS90B_HUMAN; sp|P14625|ENPL_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Endoplasmin OS=Homo sapiens GN=HSP90B1 PE=1 SV=1\t42\t98.8\t98.81\tELISNASDALDK\t\t\t\t0.00128149\t1274.636719\t638.3256\t1274.635376\t638.3250122\t2\t5\t1.1.1.17949.1\t10\t1\t30.55683\t266479.1\t\t\t\t\t1\t1\tTRUE\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-4.001\t1\t1; 80\tsp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5; Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1\t56\t99\t99\tYESLTDPSK\t\t\t\t2.03E-03\t1038.489014\t520.2518\t1038.486938\t520.2507324\t2\t2\t1.1.1.9743.1\t9\t1\t19.15072\t321876.8\t\t\t\t\t0.5247\t0.5247\tFALSE\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-5.001\t1\t1; 80\tsp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5; Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1\t56\t99\t99\tYESLTDPSK\tPhospho(Y)@1\tPhospho(Y)@56\t\t-6.54E-05\t1118.453247\t560.2339\t1118.453247\t560.2339478\t2\t5\t2.1.1.9333.1\t10\t0.0486\t18.38703\t945565.4\t\t\t\t\t1.5414\t1.5414\tFALSE\t0\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-6.001\t1\t1\tsp|P08238|HS90B_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4\t73\t99\t99\tIDIIPNPQER\t\t\t\t0.00138263\t1193.641846\t597.8282\t1193.640381\t597.8275146\t2\t2\t1.1.1.21087.1\t8\t1\t34.93665\t426070.5\t\t\t\t\t1\t1\tTRUE\t1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-7.001\t1\t1; 80\tsp|P08238|HS90B_HUMAN; sp|P07900|HS90A_HUMAN; sp|P07900-2|HS90A_HUMAN\tHeat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=4; Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5; Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapi'..b'\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n-\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\r\n'
b
diff -r 454de52dd5a8 -r 98246fd9617a zippable Kinamine/test-data/reference.fasta
--- a/zippable Kinamine/test-data/reference.fasta Tue Feb 20 14:58:51 2018 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,183132 +0,0 @@\n->sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB PE=1 SV=3\n-MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN\n->sp|P31946-2|1433B_HUMAN Isoform Short of 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB\n-MDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN\n->sp|P62258|1433E_HUMAN 14-3-3 protein epsilon OS=Homo sapiens GN=YWHAE PE=1 SV=1\n-MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGEEQNKEALQDVEDENQ\n->sp|P62258-2|1433E_HUMAN Isoform SV of 14-3-3 protein epsilon OS=Homo sapiens GN=YWHAE\n-MVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGEEQNKEALQDVEDENQ\n->sp|Q04917|1433F_HUMAN 14-3-3 protein eta OS=Homo sapiens GN=YWHAH PE=1 SV=4\n-MGDREQLLQRARLAEQAERYDDMASAMKAVTELNEPLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADGNEKKLEKVKAYREKIEKELETVCNDVLSLLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEEAGEGN\n->sp|P61981|1433G_HUMAN 14-3-3 protein gamma OS=Homo sapiens GN=YWHAG PE=1 SV=2\n-MVDREQLVQKARLAEQAERYDDMAAAMKNVTELNEPLSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTSADGNEKKIEMVRAYREKIEKELEAVCQDVLSLLDNYLIKNCSETQYESKVFYLKMKGDYYRYLAEVATGEKRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALNYSVFYYEIQNAPEQACHLAKTAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDDDGGEGNN\n->sp|P31947|1433S_HUMAN 14-3-3 protein sigma OS=Homo sapiens GN=SFN PE=1 SV=1\n-MERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEGSEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEEGGEAPQEPQS\n->sp|P31947-2|1433S_HUMAN Isoform 2 of 14-3-3 protein sigma OS=Homo sapiens GN=SFN\n-MERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEGSEEKGPEVREYRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEEGGEAPQEPQS\n->sp|P27348|1433T_HUMAN 14-3-3 protein theta OS=Homo sapiens GN=YWHAQ PE=1 SV=1\n-MEKTELIQKAKLAEQAERYDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDTSDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEECDAAEGAEN\n->sp|P63104|1433Z_HUMAN 14-3-3 protein zeta/delta OS=Homo sapiens GN=YWHAZ PE=1 SV=1\n-MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTEGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGEN\n->sp|P63104-2|1433Z_HUMAN Isoform 2 of 14-3-3 protein zeta/delta OS=Homo sapiens GN=YWHAZ\n-MSQPCRKLWRHNYETSSCIEFLKSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGEN\n->sp|P30443|1A01_HUMAN HLA class I histocompatibility antigen, A-1 alpha chain OS=Homo sapiens GN=HLA-A PE=1 SV=1\n-MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWELSSQPTIPIVGIIAGLVLLGAVIT'..b'KELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGQAGAAASESLFIS\n->sp|LYSC_CHICK|\n-MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL\n->sp|MYG_HORSE|\n-MGLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG\n->sp|OVAL_CHICK|\n-MGSIGAASMEFCFDVFKELKVHHANENIFYCPIAIMSALAMVYLGAKDSTRTQINKVVRFDKLPGFGDSIEAQCGTSVNVHSSLRDILNQITKPNDVYSFSLASRLYAEERYPILPEYLQCVKELYRGGLEPINFQTAADQARELINSWVESQTNGIIRNVLQPSSVDSQTAMVLVNAIVFKGLWEKAFKDEDTQAMPFRVTEQESKPVQMMYQIGLFRVASMASEKMKILELPFASGTMSMLVLLPDEVSGLEQLESIINFEKLTEWTSSNVMEERKIKVYLPRMKMEEKYNLTSVLMAMGITDVFSSSANLSGISSAESLKISQAVHAAHAEINEAGREVVGSAEAGVDAASVSEEFRADHPFLFCIKHIATNAVLFFGRCVSP\n->sp|BGAL_ECOLI|\n-MTMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVTVSLWQGETQVASGTAPFGGEIIDERGGYADRVTLRLNVENPKLWSAEIPNLYRAVVELHTADGTLIEAEACDVGFREVRIENGLLLLNGKPLLIRGVNRHEHHPLHGQVMDEQTMVQDILLMKQNNFNAVRCSHYPNHPLWYTLCDRYGLYVVDEANIETHGMVPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSLGNESGHGANHDALYRWIKSVDPSRPVQYEGGGADTTATDIICPMYARVDEDQPFPAVPKWSIKKWLSLPGETRPLILCEYAHAMGNSLGGFAKYWQAFRQYPRLQGGFVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDRQFCMNGLVFADRTPHPALTEAKHQQQFFQFRLSGQTIEVTSEYLFRHSDNELLHWMVALDGKPLASGEVPLDVAPQGKQLIELPELPQPESAGQLWLTVRVVQPNATAWSEAGHISAWQQWRLAENLSVTLPAASHAIPHLTTSEMDFCIELGNKRWQFNRQSGFLSQMWIGDKKQLLTPLRDQFTRAPLDNDIGVSEATRIDPNAWVERWKAAGHYQAEAALLQCTADTLADAVLITTAHAWQHQGKTLFISRKTYRIDGSGQMAITVDVEVASDTPHPARIGLNCQLAQVAERVNWLGLGPQENYPDRLTAACFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQFNISRYSQQQLMETSHRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEFQLSAGRYHYQLVWCQK\n->sp|DHE3_BOVIN|\n-MYRYLGEALLLSRAGPAALGSASADSAALLGWARGQPAAAPQPGLVPPARRHYSEAAADREDDPNFFKMVEGFFDRGASIVEDKLVEDLKTRETEEQKRNRVRSILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCITVGESDGSIWNPDGIDPKELEDFKLQHGTILGFPKAKIYEGSILEVDCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLNNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNEAGVTFT\n->sp|GFP_AEQVI|\n-MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK\n->sp|SRPP_HEVBR|\n-MAEEVEEERLKYLDFVRAAGVYAVDSFSTLYLYAKDISGPLKPGVDTIENVVKTVVTPVYYIPLEAVKFVDKTVDVSVTSLDGVVPPVIKQVSAQTYSVAQDAPRIVLDVASSVFNTGVQEGAKALYANLEPKAEQYAVITWRALNKLPLVPQVANVVVPTAVYFSEKYNDVVRGTTEQGYRVSSYLPLLPTEKITKVFGDEAS\n->sp|REF_HEVBR|\n-MAEDEDNQQGQGEGLKYLGFVQDAATYAVTTFSNVYLFAKDKSGPLQPGVDIIEGPVKNVAVPLYNRFSYIPNGALKFVDSTVVASVTIIDRSLPPIVKDASIQVVSAIRAAPEAARSLASSLPGQTKILAKVFYGEN\n->sp|PLMP_GRIFR|\n-MFSSVMVALVSLAVAVSANPGLSLKVSGPEAVDGVNNLKVVTTITNTGDETLKLLNDPRGALHTMPTDTFAITNESGETPSFIGVKVKYVPSMAAKSTGENVFAVIAPGQSVNVEHDLSAAYNFTSSGAGTYALEALNVFNYIDPETNEPVEIWADAEAHTTAVSGKLAVVRATPTLTRPVTYNGCSSSEQSALAAAASAAQSYVAESLSYLQTHTAATPRYTTWFGSYISSRHSTVLQHYTDMNSNDFSSYSFDCTCTAAGTFAYVYPNRFGTVYLCGAFWKAPTTGTDSQAGTLVHESSHFTRNGGTKDYAYGQAAAKSLATMDPDKAVMNADNHEYFSENNPAQS\n->KKA1_ECOLX\n-MSHIQRETSCSRPRLNSNLDADLYGYKWARDNVGQSGATIYRLYGKPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGKTAFQVLEEYPDSGENIVDALAVFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDASDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGIADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF\n'