Repository 'diffacto'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/diffacto

Changeset 0:3cc7ce0822a1 (2021-06-21)
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
added:
diffacto.xml
test-data/HBY20Mix.peptides.csv
test-data/HBY20Mix.peptides.tsv
test-data/HBY20Mix.samples.lst
test-data/UP000002311_559292.fasta
test-data/iPRG.novo.pep.csv
test-data/iPRG.samples.lst
b
diff -r 000000000000 -r 3cc7ce0822a1 diffacto.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/diffacto.xml Mon Jun 21 12:50:54 2021 +0000
[
b'@@ -0,0 +1,267 @@\n+<tool id="diffacto" name="Diffacto" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">\n+    <description>Comparative Protein Abundance from Covariation of Peptide Abundances</description>\n+    <macros>\n+        <token name="@TOOL_VERSION@">1.0.6</token>\n+        <token name="@VERSION_SUFFIX@">0</token>\n+    </macros>\n+    <requirements>\n+        <requirement type="package" version="@TOOL_VERSION@">diffacto</requirement>\n+    </requirements>\n+    <command detect_errors="exit_code"><![CDATA[\n+        tr \'\\t\' \',\' < \'$input\' > input.csv &&\n+        diffacto\n+        -i input.csv\n+        #if $db\n+            -db \'$db\'\n+        #end if\n+        #if $samples\n+            -samples \'$samples\'\n+        #end if\n+        -reference \'$reference\'\n+        #if $normalize\n+            -normalize $normalize\n+        #end if\n+        #if $farms_mu\n+            -farms_mu $farms_mu\n+        #end if\n+        #if $farms_alpha\n+            -farms_alpha $farms_alpha\n+        #end if\n+        -min_samples $min_samples\n+        -impute_threshold $impute_threshold\n+        -cutoff_weight $cutoff_weight\n+        $use_unique\n+        #if $scale == \'log2\'\n+            -log2 True\n+        #else\n+            -log2 False\n+        #end if\n+        $fast\n+        -out \'$output\'\n+        #if $mcfdr\n+            -mc_out \'$mc_out\'\n+        #end if\n+        #if $loadings\n+            -loadings_out \'$loadings_out\'\n+        #end if\n+    ]]></command>\n+    <inputs>\n+        <param name="input" argument="-i" type="data" format="tabular,csv" label="Peptides abundances">\n+            <help><![CDATA[\n+                Peptides abundances in tabular or csv format. \n+                <ul>\n+                <li>The first row is column headers and should contain the sample name for each sample column. </li>\n+                <li>The first column should contain unique peptide sequences. </li>\n+                <li><i>Optionally, the second column may be ProteinID assignments, else the <b>Protein database</b> input is required.</i></li>\n+                <li>Each remaining column is a sample column with numeric abundance values.</li>\n+                <li>Missing values should be empty instead of zeros.</li>\n+                </ul>\n+            ]]></help>\n+        </param>\n+        <param argument="-db" type="data" format="fasta" label="Protein database" optional="true"\n+               help="Required if the Peptide abundances input does not have Protein IDs in the second column"/> \n+        <param argument="-samples" type="data" format="tabular" label="Sample Groups" optional="true">\n+            <help><![CDATA[\n+               <i>Optional: By default, each Sample column in Peptide abundances is treated as a singleton group.</i> \n+               <br>\n+               Groups the samples from the Peptides abundance input for comparison.\n+               Each sample column from Peptides abundance input should be on a line with 2 columns:\n+               <ol> \n+               <li>Sample name for header line of the Peptides abundance input.</li>\n+               <li>Group Name assignemnt for the sample</li>\n+               </ol>\n+            ]]></help>\n+        </param>\n+        <param argument="-reference" type="text" value="" label="Reference sample groups" optional="true">\n+            <help><![CDATA[\n+            <i>Optional: By default, Diffacto uses the average of all samples/groups as the reference.</i> \n+            <br>\n+            Names of sample groups <i>(separated by semicolon)</i> treated as the comparison reference.\n+            <ul>\n+            <li>If a Sample Groups input was used, the reference names should be Group names from column 2.</li>\n+            <li>Otherwise, the reference names should be Sample names from the Peptides abundance column header line.</li>\n+\t    </ul>\n+            ]]></help>\n+        </param>\n+        <param name="scale" argument="-log2" type="select" label="Peptides abundance scale">\n+            <opt'..b'out">\n+               <assert_contents>\n+                    <has_text text="FAS2" />\n+                </assert_contents>\n+            </output>\n+        </test>\n+\n+    </tests>\n+    <help><![CDATA[\n+**Diffacto**\n+\n+Diffacto_ quantifies comparative protein abundance from the covariation of peptide abundances.\n+\n+Diffacto_ applies factor analysis to extract the covariation of peptides\' abundances. The method enables a weighted geometrical average summarization and automatic elimination of incoherent peptides, which may result from suboptimal digestion or being partially modified, and are not representative of the protein concentration.\n+\n+**Inputs**\n+\n+  - **Peptides abundances** *in tabular or csv format*\n+\n+    - The first row is column headers and should contain the sample name for each sample column.\n+    - The first column should contain unique peptide sequences.\n+    - *Optionally, the second column may be Protein ID assignments, else the* **Protein database** *input is required.*\n+    - Each remaining column is a sample column with numeric abundance values.\n+    - Missing values should be empty instead of zeros.\n+    - Example: \n+\n+      ============ ========== ========= ========= ========= =========\n+      sequences    Protein    Sample1-A Sample1_B Sample2_A Sample2_B\n+      ============ ========== ========= ========= ========= =========\n+      AAATAAMTK    EF3A       127.35209 142.58217 135.89206 162.54500\n+      AAATTGEWDK   PDC1       100.35922 114.68676 922.60617 833.97955\n+      LPVLLADACCSR HSP72;PDC1 120.21570 194.99594 977.48321 219.23281\n+      AAEEAGVTDVK  FAS2       442.67501 457.52266 448.52837 424.15980\n+      ============ ========== ========= ========= ========= =========\n+\n+\n+  - **Protein database** *(optional)*\n+\n+    - The Protein database in fasta format that has protein seqeunces containing the peptides.\n+    - Required if the **Peptides abundances** input does not have a second column containing Protein ID assignments\n+\n+\n+  - **Sample Groups** *(optional)*\n+\n+    - First column has the sample name\n+    - Second column has the group name\n+    - Example:\n+\n+      ========= ==\n+      Sample1-A S1\n+      Sample1_B S1\n+      Sample2_A S2\n+      Sample2_B S2\n+      ========= ==\n+\n+\n+**Outputs**\n+\n+  - **Protein Abundance**\n+\n+        ======= ====== ====== =================== =================== ================== ==================\n+        Protein N.Pept Q.Pept S/N                 P(PECA)\t         S1                 S2\n+        ======= ====== ====== =================== =================== ================== ==================\n+        EF3A    2      2      -2.874362404756714  0.2608189432601452  463172795.59269696 489796576.81520355\n+        FAS2    6      4      -0.5901265476375578 0.8395809777778386  52093246.23323742  53280470.3811749\n+        PDC1    3      2      6.634988423694361   0.25491030879514676 203769831.79809052 174641994.14231393\n+        ======= ====== ====== =================== =================== ================== ==================\n+\n+  - **FDR Estimate from Monte Carlo Simulation** *(optional)*\n+\n+        =======  =================== ===================\n+        Protein  P(MC)               MCFDR            \n+        =======  =================== ===================\n+        EF3A     0.1419053964023984  0.5287482885321804\n+        FAS2     0.9867109634551495  0.9132662960822688\n+        PDC1     0.3338088445078459  0.5287482885321804\n+        =======  =================== ===================\n+\n+  - **Protein Peptide Loadings** *(optional)*\n+\n+        =======  ===========  ===================\n+        EF3A     AAATAAMTK    0.5287482885321804\n+        FAS2     AAEEAGVTDVK  0.9132662960822688\n+        PDC1     AAATTGEWDK   0.5287482885321804\n+        =======  ===========  ===================\n+\n+.. _Diffacto: https://github.com/statisticalbiotechnology/diffacto\n+\n+    ]]></help>\n+    <citations>\n+        <citation type="doi">10.1074/mcp.O117.067728</citation>\n+    </citations>\n+</tool>\n'
b
diff -r 000000000000 -r 3cc7ce0822a1 test-data/HBY20Mix.peptides.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HBY20Mix.peptides.csv Mon Jun 21 12:50:54 2021 +0000
b
b'@@ -0,0 +1,101 @@\n+,20160112_P1_SEG_MID,20160112_P1_SEG_LOW,20160112_P1_SEG_HIGH,20160112_P2_SEG_LOW,20160112_P2_SEG_MID,20160112_P2_SEG_HIGH,20160112_P3_SEG_HIGH,20160112_P3_SEG_LOW,20160112_P3_SEG_MID,20160112_P4_SEG_HIGH,20160112_P4_SEG_LOW,20160112_P4_SEG_MID,20160112_P5_SEG_HIGH,20160112_P5_SEG_LOW_160121063813,20160112_P5_SEG_MID,20160112_P6_SEG_HIGH,20160112_P6_SEG_LOW,20160112_P6_SEG_MID,20160112_P7_SEG_HIGH,20160112_P7_SEG_LOW,20160112_P7_SEG_MID,20160112_P8_SEG_HIGH,20160112_P8_SEG_LOW,20160112_P8_SEG_MID_160121160232,20160112_P9_SEG_MID,20160112_P9_SEG_HIGH,20160112_P9_SEG_LOW_160121012404,20160112_P10_SEG_HIGH,20160112_P10_SEG_LOW_160120200540,20160112_P10_SEG_MID,20160112_P11_SEG_LOW_160203031257,20160112_P11_SEG_MID_160203050927,20160112_P11_SEG_HIGH_160203070611,20160112_P11_SEG_HIGH,20160112_P11_SEG_LOW,20160112_P11_SEG_MID,20160112_P12_SEG_LOW,20160112_P12_SEG_MID,20160112_P12_SEG_HIGH,20160112_P13_SEG_HIGH,20160112_P13_SEG_LOW,20160112_P13_SEG_MID,20160112_P14_SEG_HIGH,20160112_P14_SEG_MID,20160112_P14_SEG_LOW_160120174525,20160112_P15_SEG_LOW,20160112_P15_SEG_MID,20160112_P15_SEG_HIGH_160120220930,20160112_P16_SEG_LOW,20160112_P16_SEG_MID,20160112_P16_SEG_HIGH_160121181003,20160112_P17_SEG_HIGH,20160112_P17_SEG_LOW,20160112_P17_SEG_MID,20160112_P18_SEG_LOW,20160112_P18_SEG_MID,20160112_P18_SEG_HIGH,20160112_P19_SEG_MID_160121112852,20160112_P19_SEG_HIGH,20160112_P19_SEG_LOW,20160112_P20_SEG_MID,20160112_P20_SEG_LOW,20160112_P20_SEG_HIGH_160121032454\n+AAADALSDLELK,20179637.33,8224609.097,1561979.942,31535106.4,32997456.36,28266815.09,48385294.14,40570543.97,47920023.27,64937488.42,64319293.27,62234240.54,78583241.58,95847575.9,69790706.47,89426419.98,125365986.7,100146146.8,92392026.24,120271596.4,121608789.9,107234006.4,118987500.2,153517491.6,156701712.7,158609277.8,147731117,176724624.2,209172496.2,189803820.5,220521194.4,212934050.2,232694509,244718318.1,247380750.8,239556503.7,178097938.2,165542746.2,178598964.8,212596241.9,203583194.2,181876301.7,209228305.6,269713186.1,258114248.4,305764929.3,268259018.3,265167843.6,280500835.8,246090774.6,334394011.6,233180501.4,280487321.4,353982577.4,322447475.4,277793605.9,328395552,205913906.7,283676006.5,359687394.3,361659376,346308468.3,357633234.2\n+AAAEGVANLHLDEATGEMVSK,,,,20517838.93,18935503.76,20557565.86,29637933.07,26642504.09,31577250.56,42058748.64,39064350.95,37033057.53,47339481.43,53583068.12,51148998.19,67084737.22,63468394.75,61282641.93,69497708.17,76932537.28,77977853.49,83048763.08,79514546.02,106761792.2,90473986,99906526.44,108786518.5,116190863.1,,130635930.2,102474112.7,114263170.9,118842064.9,151385498.5,,130490016.4,113475082.8,119514033.6,118156393.5,140251233.5,142120011.8,131633581.1,144737807.6,149920750.8,160506476.7,207844020.5,186319406.9,182944833.7,156536076.9,159191647,222238364.6,175925430.2,162100964.9,181658443.5,169137850.6,182618860.5,205981769.6,108746879.4,208337803.2,3794375.065,250535611.7,194751336.1,234931630.5\n+AAAGSVLLEDCK,110846635.3,99867057.75,113112524.3,93179375.25,89594489.32,93427868.75,19833415.74,104022732,95715128.23,75976402.16,88291659.56,90025864.49,86772891.93,16843162.92,78029992.78,87546847.26,2434916.754,85808658.32,77409853.55,74464269.82,53548778.09,7299467.608,77918917.38,70740314.11,60000047.49,7614386.064,42073319.75,38292489.45,48514665.67,63149054.84,53874562.49,56538930.27,60038467.58,42189095.14,39573043.55,39698619.61,49045833.21,49638272.38,49305032.02,38261681.21,41868861.43,43592742.88,30624289.8,33923523.3,2043170.046,13670884.94,2071525.017,29233358.72,27994205.26,21481613.91,24282142.68,18713260.72,18316854.68,14653458.29,,7627983.038,5095231.158,7300670.713,9203277.191,2509617.804,,,\n+AAAHSADVFTTVSQLTAFEAEHLLK,,,,,3595585.727,1481916.973,5663150.116,5156293.643,3660301.644,4244553.851,4543615.099,9462813.959,7878274.079,5785260.935,4353012.58,5804436.727,8249107.17,5161623.871,6313590.583,10705269.95,7442016.063,9858596.032,9281932.784,7610166.962,10549174.28,9351480.738,12900019.14,'..b'163003.65,22522927.73,27060553.32,25779524.53,25494523.91,26050413.7,32941634.61,27297145.45,25981819.3,30996944.01,29205754.84,33724317.35,30154522.06,30569184.56,15813148.31,25740537.37,34415931.25,34476443.32,33796647.41,32390541.46\n+ADELGTPAVYWVTDHYNHR,,,,3896016.964,5571683.248,,,4404539.551,3756481.824,,6472255.346,4063263.253,5323211.223,3221310.605,3674293.993,6755792.761,4920146.734,4622272.205,5381719.254,3867034.002,,,3629295.283,4669594.82,1276307.68,6580930.406,5101532.64,6387604.933,,6951103.108,6405193.437,6398066.639,,,,7841530.224,7149941.768,6920283.484,7795865.899,8055397.07,7018242.141,7645841.166,8424221.085,,7959375.003,9588815.274,4316153.897,,8902248.701,8911542.039,10110126.15,9387507.743,10178823.14,11946160.52,11680570.64,10536573.53,6611195.004,8128423.388,,10129314.22,12309893.72,5947741.156,\n+ADELNQLFDALSYSK,2812385.765,,,799037.5494,2504529.627,1694563.495,3794052.317,2512975.711,2377661.662,3489760.519,3414197.184,3957778.864,2388567.683,410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b
diff -r 000000000000 -r 3cc7ce0822a1 test-data/HBY20Mix.peptides.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HBY20Mix.peptides.tsv Mon Jun 21 12:50:54 2021 +0000
b
b'@@ -0,0 +1,101 @@\n+\t20160112_P1_SEG_MID\t20160112_P1_SEG_LOW\t20160112_P1_SEG_HIGH\t20160112_P2_SEG_LOW\t20160112_P2_SEG_MID\t20160112_P2_SEG_HIGH\t20160112_P3_SEG_HIGH\t20160112_P3_SEG_LOW\t20160112_P3_SEG_MID\t20160112_P4_SEG_HIGH\t20160112_P4_SEG_LOW\t20160112_P4_SEG_MID\t20160112_P5_SEG_HIGH\t20160112_P5_SEG_LOW_160121063813\t20160112_P5_SEG_MID\t20160112_P6_SEG_HIGH\t20160112_P6_SEG_LOW\t20160112_P6_SEG_MID\t20160112_P7_SEG_HIGH\t20160112_P7_SEG_LOW\t20160112_P7_SEG_MID\t20160112_P8_SEG_HIGH\t20160112_P8_SEG_LOW\t20160112_P8_SEG_MID_160121160232\t20160112_P9_SEG_MID\t20160112_P9_SEG_HIGH\t20160112_P9_SEG_LOW_160121012404\t20160112_P10_SEG_HIGH\t20160112_P10_SEG_LOW_160120200540\t20160112_P10_SEG_MID\t20160112_P11_SEG_LOW_160203031257\t20160112_P11_SEG_MID_160203050927\t20160112_P11_SEG_HIGH_160203070611\t20160112_P11_SEG_HIGH\t20160112_P11_SEG_LOW\t20160112_P11_SEG_MID\t20160112_P12_SEG_LOW\t20160112_P12_SEG_MID\t20160112_P12_SEG_HIGH\t20160112_P13_SEG_HIGH\t20160112_P13_SEG_LOW\t20160112_P13_SEG_MID\t20160112_P14_SEG_HIGH\t20160112_P14_SEG_MID\t20160112_P14_SEG_LOW_160120174525\t20160112_P15_SEG_LOW\t20160112_P15_SEG_MID\t20160112_P15_SEG_HIGH_160120220930\t20160112_P16_SEG_LOW\t20160112_P16_SEG_MID\t20160112_P16_SEG_HIGH_160121181003\t20160112_P17_SEG_HIGH\t20160112_P17_SEG_LOW\t20160112_P17_SEG_MID\t20160112_P18_SEG_LOW\t20160112_P18_SEG_MID\t20160112_P18_SEG_HIGH\t20160112_P19_SEG_MID_160121112852\t20160112_P19_SEG_HIGH\t20160112_P19_SEG_LOW\t20160112_P20_SEG_MID\t20160112_P20_SEG_LOW\t20160112_P20_SEG_HIGH_160121032454\n+AAADALSDLELK\t20179637.33\t8224609.097\t1561979.942\t31535106.4\t32997456.36\t28266815.09\t48385294.14\t40570543.97\t47920023.27\t64937488.42\t64319293.27\t62234240.54\t78583241.58\t95847575.9\t69790706.47\t89426419.98\t125365986.7\t100146146.8\t92392026.24\t120271596.4\t121608789.9\t107234006.4\t118987500.2\t153517491.6\t156701712.7\t158609277.8\t147731117\t176724624.2\t209172496.2\t189803820.5\t220521194.4\t212934050.2\t232694509\t244718318.1\t247380750.8\t239556503.7\t178097938.2\t165542746.2\t178598964.8\t212596241.9\t203583194.2\t181876301.7\t209228305.6\t269713186.1\t258114248.4\t305764929.3\t268259018.3\t265167843.6\t280500835.8\t246090774.6\t334394011.6\t233180501.4\t280487321.4\t353982577.4\t322447475.4\t277793605.9\t328395552\t205913906.7\t283676006.5\t359687394.3\t361659376\t346308468.3\t357633234.2\n+AAAEGVANLHLDEATGEMVSK\t\t\t\t20517838.93\t18935503.76\t20557565.86\t29637933.07\t26642504.09\t31577250.56\t42058748.64\t39064350.95\t37033057.53\t47339481.43\t53583068.12\t51148998.19\t67084737.22\t63468394.75\t61282641.93\t69497708.17\t76932537.28\t77977853.49\t83048763.08\t79514546.02\t106761792.2\t90473986\t99906526.44\t108786518.5\t116190863.1\t\t130635930.2\t102474112.7\t114263170.9\t118842064.9\t151385498.5\t\t130490016.4\t113475082.8\t119514033.6\t118156393.5\t140251233.5\t142120011.8\t131633581.1\t144737807.6\t149920750.8\t160506476.7\t207844020.5\t186319406.9\t182944833.7\t156536076.9\t159191647\t222238364.6\t175925430.2\t162100964.9\t181658443.5\t169137850.6\t182618860.5\t205981769.6\t108746879.4\t208337803.2\t3794375.065\t250535611.7\t194751336.1\t234931630.5\n+AAAGSVLLEDCK\t110846635.3\t99867057.75\t113112524.3\t93179375.25\t89594489.32\t93427868.75\t19833415.74\t104022732\t95715128.23\t75976402.16\t88291659.56\t90025864.49\t86772891.93\t16843162.92\t78029992.78\t87546847.26\t2434916.754\t85808658.32\t77409853.55\t74464269.82\t53548778.09\t7299467.608\t77918917.38\t70740314.11\t60000047.49\t7614386.064\t42073319.75\t38292489.45\t48514665.67\t63149054.84\t53874562.49\t56538930.27\t60038467.58\t42189095.14\t39573043.55\t39698619.61\t49045833.21\t49638272.38\t49305032.02\t38261681.21\t41868861.43\t43592742.88\t30624289.8\t33923523.3\t2043170.046\t13670884.94\t2071525.017\t29233358.72\t27994205.26\t21481613.91\t24282142.68\t18713260.72\t18316854.68\t14653458.29\t\t7627983.038\t5095231.158\t7300670.713\t9203277.191\t2509617.804\t\t\t\n+AAAHSADVFTTVSQLTAFEAEHLLK\t\t\t\t\t3595585.727\t1481916.973\t5663150.116\t5156293.643\t3660301.644\t4244553.851\t4543615.099\t9462813.959\t7878274.079\t5785260.935\t4353012.58\t5804436.727\t8249107.17\t5161623.871\t6313590.583\t10705269.95\t7442016.063\t9858596.032\t9281932.784\t7610166.962\t10549174.28\t9351480.738\t12900019.14\t'..b'163003.65\t22522927.73\t27060553.32\t25779524.53\t25494523.91\t26050413.7\t32941634.61\t27297145.45\t25981819.3\t30996944.01\t29205754.84\t33724317.35\t30154522.06\t30569184.56\t15813148.31\t25740537.37\t34415931.25\t34476443.32\t33796647.41\t32390541.46\n+ADELGTPAVYWVTDHYNHR\t\t\t\t3896016.964\t5571683.248\t\t\t4404539.551\t3756481.824\t\t6472255.346\t4063263.253\t5323211.223\t3221310.605\t3674293.993\t6755792.761\t4920146.734\t4622272.205\t5381719.254\t3867034.002\t\t\t3629295.283\t4669594.82\t1276307.68\t6580930.406\t5101532.64\t6387604.933\t\t6951103.108\t6405193.437\t6398066.639\t\t\t\t7841530.224\t7149941.768\t6920283.484\t7795865.899\t8055397.07\t7018242.141\t7645841.166\t8424221.085\t\t7959375.003\t9588815.274\t4316153.897\t\t8902248.701\t8911542.039\t10110126.15\t9387507.743\t10178823.14\t11946160.52\t11680570.64\t10536573.53\t6611195.004\t8128423.388\t\t10129314.22\t12309893.72\t5947741.156\t\n+ADELNQLFDALSYSK\t2812385.765\t\t\t799037.5494\t2504529.627\t1694563.495\t3794052.317\t2512975.711\t2377661.662\t3489760.519\t3414197.184\t3957778.864\t2388567.683\t4108700.868\t5128208.165\t6466105.297\t4650291.717\t5223421.54\t5958194.238\t7023507.808\t4954675.225\t7281704.92\t8441399.072\t6632172.357\t9830773.978\t6055101.171\t8791429.04\t8101827.499\t6383227.307\t8295598.102\t8299156.402\t11311327.08\t9392820.337\t10228710.09\t15123537.93\t14799123.88\t13714303.16\t12078144.64\t11335979.47\t13400013.09\t14088751.84\t11983263.76\t12804010.35\t14140205.14\t12536866.47\t12768977.96\t14294053.14\t8253809.299\t10038358.64\t18941253.83\t10256863.31\t14594736.27\t18018018.1\t11927355.22\t20311292.46\t15120994.43\t12392247.74\t13945130.01\t9145321.155\t11929340.93\t21433472.3\t15124485.97\t14593631.9\n+ADESTDGGMVK\t\t\t\t\t2628605.648\t\t\t4015313.981\t3725384.834\t3374094.363\t\t3707802.568\t\t\t13697795.18\t12703933.9\t8363475.947\t\t9704105.41\t8097548.731\t9706145.785\t12741965.34\t11224815\t11584941.24\t17077118.74\t\t\t\t14410111.43\t\t14842723.12\t18229737.5\t15352784.25\t20757634.24\t39904021.08\t\t35459234.57\t16936028.14\t23082317.23\t\t27245525.01\t22645898.87\t19070337.1\t\t19733394.57\t\t\t20726049.55\t31559797.77\t21488576.03\t26616020.02\t25031113.58\t23100525.03\t24453408.27\t43528564.86\t33831187.4\t35719187.17\t54885991.71\t35316011.18\t27412639.05\t35399186.23\t50949472.88\t35516525.48\n+ADEVDYFHEEDR\t\t\t\t\t\t\t\t1833289.908\t\t1394918.406\t\t\t2018000.423\t\t\t1991358.717\t\t\t\t\t\t2415691.761\t1873859.498\t2455368.946\t2000720.802\t\t\t\t1940665.578\t1622560.395\t3433533.123\t2983204.956\t2012654.709\t1915814.907\t\t1311165.655\t4976472.652\t3195337.705\t\t3405316.365\t2100442.022\t4535133.973\t1147348.725\t1078799.128\t3461254.757\t\t\t4154813.458\t916985.7718\t3378042.351\t4176796.099\t6075277.488\t2517104.707\t1954179.352\t5941868.414\t3247409.59\t4480488.035\t3383660.133\t6096063.26\t\t5923732.655\t1523211.895\t1787106.356\n+ADEYGLWYFLDR\t\t\t\t\t3650187.149\t\t1060853.525\t1998571.598\t956611.4133\t1447981.207\t1966651.075\t2028003.748\t4153709.436\t1727833.447\t3322302.089\t2880776.811\t3502713.165\t3919156.484\t5219405.385\t4122494.841\t2921902.839\t1264048.184\t4549965.167\t4452576.093\t2444718.068\t3351145.123\t5074554.012\t4046048.423\t3331279.185\t2463717.505\t2617023.051\t1790974.098\t1846411.262\t6576217.761\t5715328.713\t10029621.56\t10093120.81\t7026778.894\t4747142.829\t9946799.434\t4754976.502\t12086239.99\t6224724.421\t6489874.506\t3712312.477\t6451583.645\t7200962.924\t5241699.463\t4026826.101\t13662866.81\t4606161.544\t5097149.823\t6159441.266\t4050524.266\t7364482.45\t6065614.698\t4188058.78\t4716488.741\t9121986.789\t6748271.254\t8916993.212\t4365756.79\t6680715.589\n+ADFDNCVALHPTSAEELVTMR\t\t\t\t\t10513327.68\t\t\t\t17104008.91\t16046514.07\t13927221.71\t8932536.473\t18742721.26\t19847252.94\t\t20371229.84\t18827055.43\t23904939.06\t\t\t26941998.69\t28570886.42\t24414434.41\t32238840.41\t37074599.76\t24774642.81\t35956986.92\t27949954.07\t21730497.5\t21310054.56\t33055807.77\t34141534.78\t27963837.25\t54480163.28\t59852141.37\t61620732.96\t56528126.81\t57040062.95\t46823850.63\t57729344.46\t51564823.21\t59625511.3\t57309011.11\t56326706.65\t59755384.05\t74979740.45\t72667808.3\t60085286.76\t44807660.96\t66559588.68\t59539637.73\t63935866.79\t74338978.37\t69151886.35\t78651763.78\t76619439.31\t68346408.93\t41964748.73\t65135092.8\t78888516.53\t84248944.19\t79958409.11\t71748170.8\n'
b
diff -r 000000000000 -r 3cc7ce0822a1 test-data/HBY20Mix.samples.lst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HBY20Mix.samples.lst Mon Jun 21 12:50:54 2021 +0000
b
@@ -0,0 +1,63 @@
+20160112_P1_SEG_MID P1
+20160112_P1_SEG_LOW P1
+20160112_P1_SEG_HIGH P1
+20160112_P2_SEG_LOW P2
+20160112_P2_SEG_MID P2
+20160112_P2_SEG_HIGH P2
+20160112_P3_SEG_HIGH P3
+20160112_P3_SEG_LOW P3
+20160112_P3_SEG_MID P3
+20160112_P4_SEG_HIGH P4
+20160112_P4_SEG_LOW P4
+20160112_P4_SEG_MID P4
+20160112_P5_SEG_HIGH P5
+20160112_P5_SEG_LOW_160121063813 P5
+20160112_P5_SEG_MID P5
+20160112_P6_SEG_HIGH P6
+20160112_P6_SEG_LOW P6
+20160112_P6_SEG_MID P6
+20160112_P7_SEG_HIGH P7
+20160112_P7_SEG_LOW P7
+20160112_P7_SEG_MID P7
+20160112_P8_SEG_HIGH P8
+20160112_P8_SEG_LOW P8
+20160112_P8_SEG_MID_160121160232 P8
+20160112_P9_SEG_MID P9
+20160112_P9_SEG_HIGH P9
+20160112_P9_SEG_LOW_160121012404 P9
+20160112_P10_SEG_HIGH P10
+20160112_P10_SEG_LOW_160120200540 P10
+20160112_P10_SEG_MID P10
+20160112_P11_SEG_LOW_160203031257 P11
+20160112_P11_SEG_MID_160203050927 P11
+20160112_P11_SEG_HIGH_160203070611 P11
+20160112_P11_SEG_HIGH REF
+20160112_P11_SEG_LOW REF
+20160112_P11_SEG_MID REF
+20160112_P12_SEG_LOW P12
+20160112_P12_SEG_MID P12
+20160112_P12_SEG_HIGH P12
+20160112_P13_SEG_HIGH P13
+20160112_P13_SEG_LOW P13
+20160112_P13_SEG_MID P13
+20160112_P14_SEG_HIGH P14
+20160112_P14_SEG_MID P14
+20160112_P14_SEG_LOW_160120174525 P14
+20160112_P15_SEG_LOW P15
+20160112_P15_SEG_MID P15
+20160112_P15_SEG_HIGH_160120220930 P15
+20160112_P16_SEG_LOW P16
+20160112_P16_SEG_MID P16
+20160112_P16_SEG_HIGH_160121181003 P16
+20160112_P17_SEG_HIGH P17
+20160112_P17_SEG_LOW P17
+20160112_P17_SEG_MID P17
+20160112_P18_SEG_LOW P18
+20160112_P18_SEG_MID P18
+20160112_P18_SEG_HIGH P18
+20160112_P19_SEG_MID_160121112852 P19
+20160112_P19_SEG_HIGH P19
+20160112_P19_SEG_LOW P19
+20160112_P20_SEG_MID P20
+20160112_P20_SEG_LOW P20
+20160112_P20_SEG_HIGH_160121032454 P20
\ No newline at end of file
b
diff -r 000000000000 -r 3cc7ce0822a1 test-data/UP000002311_559292.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/UP000002311_559292.fasta Mon Jun 21 12:50:54 2021 +0000
b
b'@@ -0,0 +1,14 @@\n+>sp|P00924|ENO1_YEAST Enolase 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ENO1 PE=1 SV=3\n+MAVSKVYARSVYDSRGNPTVEVELTTEKGVFRSIVPSGASTGVHEALEMRDGDKSKWMGKGVLHAVKNVNDVIAPAFVKANIDVKDQKAVDDFLISLDGTANKSKLGANAILGVSLAASRAAAAEKNVPLYKHLADLSKSKTSPYVLPVPFLNVLNGGSHAGGALALQEFMIAPTGAKTFAEALRIGSEVYHNLKSLTKKRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIKAAGHDGKIKIGLDCASSEFFKDGKYDLDFKNPNSDKSKWLTGPQLADLYHSLMKRYPIVSIEDPFAEDDWEAWSHFFKTAGIQIVADDLTVTNPKRIATAIEKKAADALLLKVNQIGTLSESIKAAQDSFAAGWGVMVSHRSGETEDTFIADLVVGLRTGQIKTGAPARSERLAKLNQLLRIEEELGDNAVFAGENFHHGDKL\n+>sp|P07149|FAS1_YEAST Fatty acid synthase subunit beta OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=FAS1 PE=1 SV=2\n+MDAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINPDDDYGFKQEIFDVTSNGLKKNPNWLEEYHPKLIKNKSGKIFVETKFSKLIGRPPLLVPGMTPCTVSPDFVAATTNAGYTIELAGGGYFSAAGMTAAIDSVVSQIEKGSTFGINLIYVNPFMLQWGIPLIKELRSKGYPIQFLTIGAGVPSLEVASEYIETLGLKYLGLKPGSIDAISQVINIAKAHPNFPIALQWTGGRGGGHHSFEDAHTPMLQMYSKIRRHPNIMLIFGSGFGSADDTYPYLTGEWSTKFDYPPMPFDGFLFGSRVMIAKEVKTSPDAKKCIAACTGVPDDKWEQTYKKPTGGIVTVRSEMGEPIHKIATRGVMLWKEFDETIFNLPKNKLVPTLEAKRDYIISRLNADFQKPWFATVNGQARDLATMTYEEVAKRLVELMFIRSTNSWFDVTWRTFTGDFLRRVEERFTKSKTLSLIQSYSLLDKPDEAIEKVFNAYPAAREQFLNAQDIDHFLSMCQNPMQKPVPFVPVLDRRFEIFFKKDSLWQSEHLEAVVDQDVQRTCILHGPVAAQFTKVIDEPIKSIMDGIHDGHIKKLLHQYYGDDESKIPAVEYFGGESPVDVQSQVDSSSVSEDSAVFKATSSTDEESWFKALAGSEINWRHASFLCSFITQDKMFVSNPIRKVFKPSQGMVVEISNGNTSSKTVVTLSEPVQGELKPTVILKLLKENIIQMEMIENRTMDGKPVSLPLLYNFNPDNGFAPISEVMEDRNQRIKEMYWKLWIDEPFNLDFDPRDVIKGKDFEITAKEVYDFTHAVGNNCEDFVSRPDRTMLAPMDFAIVVGWRAIIKAIFPNTVDGDLLKLVHLSNGYKMIPGAKPLQVGDVVSTTAVIESVVNQPTGKIVDVVGTLSRNGKPVMEVTSSFFYRGNYTDFENTFQKTVEPVYQMHIKTSKDIAVLRSKEWFQLDDEDFDLLNKTLTFETETEVTFKNANIFSSVKCFGPIKVELPTKETVEIGIVDYEAGASHGNPVVDFLKRNGSTLEQKVNLENPIPIAVLDSYTPSTNEPYARVSGDLNPIHVSRHFASYANLPGTITHGMFSSASVRALIENWAADSVSSRVRGYTCQFVDMVLPNTALKTSIQHVGMINGRKLIKFETRNEDDVVVLTGEAEIEQPVTTFVFTGQGSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEGHLFEIIDEASKKSAVKPRPLKLERGFACIPLVGISVPFHSTYLMNGVKPFKSFLKKNIIKENVKVARLAGKYIPNLTAKPFQVTKEYFQDVYDLTGSEPIKEIIDNWEKYEQS\n+>sp|P07245|C1TC_YEAST C-1-tetrahydrofolate synthase, cytoplasmic OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ADE3 PE=1 SV=1\n+MAGQVLDGKACAQQFRSNIANEIKSIQGHVPGFAPNLAIIQVGNRPDSATYVRMKRKAAEEAGIVANFIHLDESATEFEVLRYVDQLNEDPHTHGIIVQLPLPAHLDEDRITSRVLAEKDVDGFGPTNIGELNKKNGHPFFLPCTPKGIIELLHKANVTIEGSRSVVIGRSDIVGSPVAELLKSLNSTVTITHSKTRDIASYLHDADIVVVAIGQPEFVKGEWFKPRDGTSSDKKTVVIDVGTNYVADPSKKSGFKCVGDVEFNEAIKYVHLITPVPGGVGPMTVAMLMQNTLIAAKRQMEESSKPLQIPPLPLKLLTPVPSDIDISRAQQPKLINQLAQELGIYSHELELYGHYKAKISPKVIERLQTRQNGKYILVSGITPTPLGEGKSTTTMGLVQALTAHLGKPAIANVRQPSLGPTLGVKGGAAGGGYSQVIPMDEFNLHLTGDIHAIGAANNLLAAAIDTRMFHETTQKNDATFYNRLVPRKNGKRKFTPSMQRRLNRLGIQKTNPDDLTPEEINKFARLNIDPDTITIKRVVDINDRMLRQITIGQAPTEKNHTRVTGFDITVASELMAILALSKDLRDMKERIGRVVVAADVNRSPVTVEDVGCTGALTALLRDAIKPNLMQTLEGTPVLVHAGPFANISIGASSVIADRVALKLVGTEPEAKTEAGYVVTEAGFDFTMGGERFFNIKCRSSGLTPNAVVLVATVRALKSHGGAPDVKPGQPLPSAYTEENIEFVEKGAANMCKQIANIKQFGVPVVVAINKFETDTEGEIAAIRKAALEAGAFEAVTSNHWAEGGKGAIDLAKAVIEASNQPVDFHFLYDVNSSVEDKLTTIVQKMYGGAAIDILPEAQRKIDMYKEQGFGNLPICIAKTQYSLSHDATLKGVPTGFTFPIRDVRLSNGAGYLYALAAEIQTIPGLATYAGYMAVEVDDDGEIDGLF\n+>sp|P16862|PFKA2_YEAST ATP-dependent 6-phosphofructokinase subunit beta OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PFK2 PE=1 SV=4\n+MTVTTPFVNGTSY'..b'SSPDENSTLLSNDSISLKILLRPDEKINKNVEAHLKELNSITKTQDWRSHATQSLVFNTSDILAVKDTLNAMNAPLQGYPTELFPMQLYTLDPLGNVVGVTSTKNAVSTKPTPPPAPEASAESGLSSKVHSYTDLAYRMKTTDTYPSLPKPLNRPQKAIAVMTSGGDAPGMNSNVRAIVRSAIFKGCRAFVVMEGYEGLVRGGPEYIKEFHWEDVRGWSAEGGTNIGTARCMEFKKREGRLLGAQHLIEAGVDALIVCGGDGSLTGADLFRSEWPSLIEELLKTNRISNEQYERMKHLNICGTVGSIDNDMSTTDATIGAYSALDRICKAIDYVEATANSHSRAFVVEVMGRNCGWLALLAGIATSADYIFIPEKPATSSEWQDQMCDIVSKHRSRGKRTTIVVVAEGAIAADLTPISPSDVHKVLVDRLGLDTRITTLGHVQRGGTAVAYDRILATLQGLEAVNAVLESTPDTPSPLIAVNENKIVRKPLMESVKLTKAVAEAIQAKDFKRAMSLRDTEFIEHLNNFMAINSADHNEPKLPKDKRLKIAIVNVGAPAGGINSAVYSMATYCMSQGHRPYAIYNGWSGLARHESVRSLNWKDMLGWQSRGGSEIGTNRVTPEEADLGMIAYYFQKYEFDGLIIVGGFEAFESLHQLERARESYPAFRIPMVLIPATLSNNVPGTEYSLGSDTALNALMEYCDVVKQSASSTRGRAFVVDCQGGNSGYLATYASLAVGAQVSYVPEEGISLEQLSEDIEYLAQSFEKAEGRGRFGKLILKSTNASKALSATKLAEVITAEADGRFDAKPAYPGHVQQGGLPSPIDRTRATRMAIKAVGFIKDNQAAIAEARAAEENFNADDKTISDTAAVVGVKGSHVVYNSIRQLYDYETEVSMRMPKVIHWQATRLIADHLVGRKRVD\n+>sp|P19097|FAS2_YEAST Fatty acid synthase subunit alpha OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=FAS2 PE=1 SV=2\n+MKPEVEQELAHILLTELLAYQFASPVRWIETQDVFLKDFNTERVVEIGPSPTLAGMAQRTLKNKYESYDAALSLHREILCYSKDAKEIYYTPDPSELAAKEEPAKEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAAEIADEPVKASLLLHVLVAHKLKKSLDSIPMSKTIKDLVGGKSTVQNEILGDLGKEFGTTPEKPEETPLEELAETFQDTFSGALGKQSSSLLSRLISSKMPGGFTITVARKYLQTRWGLPSGRQDGVLLVALSNEPAARLGSEADAKAFLDSMAQKYASIVGVDLSSAASASGAAGAGAAAGAAMIDAGALEEITKDHKVLARQQLQVLARYLKMDLDNGERKFLKEKDTVAELQAQLDYLNAELGEFFVNGVATSFSRKKARTFDSSWNWAKQSLLSLYFEIIHGVLKNVDREVVSEAINIMNRSNDALIKFMEYHISNTDETKGENYQLVKTLGEQLIENCKQVLDVDPVYKDVAKPTGPKTAIDKNGNITYSEEPREKVRKLSQYVQEMALGGPITKESQPTIEEDLTRVYKAISAQADKQDISSSTRVEFEKLYSDLMKFLESSKEIDPSQTTQLAGMDVEDALDKDSTKEVASLPNKSTISKTVSSTIPRETIPFLHLRKKTPAGDWKYDRQLSSLFLDGLEKAAFNGVTFKDKYVLITGAGKGSIGAEVLQGLLQGGAKVVVTTSRFSKQVTDYYQSIYAKYGAKGSTLIVVPFNQGSKQDVEALIEFIYDTEKNGGLGWDLDAIIPFAAIPEQGIELEHIDSKSEFAHRIMLTNILRMMGCVKKQKSARGIETRPAQVILPMSPNHGTFGGDGMYSESKLSLETLFNRWHSESWANQLTVCGAIIGWTRGTGLMSANNIIAEGIEKMGVRTFSQKEMAFNLLGLLTPEVVELCQKSPVMADLNGGLQFVPELKEFTAKLRKELVETSEVRKAVSIETALEHKVVNGNSADAAYAQVEIQPRANIQLDFPELKPYKQVKQIAPAELEGLLDLERVIVVTGFAEVGPWGSARTRWEMEAFGEFSLEGCVEMAWIMGFISYHNGNLKGRPYTGWVDSKTKEPVDDKDVKAKYETSILEHSGIRLIEPELFNGYNPEKKEMIQEVIVEEDLEPFEASKETAEQFKHQHGDKVDIFEIPETGEYSVKLLKGATLYIPKALRFDRLVAGQIPTGWNAKTYGISDDIISQVDPITLFVLVSVVEAFIASGITDPYEMYKYVHVSEVGNCSGSGMGGVSALRGMFKDRFKDEPVQNDILQESFINTMSAWVNMLLISSSGPIKTPVGACATSVESVDIGVETILSGKARICIVGGYDDFQEEGSFEFGNMKATSNTLEEFEHGRTPAEMSRPATTTRNGFMEAQGAGIQIIMQADLALKMGVPIYGIVAMAATATDKIGRSVPAPGKGILTTAREHHSSVKYASPNLNMKYRKRQLVTREAQIKDWVENELEALKLEAEEIPSEDQNEFLLERTREIHNEAESQLRAAQQQWGNDFYKRDPRIAPLRGALATYGLTIDDLGVASFHGTSTKANDKNESATINEMMKHLGRSEGNPVIGVFQKFLTGHPKGAAGAWMMNGALQILNSGIIPGNRNADNVDKILEQFEYVLYPSKTLKTDGVRAVSITSFGFGQKGGQAIVVHPDYLYGAITEDRYNEYVAKVSAREKSAYKFFHNGMIYNKLFVSKEHAPYTDELEEDVYLDPLARVSKDKKSGSLTFNSKNIQSKDSYINANTIETAKMIENMTKEKVSNGGVGVDVELITSINVENDTFIERNFTPQEIEYCSAQPSVQSSFAGTWSAKEAVFKSLGVKSLGGGAALKDIEIVRVNKNAPAVELHGNAKKAAEEAGVTDVKVSISHDDLQAVAVAVSTKK\n+>sp|P38011|GBLP_YEAST Guanine nucleotide-binding protein subunit beta-like protein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ASC1 PE=1 SV=4\n+MASNEVLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRSFKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKASMIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVVPNEKADDDSVTIISAGNDKMVKAWNLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEVFSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQTLFAGYTDNVIRVWQVMTAN\n+>sp|Q07478|SUB2_YEAST ATP-dependent RNA helicase SUB2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SUB2 PE=1 SV=1\n+MSHEGEEDLLEYSDNEQEIQIDASKAAEAGETGAATSATEGDNNNNTAAGDKKGSYVGIHSTGFKDFLLKPELSRAIIDCGFEHPSEVQQHTIPQSIHGTDVLCQAKSGLGKTAVFVLSTLQQLDPVPGEVAVVVICNARELAYQIRNEYLRFSKYMPDVKTAVFYGGTPISKDAELLKNKDTAPHIVVATPGRLKALVREKYIDLSHVKNFVIDECDKVLEELDMRRDVQEIFRATPRDKQVMMFSATLSQEIRPICRRFLQNPLEIFVDDEAKLTLHGLQQYYIKLEEREKNRKLAQLLDDLEFNQVIIFVKSTTRANELTKLLNASNFPAITVHGHMKQEERIARYKAFKDFEKRICVSTDVFGRGIDIERINLAINYDLTNEADQYLHRVGRAGRFGTKGLAISFVSSKEDEEVLAKIQERFDVKIAEFPEEGIDPSTYLNN\n'
b
diff -r 000000000000 -r 3cc7ce0822a1 test-data/iPRG.novo.pep.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/iPRG.novo.pep.csv Mon Jun 21 12:50:54 2021 +0000
b
@@ -0,0 +1,18 @@
+sequences,Protein,JD_06232014_sample1-A,JD_06232014_sample1_B,JD_06232014_sample1_C,JD_06232014_sample2_A,JD_06232014_sample2_B,JD_06232014_sample2_C,JD_06232014_sample3_A,JD_06232014_sample3_B,JD_06232014_sample3_C,JD_06232014_sample4-A,JD_06232014_sample4_B,JD_06232014_sample4_C
+//AAATAAMTK//AAATAAMTK//AAATAAMTK//AAATAAMTK//AAATAAMTK//AAATAAMTK//AAATAAMTK//AAATAAMTK//AAATAAMTK//AAATAAMTK//AAATAAMTK//AAATAAMTK//AAATAAMTK//AAATAAMTK//AAATAAMTK,EF3A,1278904798.352093,1427735490.5821738,1651734950.8442984,1350697224.892064,1620517291.5450056,1518469630.5830846,1228067723.4756167,1317714636.3749988,1433324632.7195153,1361724951.3585825,1214799744.227304,1462954448.3123019
+//AAATTGEWDK//AAATTGEWDK//AAATTGEWDK,PDC1,100425510.35922688,114417799.68676732,85878795.28670345,92235767.60617056,83399677.97955546,67858698.16706964,76204907.05197212,89077743.80377103,89213023.53436682,91003344.6368312,100441256.52999114,78723601.97783917
+//AADLEVANPLMSK//LPVLLADACCSR//EQLEVANPLMSK//LPVLLADACCSR//AADLEVANPLMSK//LPVLLADACCSR//QLEEVANPLMSK//LPVLLADACCSR//AADLEVANPLMSK//LPVLLADACCSR//ELQEVANPLMSK//LPVLLADACCSR//AADLEVANPSPYK//LPVLLADACCSR,HSP72;PDC5;PDC1,120157534.21570496,194272907.99594408,154680669.1026353,97701432.48321408,219239163.23281592,233483616.5476059,63126103.87236808,161982517.81979004,152675876.09971395,85941051.12185937,108130056.95372535,175345929.7109972
+//AAEEAGVTDVK//AAEEAGVTDVK//AAEEAGVTDVK//AAEEAGVTDVK//AAEEAGVTDVK//AAEEAGVTDVK//AAEEAGVTDVK//AAEEAGVTDVK,FAS2,442360165.6750173,457305786.52266735,465345269.13223624,448651431.528376,424136803.15980566,467586002.3448458,455675833.96847945,442867602.33366835,521637639.32504255,420010867.33587474,468227118.1702109,512066123.7211542
+//AAEEAGVTDVKK//LLSSLEEAEAR//AAEEAGVTDVKK//LLSSLEEAEAR//AAEEAPSSTVKK//AAEEAGVTDVKK//LLSSLEEAEAR//LLSSLEEAEAR//AAEEARMPAKK//LLSSLEEAEAR,TX305;FAS2;TF3C1,24354771.261380896,21061028.616257805,28236239.40666713,26636531.22618304,26065508.35520007,33892878.18294381,27519686.869994573,25906913.301286865,35593119.01982433,26865815.52682249,25517154.847027604,28858577.78581238
+//AAEENFNADDK//AAEENFNADDK//AAEENFNADDK//EAAENFNADDK//AAEENFNADDK//AAEENFNADDK//AAEENFNADDK//AAEENFNADDK//AAEENFNADDK//AAEENFNADDK//AAEENFNADDK,PFKA2,551803576.1908661,537075478.6009598,555865957.5368063,528394539.35890007,503749410.91988915,532103702.5912981,448575605.1854078,566116740.5009402,595942862.162208,540488580.5096843,566345016.7071806,490748824.2036419
+//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK,FAS2,27039707.207323667,29414313.931416154,28414082.464689113,19732067.78947082,28176401.65937588,27781342.822167225,47836733.36738475,21048686.99007524,24898886.5871167,26355565.88645301,26990592.53895186,21176477.60553841
+//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGSLFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK//AAFDGVTFK,FAS2,44547453.02294096,63771095.46465,56689892.7794255,44924529.1976753,64434008.86767921,71969153.97798398,41746359.55296365,50236027.09333874,57996548.90325943,54416151.27219448,60847671.90786173,55102913.81560656
+//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK//AAFNGVTFK,FAS2,333076516.32330287,373641432.9995464,376340442.48505986,375358796.2848605,370859742.4388924,362437024.40977263,332959378.277259,381377015.2357336,363719711.724041,388593605.68626547,372058304.7000809,310607051.42201346
+//AAGANSQASFVLDDWK//AQANVDNVWADVYSK//AAGANVDNVWSDVYAK//AAQNVDNVWADVYSK//QAAAAADNVWADVYSK//AAQNVDNVWADVYSK//AAQNVDNVWADVYSK,RLA3,44075455.32085449,24602036.561143603,119139140.12762956,28711921.60376516,95434611.53181049,84771065.77454764,96217499.20766228,96505462.11305544,83200248.56029966,52305673.84248466,51766085.2536725,77762864.11713791
+//AAGANVDNVWADVYAK//AAGANVDNVWADVYAK//AAQNVDNVWADVYAK//SPEAVDNVWADVYAK//AAQNVDNVWADVYAK//AAGANVDNVWADVYAK//AAGANVDNVWADVYAK//AAGANVDNVWADVYAK//SPEERNVWADVYAK//AAQNVDNVWADVYAK//TPADVDNVWADVYAK//AAGANVDNVWADVYAK//AAQNVDNVWADVYAK//AAGANVDNVWADVYAK//AAGANVDNVWADVYAK//AAGANVDNVWADVYAK//AAGANVDNVWADVYAK//AAGANVDNVWADVYAK//AAGANVDNVWADVYAK//AAQNVDNVWADVYAK//AAGANVDNVWADVYAK//AAQNVDNVWADVYAK,RLA3,2680320918.7891088,2771017227.056105,2757242411.006762,2699976724.327591,2839536584.582058,2697039277.483688,2816236767.3948464,2768680349.606903,2993515452.082947,2711320283.7673416,2645100250.2447767,2833904283.241229
+//AAKEAGVTDVK//LLSDSLSPTR,KATG;FAS2,13668754.808492854,13554722.913036196,14886658.860913232,10355546.796800312,13127310.784125125,14718450.09121781,8293895.972042983,14041832.902256144,16917256.065108504,11701357.038525267,11283035.264469687,14372005.78692098
+//AAKREFPGVQMK//KAAREFPGVQMK//SAQRLMLGVQMK//GTQRLFPGVQMK//QVRATFPGVQMK//NLRATFPGVQMK//KAAREFPGVQMK//RLNATFPGVQMK//KAAREFPGVQMK//GLGRATMLGVQMK,PDC1,441715145.7259384,428353458.6869943,383416828.3047158,435056137.2240772,387835175.7702839,322129375.61883396,303962465.01307386,355878747.5855891,322800887.17144537,428677340.26972365,420715883.92310417,288000748.86515296
+//AALDFYTK,PFKA2,221099624.09650093,205511707.310624,40314252.73443493,20866646.91756964,24463699.10042244,37238946.87482881,57497721.24803855,59345514.89208978,34914512.837780096,27429989.55268396,23233970.182464056,42146903.05880317
+//AALDFYTK//AALDFYTK,PFKA2,32762140.1259433,712056057.9297818,179041646.47822842,216464521.62904957,199866552.7998617,206252443.24274975,963602869.2407126,181126222.24709657,189080170.20926657,623207775.8048165,31802839.805092037,862247098.4143429
+//AALDFYTK//AALDFYTK//AALDFYTK//AALDFYTK//AALDFYTK//AALDFYTK//AALDFYTK//AALDFYTK//AALDFYTK//AALDFYTK//AALDFYTK//AALDFYTK,PFKA2,682268979.7907418,773270942.1858556,642644679.9305599,642462442.0714186,695237927.7320273,642020527.1684303,526418094.44757,634606608.746667,640887878.3081707,773915691.3316836,765754836.5765419,670403996.9086295
+//AALSAMVDAAK//AALSAMVDAAK//AALSAMVDAAK//AALSAMVDAAK//AALSAMVDAAK//AALSAMVDAAK//AALSAMVDAAK//AALSAMVDAAK//AALSAMVDAAK//AALSAMDQLK//AALSAMVDAAK,EF3A;EF3;METE,152569269.17351758,142739217.79650542,150321655.56263795,151685535.7651258,173722927.86660102,157643248.46325687,152042108.95472035,132843296.39897732,151415143.9925864,152335809.9737917,140587662.01396108,130366841.93828247
b
diff -r 000000000000 -r 3cc7ce0822a1 test-data/iPRG.samples.lst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/iPRG.samples.lst Mon Jun 21 12:50:54 2021 +0000
b
@@ -0,0 +1,12 @@
+JD_06232014_sample1-A S1
+JD_06232014_sample1_B S1
+JD_06232014_sample1_C S1
+JD_06232014_sample2_A S2
+JD_06232014_sample2_B S2
+JD_06232014_sample2_C S2
+JD_06232014_sample3_A S3
+JD_06232014_sample3_B S3
+JD_06232014_sample3_C S3
+JD_06232014_sample4-A S4
+JD_06232014_sample4_B S4
+JD_06232014_sample4_C S4
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