changeset 0:174cfed15fe2 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/diffacto.xml	Mon Jun 21 12:50:29 2021 +0000
@@ -0,0 +1,267 @@
+<tool id="diffacto" name="Diffacto" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
+    <description>Comparative Protein Abundance from Covariation of Peptide Abundances</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.6</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">diffacto</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        tr '\t' ',' < '$input' > input.csv &&
+        diffacto
+        -i input.csv
+        #if $db
+            -db '$db'
+        #end if
+        #if $samples
+            -samples '$samples'
+        #end if
+        -reference '$reference'
+        #if $normalize
+            -normalize $normalize
+        #end if
+        #if $farms_mu
+            -farms_mu $farms_mu
+        #end if
+        #if $farms_alpha
+            -farms_alpha $farms_alpha
+        #end if
+        -min_samples $min_samples
+        -impute_threshold $impute_threshold
+        -cutoff_weight $cutoff_weight
+        $use_unique
+        #if $scale == 'log2'
+            -log2 True
+        #else
+            -log2 False
+        #end if
+        $fast
+        -out '$output'
+        #if $mcfdr
+            -mc_out '$mc_out'
+        #end if
+        #if $loadings
+            -loadings_out '$loadings_out'
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="input" argument="-i" type="data" format="tabular,csv" label="Peptides abundances">
+            <help><![CDATA[
+                Peptides abundances in tabular or csv format. 
+                <ul>
+                <li>The first row is column headers and should contain the sample name for each sample column. </li>
+                <li>The first column should contain unique peptide sequences. </li>
+                <li><i>Optionally, the second column may be ProteinID assignments, else the <b>Protein database</b> input is required.</i></li>
+                <li>Each remaining column is a sample column with numeric abundance values.</li>
+                <li>Missing values should be empty instead of zeros.</li>
+                </ul>
+            ]]></help>
+        </param>
+        <param argument="-db" type="data" format="fasta" label="Protein database" optional="true"
+               help="Required if the Peptide abundances input does not have Protein IDs in the second column"/> 
+        <param argument="-samples" type="data" format="tabular" label="Sample Groups" optional="true">
+            <help><![CDATA[
+               <i>Optional: By default, each Sample column in Peptide abundances is treated as a singleton group.</i> 
+               <br>
+               Groups the samples from the Peptides abundance input for comparison.
+               Each sample column from Peptides abundance input should be on a line with 2 columns:
+               <ol> 
+               <li>Sample name for header line of the Peptides abundance input.</li>
+               <li>Group Name assignemnt for the sample</li>
+               </ol>
+            ]]></help>
+        </param>
+        <param argument="-reference" type="text" value="" label="Reference sample groups" optional="true">
+            <help><![CDATA[
+            <i>Optional: By default, Diffacto uses the average of all samples/groups as the reference.</i> 
+            <br>
+            Names of sample groups <i>(separated by semicolon)</i> treated as the comparison reference.
+            <ul>
+            <li>If a Sample Groups input was used, the reference names should be Group names from column 2.</li>
+            <li>Otherwise, the reference names should be Sample names from the Peptides abundance column header line.</li>
+	    </ul>
+            ]]></help>
+        </param>
+        <param name="scale" argument="-log2" type="select" label="Peptides abundance scale">
+            <option value="linear">linear</option>
+            <option value="log2">log2</option>
+        </param>
+        <param argument="-normalize" type="select" label="Sample-wise normalization" optional="true">
+            <option value="average">average</option>
+            <option value="median">median</option>
+            <option value="GMM">GMM</option>
+        </param>
+        <param argument="-farms_mu" type="float" value="0.1" min="0.0" max="1.0" optional="true" label="Hyperparameter mu"
+            help="Hyperparameter mu (default: 0.1)"/>
+        <param argument="-farms_alpha" type="float" value="0.1" min="0.0" max="1.0" optional="true" label="Hyperparameter alpha"
+            help="Hyperparameter weight of prior probability (default: 0.1)"/>
+        <param argument="-min_samples" type="integer" value="1" min="1" label="Minimum samples for peptide"
+            help="Minimum number of samples peptides needed to be quantified in"/>
+        <param argument="-impute_threshold" type="float" value="0.99" min="0.1" max="1.0" label="Minimum fraction of missing values in the group"
+            help="Impute missing values if missing fraction is larger than the threshold."/>
+        <param argument="-cutoff_weight" type="float" value="0.5" min="0." max="1.0" label="Peptide cutoff weight"
+            help="Peptides weighted lower than the cutoff will be excluded."/>
+        <param argument="-use_unique" type="boolean" truevalue="-use_unique True" falsevalue="" checked="false" label="Use unique peptides only"/>
+        <param argument="-fast" type="boolean" truevalue="-fast True" falsevalue="" checked="false" label="Allow early termination in EM calculation when noise is sufficiently small."/>
+        <param name="mcfdr" argument="-mc_out" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Perform Monte Carlo FDR simulation"/>
+        <param name="loadings" argument="-loadings_out" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Output Protein Peptide loadings file"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Protein Abundance">
+            <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="Protein,N.Pept,Q.Pept,S/N,P(PECA)" />
+            </actions>
+        </data>
+        <data name="mc_out" format="tabular" label="${tool.name} on ${on_string}: MC FDR">
+            <filter>mcfdr == True</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="Protein,P(MC),MCFDR" />
+            </actions>
+        </data>
+        <data name="loadings_out" format="tabular" label="${tool.name} on ${on_string}: Protein Peptide loading">
+            <filter>loadings == True</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="Protein,Peptide,Loading" />
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="csv" value="HBY20Mix.peptides.csv"/>
+            <param name="db" ftype="fasta" value="UP000002311_559292.fasta"/>
+            <param name="samples" ftype="tabular" value="HBY20Mix.samples.lst"/>
+            <output name="output">
+               <assert_contents>
+                    <has_text text="P19097" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" ftype="tabular" value="HBY20Mix.peptides.tsv"/>
+            <param name="db" ftype="fasta" value="UP000002311_559292.fasta"/>
+            <param name="samples" ftype="tabular" value="HBY20Mix.samples.lst"/>
+            <output name="output">
+               <assert_contents>
+                    <has_text text="P19097" />
+                </assert_contents>
+            </output>
+        </test>
+
+        <test>
+            <param name="input" ftype="csv" value="iPRG.novo.pep.csv"/>
+            <param name="samples" ftype="tabular" value="iPRG.samples.lst"/>
+            <param name="min_samples" value="2"/>
+            <output name="output">
+               <assert_contents>
+                    <has_text text="FAS2" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" ftype="csv" value="iPRG.novo.pep.csv"/>
+            <param name="samples" ftype="tabular" value="iPRG.samples.lst"/>
+            <param name="min_samples" value="4"/>
+            <param name="use_unique" value="True"/>
+            <param name="mcfdr" value="True"/>
+            <output name="output">
+               <assert_contents>
+                    <has_text text="FAS2" />
+                </assert_contents>
+            </output>
+            <output name="mc_out">
+               <assert_contents>
+                    <has_text text="FAS2" />
+                </assert_contents>
+            </output>
+        </test>
+
+    </tests>
+    <help><![CDATA[
+**Diffacto**
+
+Diffacto_ quantifies comparative protein abundance from the covariation of peptide abundances.
+
+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.
+
+**Inputs**
+
+  - **Peptides abundances** *in tabular or csv format*
+
+    - The first row is column headers and should contain the sample name for each sample column.
+    - The first column should contain unique peptide sequences.
+    - *Optionally, the second column may be Protein ID assignments, else the* **Protein database** *input is required.*
+    - Each remaining column is a sample column with numeric abundance values.
+    - Missing values should be empty instead of zeros.
+    - Example: 
+
+      ============ ========== ========= ========= ========= =========
+      sequences    Protein    Sample1-A Sample1_B Sample2_A Sample2_B
+      ============ ========== ========= ========= ========= =========
+      AAATAAMTK    EF3A       127.35209 142.58217 135.89206 162.54500
+      AAATTGEWDK   PDC1       100.35922 114.68676 922.60617 833.97955
+      LPVLLADACCSR HSP72;PDC1 120.21570 194.99594 977.48321 219.23281
+      AAEEAGVTDVK  FAS2       442.67501 457.52266 448.52837 424.15980
+      ============ ========== ========= ========= ========= =========
+
+
+  - **Protein database** *(optional)*
+
+    - The Protein database in fasta format that has protein seqeunces containing the peptides.
+    - Required if the **Peptides abundances** input does not have a second column containing Protein ID assignments
+
+
+  - **Sample Groups** *(optional)*
+
+    - First column has the sample name
+    - Second column has the group name
+    - Example:
+
+      ========= ==
+      Sample1-A S1
+      Sample1_B S1
+      Sample2_A S2
+      Sample2_B S2
+      ========= ==
+
+
+**Outputs**
+
+  - **Protein Abundance**
+
+        ======= ====== ====== =================== =================== ================== ==================
+        Protein N.Pept Q.Pept S/N                 P(PECA)	         S1                 S2
+        ======= ====== ====== =================== =================== ================== ==================
+        EF3A    2      2      -2.874362404756714  0.2608189432601452  463172795.59269696 489796576.81520355
+        FAS2    6      4      -0.5901265476375578 0.8395809777778386  52093246.23323742  53280470.3811749
+        PDC1    3      2      6.634988423694361   0.25491030879514676 203769831.79809052 174641994.14231393
+        ======= ====== ====== =================== =================== ================== ==================
+
+  - **FDR Estimate from Monte Carlo Simulation** *(optional)*
+
+        =======  =================== ===================
+        Protein  P(MC)               MCFDR            
+        =======  =================== ===================
+        EF3A     0.1419053964023984  0.5287482885321804
+        FAS2     0.9867109634551495  0.9132662960822688
+        PDC1     0.3338088445078459  0.5287482885321804
+        =======  =================== ===================
+
+  - **Protein Peptide Loadings** *(optional)*
+
+        =======  ===========  ===================
+        EF3A     AAATAAMTK    0.5287482885321804
+        FAS2     AAEEAGVTDVK  0.9132662960822688
+        PDC1     AAATTGEWDK   0.5287482885321804
+        =======  ===========  ===================
+
+.. _Diffacto: https://github.com/statisticalbiotechnology/diffacto
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1074/mcp.O117.067728</citation>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HBY20Mix.peptides.csv	Mon Jun 21 12:50:29 2021 +0000
@@ -0,0 +1,101 @@
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+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
+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,,,
+AAAHSADVFTTVSQLTAFEAEHLLK,,,,,3595585.727,1481916.973,5663150.116,5156293.643,3660301.644,4244553.851,4543615.099,9462813.959,7878274.079,5785260.935,4353012.58,5804436.727,8249107.17,5161623.871,6313590.583,10705269.95,7442016.063,9858596.032,9281932.784,7610166.962,10549174.28,9351480.738,12900019.14,9654444.796,14186965.21,8749893.671,9972881.86,13055249.08,9606675.256,14618637.36,19458447.13,21899320.69,15559012.41,15775796.54,14383959,15306261.53,20972851.62,17005040.3,15786813.02,17858491.05,19424220.97,17988316.75,19866857.72,19872110.41,17070849.51,22771478.32,19713414.78,18510120.12,22324026.78,27413707.14,29604860.11,20224560.85,19032608.97,13690285.25,36477953.25,35812811.08,28029490.27,20962081.84,33856762.66
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HBY20Mix.peptides.tsv	Mon Jun 21 12:50:29 2021 +0000
@@ -0,0 +1,101 @@
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+ADDLHHLLVLALEPPLR										4281734.957	913120.7592			3083105.923			373386.0592	5582953.561		6889384.88	3449984.581	2593183.435	5648802.377	4913452.861	2399516.155	6122152.197	4191551.066	3109920.926	4845992.383	4042941.557	4612440.805	5423124.039		6111259.359	8217105.477	7159409.409	6542779.586		6242614.064	6821467.115	7685315.049	5109707.761	3159597.878	6521879.201	6733478.443	8452980.688	9283797.115	7537096.95	7906887.764	7256664.909	8739155.584	6478155.381	8532380.59	9882971.866	10344225.92	10002013.17	9062539.275	5116164.623	8868828.455	11653189.58	10829226.9	8036576.454	10293789.32
+ADDMPVVQADNQTSSSK											849887.5854									1231231.042				599031.888	1481768.511	2033956.733	1668450.83	2424233.905	1589002.52	1015867.2				1838216.947	3423921.451		1033881.951	2086738.387	1086218.007	1326578.722	1890164.636	666264.5734	1329135.068	2420457.362	1311807.172	1433883.157	1526748.328	1166595.857	4581016.424	1386766.434	1526979.356	2453199.754	2468511.397	1583339.586	2629974.754	1619027.983	4083404.468	2403855.515	2748833.658	2751689.759	1286890.816	3726386.031	2532432.5
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HBY20Mix.samples.lst	Mon Jun 21 12:50:29 2021 +0000
@@ -0,0 +1,63 @@
[phone]_P1_SEG_MID	P1
[phone]_P1_SEG_LOW	P1
[phone]_P1_SEG_HIGH	P1
[phone]_P2_SEG_LOW	P2
[phone]_P2_SEG_MID	P2
[phone]_P2_SEG_HIGH	P2
[phone]_P3_SEG_HIGH	P3
[phone]_P3_SEG_LOW	P3
[phone]_P3_SEG_MID	P3
[phone]_P4_SEG_HIGH	P4
[phone]_P4_SEG_LOW	P4
[phone]_P4_SEG_MID	P4
[phone]_P5_SEG_HIGH	P5
[phone]_P5_SEG_LOW_160121063813	P5
[phone]_P5_SEG_MID	P5
[phone]_P6_SEG_HIGH	P6
[phone]_P6_SEG_LOW	P6
[phone]_P6_SEG_MID	P6
[phone]_P7_SEG_HIGH	P7
[phone]_P7_SEG_LOW	P7
[phone]_P7_SEG_MID	P7
[phone]_P8_SEG_HIGH	P8
[phone]_P8_SEG_LOW	P8
[phone]_P8_SEG_MID_160121160232	P8
[phone]_P9_SEG_MID	P9
[phone]_P9_SEG_HIGH	P9
[phone]_P9_SEG_LOW_160121012404	P9
[phone]_P10_SEG_HIGH	P10
[phone]_P10_SEG_LOW_160120200540	P10
[phone]_P10_SEG_MID	P10
[phone]_P11_SEG_LOW_160203031257	P11
[phone]_P11_SEG_MID_160203050927	P11
[phone]_P11_SEG_HIGH_160203070611	P11
[phone]_P11_SEG_HIGH	REF
[phone]_P11_SEG_LOW	REF
[phone]_P11_SEG_MID	REF
[phone]_P12_SEG_LOW	P12
[phone]_P12_SEG_MID	P12
[phone]_P12_SEG_HIGH	P12
[phone]_P13_SEG_HIGH	P13
[phone]_P13_SEG_LOW	P13
[phone]_P13_SEG_MID	P13
[phone]_P14_SEG_HIGH	P14
[phone]_P14_SEG_MID	P14
[phone]_P14_SEG_LOW_160120174525	P14
[phone]_P15_SEG_LOW	P15
[phone]_P15_SEG_MID	P15
[phone]_P15_SEG_HIGH_160120220930	P15
[phone]_P16_SEG_LOW	P16
[phone]_P16_SEG_MID	P16
[phone]_P16_SEG_HIGH_160121181003	P16
[phone]_P17_SEG_HIGH	P17
[phone]_P17_SEG_LOW	P17
[phone]_P17_SEG_MID	P17
[phone]_P18_SEG_LOW	P18
[phone]_P18_SEG_MID	P18
[phone]_P18_SEG_HIGH	P18
[phone]_P19_SEG_MID_160121112852	P19
[phone]_P19_SEG_HIGH	P19
[phone]_P19_SEG_LOW	P19
[phone]_P20_SEG_MID	P20
[phone]_P20_SEG_LOW	P20
[phone]_P20_SEG_HIGH_160121032454	P20
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/UP000002311_559292.fasta	Mon Jun 21 12:50:29 2021 +0000
@@ -0,0 +1,14 @@
+>sp|P00924|ENO1_YEAST Enolase 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ENO1 PE=1 SV=3
+MAVSKVYARSVYDSRGNPTVEVELTTEKGVFRSIVPSGASTGVHEALEMRDGDKSKWMGKGVLHAVKNVNDVIAPAFVKANIDVKDQKAVDDFLISLDGTANKSKLGANAILGVSLAASRAAAAEKNVPLYKHLADLSKSKTSPYVLPVPFLNVLNGGSHAGGALALQEFMIAPTGAKTFAEALRIGSEVYHNLKSLTKKRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIKAAGHDGKIKIGLDCASSEFFKDGKYDLDFKNPNSDKSKWLTGPQLADLYHSLMKRYPIVSIEDPFAEDDWEAWSHFFKTAGIQIVADDLTVTNPKRIATAIEKKAADALLLKVNQIGTLSESIKAAQDSFAAGWGVMVSHRSGETEDTFIADLVVGLRTGQIKTGAPARSERLAKLNQLLRIEEELGDNAVFAGENFHHGDKL
+>sp|P07149|FAS1_YEAST Fatty acid synthase subunit beta OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=FAS1 PE=1 SV=2
+MDAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINPDDDYGFKQEIFDVTSNGLKKNPNWLEEYHPKLIKNKSGKIFVETKFSKLIGRPPLLVPGMTPCTVSPDFVAATTNAGYTIELAGGGYFSAAGMTAAIDSVVSQIEKGSTFGINLIYVNPFMLQWGIPLIKELRSKGYPIQFLTIGAGVPSLEVASEYIETLGLKYLGLKPGSIDAISQVINIAKAHPNFPIALQWTGGRGGGHHSFEDAHTPMLQMYSKIRRHPNIMLIFGSGFGSADDTYPYLTGEWSTKFDYPPMPFDGFLFGSRVMIAKEVKTSPDAKKCIAACTGVPDDKWEQTYKKPTGGIVTVRSEMGEPIHKIATRGVMLWKEFDETIFNLPKNKLVPTLEAKRDYIISRLNADFQKPWFATVNGQARDLATMTYEEVAKRLVELMFIRSTNSWFDVTWRTFTGDFLRRVEERFTKSKTLSLIQSYSLLDKPDEAIEKVFNAYPAAREQFLNAQDIDHFLSMCQNPMQKPVPFVPVLDRRFEIFFKKDSLWQSEHLEAVVDQDVQRTCILHGPVAAQFTKVIDEPIKSIMDGIHDGHIKKLLHQYYGDDESKIPAVEYFGGESPVDVQSQVDSSSVSEDSAVFKATSSTDEESWFKALAGSEINWRHASFLCSFITQDKMFVSNPIRKVFKPSQGMVVEISNGNTSSKTVVTLSEPVQGELKPTVILKLLKENIIQMEMIENRTMDGKPVSLPLLYNFNPDNGFAPISEVMEDRNQRIKEMYWKLWIDEPFNLDFDPRDVIKGKDFEITAKEVYDFTHAVGNNCEDFVSRPDRTMLAPMDFAIVVGWRAIIKAIFPNTVDGDLLKLVHLSNGYKMIPGAKPLQVGDVVSTTAVIESVVNQPTGKIVDVVGTLSRNGKPVMEVTSSFFYRGNYTDFENTFQKTVEPVYQMHIKTSKDIAVLRSKEWFQLDDEDFDLLNKTLTFETETEVTFKNANIFSSVKCFGPIKVELPTKETVEIGIVDYEAGASHGNPVVDFLKRNGSTLEQKVNLENPIPIAVLDSYTPSTNEPYARVSGDLNPIHVSRHFASYANLPGTITHGMFSSASVRALIENWAADSVSSRVRGYTCQFVDMVLPNTALKTSIQHVGMINGRKLIKFETRNEDDVVVLTGEAEIEQPVTTFVFTGQGSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEGHLFEIIDEASKKSAVKPRPLKLERGFACIPLVGISVPFHSTYLMNGVKPFKSFLKKNIIKENVKVARLAGKYIPNLTAKPFQVTKEYFQDVYDLTGSEPIKEIIDNWEKYEQS
+>sp|P07245|C1TC_YEAST C-1-tetrahydrofolate synthase, cytoplasmic OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ADE3 PE=1 SV=1
+MAGQVLDGKACAQQFRSNIANEIKSIQGHVPGFAPNLAIIQVGNRPDSATYVRMKRKAAEEAGIVANFIHLDESATEFEVLRYVDQLNEDPHTHGIIVQLPLPAHLDEDRITSRVLAEKDVDGFGPTNIGELNKKNGHPFFLPCTPKGIIELLHKANVTIEGSRSVVIGRSDIVGSPVAELLKSLNSTVTITHSKTRDIASYLHDADIVVVAIGQPEFVKGEWFKPRDGTSSDKKTVVIDVGTNYVADPSKKSGFKCVGDVEFNEAIKYVHLITPVPGGVGPMTVAMLMQNTLIAAKRQMEESSKPLQIPPLPLKLLTPVPSDIDISRAQQPKLINQLAQELGIYSHELELYGHYKAKISPKVIERLQTRQNGKYILVSGITPTPLGEGKSTTTMGLVQALTAHLGKPAIANVRQPSLGPTLGVKGGAAGGGYSQVIPMDEFNLHLTGDIHAIGAANNLLAAAIDTRMFHETTQKNDATFYNRLVPRKNGKRKFTPSMQRRLNRLGIQKTNPDDLTPEEINKFARLNIDPDTITIKRVVDINDRMLRQITIGQAPTEKNHTRVTGFDITVASELMAILALSKDLRDMKERIGRVVVAADVNRSPVTVEDVGCTGALTALLRDAIKPNLMQTLEGTPVLVHAGPFANISIGASSVIADRVALKLVGTEPEAKTEAGYVVTEAGFDFTMGGERFFNIKCRSSGLTPNAVVLVATVRALKSHGGAPDVKPGQPLPSAYTEENIEFVEKGAANMCKQIANIKQFGVPVVVAINKFETDTEGEIAAIRKAALEAGAFEAVTSNHWAEGGKGAIDLAKAVIEASNQPVDFHFLYDVNSSVEDKLTTIVQKMYGGAAIDILPEAQRKIDMYKEQGFGNLPICIAKTQYSLSHDATLKGVPTGFTFPIRDVRLSNGAGYLYALAAEIQTIPGLATYAGYMAVEVDDDGEIDGLF
+>sp|P16862|PFKA2_YEAST ATP-dependent 6-phosphofructokinase subunit beta OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PFK2 PE=1 SV=4
+MTVTTPFVNGTSYCTVTAYSVQSYKAAIDFYTKFLSLENRSSPDENSTLLSNDSISLKILLRPDEKINKNVEAHLKELNSITKTQDWRSHATQSLVFNTSDILAVKDTLNAMNAPLQGYPTELFPMQLYTLDPLGNVVGVTSTKNAVSTKPTPPPAPEASAESGLSSKVHSYTDLAYRMKTTDTYPSLPKPLNRPQKAIAVMTSGGDAPGMNSNVRAIVRSAIFKGCRAFVVMEGYEGLVRGGPEYIKEFHWEDVRGWSAEGGTNIGTARCMEFKKREGRLLGAQHLIEAGVDALIVCGGDGSLTGADLFRSEWPSLIEELLKTNRISNEQYERMKHLNICGTVGSIDNDMSTTDATIGAYSALDRICKAIDYVEATANSHSRAFVVEVMGRNCGWLALLAGIATSADYIFIPEKPATSSEWQDQMCDIVSKHRSRGKRTTIVVVAEGAIAADLTPISPSDVHKVLVDRLGLDTRITTLGHVQRGGTAVAYDRILATLQGLEAVNAVLESTPDTPSPLIAVNENKIVRKPLMESVKLTKAVAEAIQAKDFKRAMSLRDTEFIEHLNNFMAINSADHNEPKLPKDKRLKIAIVNVGAPAGGINSAVYSMATYCMSQGHRPYAIYNGWSGLARHESVRSLNWKDMLGWQSRGGSEIGTNRVTPEEADLGMIAYYFQKYEFDGLIIVGGFEAFESLHQLERARESYPAFRIPMVLIPATLSNNVPGTEYSLGSDTALNALMEYCDVVKQSASSTRGRAFVVDCQGGNSGYLATYASLAVGAQVSYVPEEGISLEQLSEDIEYLAQSFEKAEGRGRFGKLILKSTNASKALSATKLAEVITAEADGRFDAKPAYPGHVQQGGLPSPIDRTRATRMAIKAVGFIKDNQAAIAEARAAEENFNADDKTISDTAAVVGVKGSHVVYNSIRQLYDYETEVSMRMPKVIHWQATRLIADHLVGRKRVD
+>sp|P19097|FAS2_YEAST Fatty acid synthase subunit alpha OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=FAS2 PE=1 SV=2
+MKPEVEQELAHILLTELLAYQFASPVRWIETQDVFLKDFNTERVVEIGPSPTLAGMAQRTLKNKYESYDAALSLHREILCYSKDAKEIYYTPDPSELAAKEEPAKEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAAEIADEPVKASLLLHVLVAHKLKKSLDSIPMSKTIKDLVGGKSTVQNEILGDLGKEFGTTPEKPEETPLEELAETFQDTFSGALGKQSSSLLSRLISSKMPGGFTITVARKYLQTRWGLPSGRQDGVLLVALSNEPAARLGSEADAKAFLDSMAQKYASIVGVDLSSAASASGAAGAGAAAGAAMIDAGALEEITKDHKVLARQQLQVLARYLKMDLDNGERKFLKEKDTVAELQAQLDYLNAELGEFFVNGVATSFSRKKARTFDSSWNWAKQSLLSLYFEIIHGVLKNVDREVVSEAINIMNRSNDALIKFMEYHISNTDETKGENYQLVKTLGEQLIENCKQVLDVDPVYKDVAKPTGPKTAIDKNGNITYSEEPREKVRKLSQYVQEMALGGPITKESQPTIEEDLTRVYKAISAQADKQDISSSTRVEFEKLYSDLMKFLESSKEIDPSQTTQLAGMDVEDALDKDSTKEVASLPNKSTISKTVSSTIPRETIPFLHLRKKTPAGDWKYDRQLSSLFLDGLEKAAFNGVTFKDKYVLITGAGKGSIGAEVLQGLLQGGAKVVVTTSRFSKQVTDYYQSIYAKYGAKGSTLIVVPFNQGSKQDVEALIEFIYDTEKNGGLGWDLDAIIPFAAIPEQGIELEHIDSKSEFAHRIMLTNILRMMGCVKKQKSARGIETRPAQVILPMSPNHGTFGGDGMYSESKLSLETLFNRWHSESWANQLTVCGAIIGWTRGTGLMSANNIIAEGIEKMGVRTFSQKEMAFNLLGLLTPEVVELCQKSPVMADLNGGLQFVPELKEFTAKLRKELVETSEVRKAVSIETALEHKVVNGNSADAAYAQVEIQPRANIQLDFPELKPYKQVKQIAPAELEGLLDLERVIVVTGFAEVGPWGSARTRWEMEAFGEFSLEGCVEMAWIMGFISYHNGNLKGRPYTGWVDSKTKEPVDDKDVKAKYETSILEHSGIRLIEPELFNGYNPEKKEMIQEVIVEEDLEPFEASKETAEQFKHQHGDKVDIFEIPETGEYSVKLLKGATLYIPKALRFDRLVAGQIPTGWNAKTYGISDDIISQVDPITLFVLVSVVEAFIASGITDPYEMYKYVHVSEVGNCSGSGMGGVSALRGMFKDRFKDEPVQNDILQESFINTMSAWVNMLLISSSGPIKTPVGACATSVESVDIGVETILSGKARICIVGGYDDFQEEGSFEFGNMKATSNTLEEFEHGRTPAEMSRPATTTRNGFMEAQGAGIQIIMQADLALKMGVPIYGIVAMAATATDKIGRSVPAPGKGILTTAREHHSSVKYASPNLNMKYRKRQLVTREAQIKDWVENELEALKLEAEEIPSEDQNEFLLERTREIHNEAESQLRAAQQQWGNDFYKRDPRIAPLRGALATYGLTIDDLGVASFHGTSTKANDKNESATINEMMKHLGRSEGNPVIGVFQKFLTGHPKGAAGAWMMNGALQILNSGIIPGNRNADNVDKILEQFEYVLYPSKTLKTDGVRAVSITSFGFGQKGGQAIVVHPDYLYGAITEDRYNEYVAKVSAREKSAYKFFHNGMIYNKLFVSKEHAPYTDELEEDVYLDPLARVSKDKKSGSLTFNSKNIQSKDSYINANTIETAKMIENMTKEKVSNGGVGVDVELITSINVENDTFIERNFTPQEIEYCSAQPSVQSSFAGTWSAKEAVFKSLGVKSLGGGAALKDIEIVRVNKNAPAVELHGNAKKAAEEAGVTDVKVSISHDDLQAVAVAVSTKK
+>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
+MASNEVLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRSFKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKASMIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVVPNEKADDDSVTIISAGNDKMVKAWNLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEVFSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQTLFAGYTDNVIRVWQVMTAN
+>sp|Q07478|SUB2_YEAST ATP-dependent RNA helicase SUB2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SUB2 PE=1 SV=1
+MSHEGEEDLLEYSDNEQEIQIDASKAAEAGETGAATSATEGDNNNNTAAGDKKGSYVGIHSTGFKDFLLKPELSRAIIDCGFEHPSEVQQHTIPQSIHGTDVLCQAKSGLGKTAVFVLSTLQQLDPVPGEVAVVVICNARELAYQIRNEYLRFSKYMPDVKTAVFYGGTPISKDAELLKNKDTAPHIVVATPGRLKALVREKYIDLSHVKNFVIDECDKVLEELDMRRDVQEIFRATPRDKQVMMFSATLSQEIRPICRRFLQNPLEIFVDDEAKLTLHGLQQYYIKLEEREKNRKLAQLLDDLEFNQVIIFVKSTTRANELTKLLNASNFPAITVHGHMKQEERIARYKAFKDFEKRICVSTDVFGRGIDIERINLAINYDLTNEADQYLHRVGRAGRFGTKGLAISFVSSKEDEEVLAKIQERFDVKIAEFPEEGIDPSTYLNN

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/iPRG.novo.pep.csv	Mon Jun 21 12:50:29 2021 +0000
@@ -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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/iPRG.samples.lst	Mon Jun 21 12:50:29 2021 +0000
@@ -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
\ No newline at end of file