# HG changeset patch # User galaxyp # Date 1624279829 0 # Node ID 174cfed15fe2c3e215ebb1de637f74b48690b90c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6" diff -r 000000000000 -r 174cfed15fe2 diffacto.xml --- /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 @@ + + Comparative Protein Abundance from Covariation of Peptide Abundances + + 1.0.6 + 0 + + + diffacto + + 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 + ]]> + + + +
  • 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 ProteinID 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.
    • + + ]]>     + + + + Optional: By default, each Sample column in Peptide abundances is treated as a singleton group. +
    + 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: +
      +
    1. Sample name for header line of the Peptides abundance input.
      2. +
    2. Group Name assignemnt for the sample
      3. +
    + ]]>     + + + Optional: By default, Diffacto uses the average of all samples/groups as the reference. +
    + Names of sample groups (separated by semicolon) treated as the comparison reference. +
      +
    • If a Sample Groups input was used, the reference names should be Group names from column 2.
      • +
    • Otherwise, the reference names should be Sample names from the Peptides abundance column header line.
      • +
    + ]]>     + + + + + + + + + + + + + + + + + + + +     + + + + + + + + + mcfdr == True + + + + + + + loadings == True + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1074/mcp.O117.067728 + +     diff -r 000000000000 -r 174cfed15fe2 test-data/HBY20Mix.peptides.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HBY20Mix.peptides.csv Mon Jun 21 12:50:29 2021 +0000 @@ -0,0 +1,101 @@ 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+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 diff -r 000000000000 -r 174cfed15fe2 test-data/UP000002311_559292.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/UP000002311_559292.fasta Mon Jun 21 12:50:29 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 diff -r 000000000000 -r 174cfed15fe2 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 12:50:29 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 diff -r 000000000000 -r 174cfed15fe2 test-data/iPRG.samples.lst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/iPRG.samples.lst Mon Jun 21 12:50:29 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