changeset 0:ce13b4c42256 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,15 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.3.0</token>
+
+    <xml name="requirements">
+        <requirement type="package" version="@TOOL_VERSION@">omark</requirement>
+        <requirement type="package" version="2.0.2">omamer</requirement>
+    </xml>
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1101/2022.11.25.517970</citation> 
+        </citations>
+    </xml>
+
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/omark.xml	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,108 @@
+<?xml version="1.0"?>
+<tool id="omark" name="OMArk" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+    <description>proteome quality assessment</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="requirements" />
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+    omamer search --db '$database' --query '$input' --out 'output_omamer'
+    &&
+
+    omark
+    -f 'output_omamer'
+    -d '$database'
+    $omark_mode
+    -i '$input_iso'
+    -t 't'
+    -r 'r'
+    -o omark_galaxy
+
+    ]]></command>
+
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Protein sequences"/>
+        <param name="input_iso" type="data" format="txt" optional="true" label="Input isoform file" help="A semi-colon separated file, listing all isoforms of each genes, with one gene per line."/>
+        <param argument="-c" name="omark_mode" type="boolean" checked="false" label="Only compute a list of conserved HOGs" help="Can be used to obtain a set of genes on which to train"/>
+        <param name="database" label="OMAmer database" type="select">
+            <options from_data_table="omamer"/>
+        </param>
+
+        <param argument="-t" type="text" optional="true" label="Taxonomic identifier" help="NCBI taxid corresponding to the input proteome">
+            <sanitizer invalid_char="">
+                <valid initial="string.letters,string.digits">
+                    <add value="_" />
+                </valid>
+            </sanitizer>
+            <validator type="regex">[0-9a-zA-Z_]+</validator>
+        </param>
+        <param argument="-r" type="text" optional="true" label="Taxonomic rank">
+            <sanitizer invalid_char="">
+                <valid initial="string.letters,string.digits">
+                    <add value="_" />
+                </valid>
+            </sanitizer>
+            <validator type="regex">[0-9a-zA-Z_]+</validator>
+        </param>
+        
+        <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
+            <option value="detail_sum" selected="true">Detailed summary</option>
+            <option value="hog">HOG identifiers</option>
+            <option value="pdf">PDF Graphic representation </option>
+            <option value="png">PNG Graphic representation </option>
+            <option value="sum">Comparative proteome analysis</option>
+            <option value="tax">Taxomony</option>
+            <option value="ump">Protein identifiers</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="omark_detail_sum" format="txt" label="${tool.name} on ${on_string}: Detailed summary" from_work_dir="omark_galaxy/*detailed_summary.txt">
+            <filter>outputs and 'detail_sum' in outputs</filter>
+        </data>
+        <data name="omark_hog" format="omq" label="${tool.name} on ${on_string}: HOG identifiers" from_work_dir="omark_galaxy/*.omq">
+            <filter>outputs and 'hog' in outputs</filter>
+        </data>
+        <data name="omark_pdf" format="pdf" label="${tool.name} on ${on_string}: Graphic representation (pdf)" from_work_dir="omark_galaxy/*.pdf">
+            <filter>outputs and 'pdf' in outputs</filter>
+        </data>
+        <data name="omark_png" format="png" label="${tool.name} on ${on_string}: Graphic representation (png)" from_work_dir="omark_galaxy/*.png">
+            <filter>outputs and 'png' in outputs</filter>
+        </data>
+        <data name="omark_sum" format="sum" label="${tool.name} on ${on_string}: Comparative proteome analysis" from_work_dir="omark_galaxy/*.sum">
+            <filter>outputs and 'sum' in outputs</filter>
+        </data>
+        <data name="omark_tax" format="txt" label="${tool.name} on ${on_string}: Taxomony" from_work_dir="omark_galaxy/*.tax">
+            <filter>outputs and 'tax' in outputs</filter>
+        </data>
+        <data name="omark_ump" format="ump" label="${tool.name} on ${on_string}: Protein identifiers" from_work_dir="omark_galaxy/*.ump">
+            <filter>outputs and 'ump' in outputs</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test expect_failure="true">
+            <param name="input" value="input.fasta"/>
+            <param name="outputs" value="sum,detail_sum,png,hog,pdf,ump,tax"/>
+            <param name="database" value="test"/>
+        </test>
+    </tests>
+
+
+    <help><![CDATA[
+        OMark_: is a software for proteome quality assessment. 
+        It provides measures of proteome completeness, characterizes the consistency
+        of all protein coding genes with regard to their homologs, and identifies the
+        presence of contamination from other species. 
+
+        OMArk relies on the OMA orthology database.
+        For more information, please refer to the OMamer_ documentaion.
+
+        .. _OMark: https://github.com/DessimozLab/OMArk
+        .. _OMamer: https://github.com/DessimozLab/omamer
+    ]]></help>
+    <expand macro="citation"/>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fasta	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,403 @@
+>tr|A0A2R8YED5|A0A2R8YED5_HUMAN Olfactory receptor OS=Homo sapiens OX=9606 GN=OR5BS1P PE=3 SV=1
+MEVSNMTTVTVFILLGLSNNPQVQALLFVLFLVIYLLTLLGNLLMVLVISTDSHLCTPMY
+FFLRQLSFLDAFYSSIIVPKLLENLLSKGETISFLECFTQISLVIFSGATEACLLSVMAY
+DRFQAMCHPLLYVVIINRRVCAGLVGASWAIGMGTGLINTLLLAQQHFCGPNVIHSFACE
+LPPVLLLTCSDPCASIVSILTTMSVLGLGTLVLLLGSYSCIIMTALRINSATGRSKIFST
+CSSHFLVVTIFYTSGVLRYMIPASGSALEQVLSVQYSVITPLLNPLIYSLKSQEVKVALR
+RMLARKSRLPL
+>sp|A0JD32|TV382_HUMAN T cell receptor alpha variable 38-2/delta variable 8 OS=Homo sapiens OX=9606 GN=TRAV38-2DV8 PE=3 SV=1
+MACPGFLWALVISTCLEFSMAQTVTQSQPEMSVQEAETVTLSCTYDTSESDYYLFWYKQP
+PSRQMILVIRQEAYKQQNATENRFSVNFQKAAKSFSLKISDSQLGDAAMYFCAYRS
+>sp|A5D6W6|FITM1_HUMAN Fat storage-inducing transmembrane protein 1 OS=Homo sapiens OX=9606 GN=FITM1 PE=2 SV=1
+MERGPVVGAGLGAGARIQALLGCLLKVLLWVASALLYFGSEQAARLLGSPCLRRLYHAWL
+AAVVIFGPLLQFHVNPRTIFASHGNFFNIKFVNSAWGWTCTFLGGFVLLVVFLATRRVAV
+TARHLSRLVVGAAVWRGAGRAFLLIEDLTGSCFEPLPQGLLLHELPDRRSCLAAGHQWRG
+YTVSSHTFLLTFCCLLMAEEAAVFAKYLAHGLPAGAPLRLVFLLNVLLLGLWNFLLLCTV
+IYFHQYTHKVVGAAVGTFAWYLTYGSWYHQPWSPGSPGHGLFPRPHSSRKHN
+>sp|A6NH00|OR2T8_HUMAN Olfactory receptor 2T8 OS=Homo sapiens OX=9606 GN=OR2T8 PE=3 SV=1
+MENGSYTSYFILLGLFNHTRAHQVLFMMVLSIVLTSLFGNSLMILLIHWDHRLHTPMYFL
+LSQLSLMDVMLVSTTVPKMAADYLTGSKAISRAGCGAQIFFLPTLGGGECFLLAAMAYDR
+YAAVCHPLRYPTLMSWQLCLRMNLSCWLLGAADGLLQAVATLSFPYCGAHEIDHFFCETP
+VLVRLACADTSVFENAMYICCVLMLLVPFSLILSSYGLILAAVLHMRSTEARKKAFATCS
+SHVAVVGLFYGAAIFTYMRPKSHRSTNHDKVVSAFYTMFTPLLNPLIYSVKNSEVKGALT
+RCMGRCVALSRE
+>sp|B3EWG5|FM25C_HUMAN Protein FAM25C OS=Homo sapiens OX=9606 GN=FAM25C PE=1 SV=1
+MLGGLGKLAAEGLAHRTEKATEGAIHAVEEVVKEVVGHAKETGEKAIAEAIKKAQESGDK
+KMKEITETVTNTVTNAITHAAESLDKLGQ
+>sp|D6RGX4|F90AP_HUMAN Putative protein FAM90A26 OS=Homo sapiens OX=9606 GN=FAM90A26 PE=5 SV=1
+MMACRDPKPGAKRLVRAQTLQKQRRAPVGPRAPPPDEEDPRLKCKNCGAFGHMARSTRCP
+MKCWKAALVPPTLGKKEGKENLKPWKPQVEANPGPLNKDKGEKEERPRQQDPQRKALLHI
+FSGKPPEKPLPNRKGSTESSVYLRVASGPMPVHTTSKRPRVDPVLADRSATEMSDRGSAL
+ASLSPLRKASLSSSSSLGPKERQTGAAADIPQPAVRHQGPEPLLVVKPTHSSPEGGCREV
+PQAASKTHGLLQAISPQAQDKRPAVTSQPCPPAATHSLGLGSNLSFGPGAKRPAQAPIQA
+CLNFPKKPRLGPFQIPESAIQGGELGAPEYLQPPPATTELGPSTSPQMGRRTPAQVSSVD
+RQPPHSRPCLPTAQACTMSHHPATSHDGAQPLRVLFRRLENGRWSSSLLAAPSFHSPEKP
+GAFLAQSPHVSEKSEVPRVRVPPNVLYEDLQVSSSSEDSDSDLE
+>sp|O00451|GFRA2_HUMAN GDNF family receptor alpha-2 OS=Homo sapiens OX=9606 GN=GFRA2 PE=1 SV=2
+MILANVFCLFFFLDETLRSLASPSSLQGPELHGWRPPVDCVRANELCAAESNCSSRYRTL
+RQCLAGRDRNTMLANKECQAALEVLQESPLYDCRCKRGMKKELQCLQIYWSIHLGLTEGE
+EFYEASPYEPVTSRLSDIFRLASIFSGTGADPVVSAKSNHCLDAAKACNLNDNCKKLRSS
+YISICNREISPTERCNRRKCHKALRQFFDRVPSEYTYRMLFCSCQDQACAERRRQTILPS
+CSYEDKEKPNCLDLRGVCRTDHLCRSRLADFHANCRASYQTVTSCPADNYQACLGSYAGM
+IGFDMTPNYVDSSPTGIVVSPWCSCRGSGNMEEECEKFLRDFTENPCLRNAIQAFGNGTD
+VNVSPKGPSFQATQAPRVEKTPSLPDDLSDSTSLGTSVITTCTSVQEQGLKANNSKELSM
+CFTELTTNIIPGSNKVIKPNSGPSRARPSAALTVLSVLMLKLAL
+>sp|O14817|TSN4_HUMAN Tetraspanin-4 OS=Homo sapiens OX=9606 GN=TSPAN4 PE=1 SV=1
+MARACLQAVKYLMFAFNLLFWLGGCGVLGVGIWLAATQGSFATLSSSFPSLSAANLLIIT
+GAFVMAIGFVGCLGAIKENKCLLLTFFLLLLLVFLLEATIAILFFAYTDKIDRYAQQDLK
+KGLHLYGTQGNVGLTNAWSIIQTDFRCCGVSNYTDWFEVYNATRVPDSCCLEFSESCGLH
+APGTWWKAPCYETVKVWLQENLLAVGIFGLCTALVQILGLTFAMTMYCQVVKADTYCA
+>sp|O14901|KLF11_HUMAN Krueppel-like factor 11 OS=Homo sapiens OX=9606 GN=KLF11 PE=1 SV=2
+MHTPDFAGPDDARAVDIMDICESILERKRHDSERSTCSILEQTDMEAVEALVCMSSWGQR
+SQKGDLLRIRPLTPVSDSGDVTTTVHMDAATPELPKDFHSLSTLCITPPQSPDLVEPSTR
+TPVSPQVTDSKACTATDVLQSSAVVARALSGGAERGLLGLEPVPSSPCRAKGTSVIRHTG
+ESPAACFPTIQTPDCRLSDSREGEEQLLGHFETLQDTHLTDSLLSTNLVSCQPCLHKSGG
+LLLTDKGQQAGWPGAVQTCSPKNYENDLPRKTTPLISVSVPAPPVLCQMIPVTGQSSMLP
+AFLKPPPQLSVGTVRPILAQAAPAPQPVFVGPAVPQGAVMLVLPQGALPPPAPCAANVMA
+AGNTKLLPLAPAPVFITSSQNCVPQVDFSRRRNYVCSFPGCRKTYFKSSHLKAHLRTHTG
+EKPFNCSWDGCDKKFARSDELSRHRRTHTGEKKFVCPVCDRRFMRSDHLTKHARRHMTTK
+KIPGWQAEVGKLNRIASAESPGSPLVSMPASA
+>sp|O15079|SNPH_HUMAN Syntaphilin OS=Homo sapiens OX=9606 GN=SNPH PE=1 SV=2
+MAMSLPGSRRTSAGSRRRTSPPVSVRDAYGTSSLSSSSNSGSYKGSDSSPTPRRSMKYTL
+CSDNHGIKPPTPEQYLTPLQQKEVCIRHLKARLKDTQDRLQDRDTEIDDLKTQLSRMQED
+WIEEECHRVEAQLALKEARKEIKQLKQVIDTVKNNLIDKDKGLQKYFVDINIQNKKLETL
+LHSMEVAQNGMAKEDGTGESAGGSPARSLTRSSTYTKLSDPAVCGDRQPGDPSSGSAEDG
+ADSGFAAADDTLSRTDALEASSLLSSGVDCGTEETSLHSSFGLGPRFPASNTYEKLLCGM
+EAGVQASCMQERAIQTDFVQYQPDLDTILEKVTQAQVCGTDPESGDRCPELDAHPSGPRD
+PNSAVVVTVGDELEAPEPITRGPTPQRPGANPNPGQSVSVVCPMEEEEEAAVAEKEPKSY
+WSRHYIVDLLAVVVPAVPTVAWLCRSQRRQGQPIYNISSLLRGCCTVALHSIRRISCRSL
+SQPSPSPAGGGSQL
+>sp|O15400|STX7_HUMAN Syntaxin-7 OS=Homo sapiens OX=9606 GN=STX7 PE=1 SV=4
+MSYTPGVGGDPAQLAQRISSNIQKITQCSVEIQRTLNQLGTPQDSPELRQQLQQKQQYTN
+QLAKETDKYIKEFGSLPTTPSEQRQRKIQKDRLVAEFTTSLTNFQKVQRQAAEREKEFVA
+RVRASSRVSGSFPEDSSKERNLVSWESQTQPQVQVQDEEITEDDLRLIHERESSIRQLEA
+DIMDINEIFKDLGMMIHEQGDVIDSIEANVENAEVHVQQANQQLSRAADYQRKSRKTLCI
+IILILVIGVAIISLIIWGLNH
+>sp|O15547|P2RX6_HUMAN P2X purinoceptor 6 OS=Homo sapiens OX=9606 GN=P2RX6 PE=1 SV=2
+MCPQLAGAGSMGSPGATTGWGLLDYKTEKYVMTRNWRVGALQRLLQFGIVVYVVGWALLA
+KKGYQERDLEPQFSIITKLKGVSVTQIKELGNRLWDVADFVKPPQGENVFFLVTNFLVTP
+AQVQGRCPEHPSVPLANCWVDEDCPEGEGGTHSHGVKTGQCVVFNGTHRTCEIWSWCPVE
+SGVVPSRPLLAQAQNFTLFIKNTVTFSKFNFSKSNALETWDPTYFKHCRYEPQFSPYCPV
+FRIGDLVAKAGGTFEDLALLGGSVGIRVHWDCDLDTGDSGCWPHYSFQLQEKSYNFRTAT
+HWWEQPGVEARTLLKLYGIRFDILVTGQAGKFGLIPTAVTLGTGAAWLGVVTFFCDLLLL
+YVDREAHFYWRTKYEEAKAPKATANSVWRELALASQARLAECLRRSSAPAPTATAAGSQT
+QTPGWPCPSSDTHLPTHSGSL
+>sp|O43598|DNPH1_HUMAN 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 OS=Homo sapiens OX=9606 GN=DNPH1 PE=1 SV=1
+MAAAMVPGRSESWERGEPGRPALYFCGSIRGGREDRTLYERIVSRLRRFGTVLTEHVAAA
+ELGARGEEAAGGDRLIHEQDLEWLQQADVVVAEVTQPSLGVGYELGRAVAFNKRILCLFR
+PQSGRVLSAMIRGAADGSRFQVWDYEEGEVEALLDRYFEADPPGQVAASPDPTT
+>sp|O75078|ADA11_HUMAN Disintegrin and metalloproteinase domain-containing protein 11 OS=Homo sapiens OX=9606 GN=ADAM11 PE=2 SV=3
+MRLLRRWAFAALLLSLLPTPGLGTQGPAGALRWGGLPQLGGPGAPEVTEPSRLVRESSGG
+EVRKQQLDTRVRQEPPGGPPVHLAQVSFVIPAFNSNFTLDLELNHHLLSSQYVERHFSRE
+GTTQHSTGAGDHCYYQGKLRGNPHSFAALSTCQGLHGVFSDGNLTYIVEPQEVAGPWGAP
+QGPLPHLIYRTPLLPDPLGCREPGCLFAVPAQSAPPNRPRLRRKRQVRRGHPTVHSETKY
+VELIVINDHQLFEQMRQSVVLTSNFAKSVVNLADVIYKEQLNTRIVLVAMETWADGDKIQ
+VQDDLLETLARLMVYRREGLPEPSDATHLFSGRTFQSTSSGAAYVGGICSLSHGGGVNEY
+GNMGAMAVTLAQTLGQNLGMMWNKHRSSAGDCKCPDIWLGCIMEDTGFYLPRKFSRCSID
+EYNQFLQEGGGSCLFNKPLKLLDPPECGNGFVEAGEECDCGSVQECSRAGGNCCKKCTLT
+HDAMCSDGLCCRRCKYEPRGVSCREAVNECDIAETCTGDSSQCPPNLHKLDGYYCDHEQG
+RCYGGRCKTRDRQCQVLWGHAAADRFCYEKLNVEGTERGSCGRKGSGWVQCSKQDVLCGF
+LLCVNISGAPRLGDLVGDISSVTFYHQGKELDCRGGHVQLADGSDLSYVEDGTACGPNML
+CLDHRCLPASAFNFSTCPGSGERRICSHHGVCSNEGKCICQPDWTGKDCSIHNPLPTSPP
+TGETERYKGPSGTNIIIGSIAGAVLVAAIVLGGTGWGFKNIRRGRSGGA
+>sp|O75347|TBCA_HUMAN Tubulin-specific chaperone A OS=Homo sapiens OX=9606 GN=TBCA PE=1 SV=3
+MADPRVRQIKIKTGVVKRLVKEKVMYEKEAKQQEEKIEKMRAEDGENYDIKKQAEILQES
+RMMIPDCQRRLEAAYLDLQRILENEKDLEEAEEYKEARLVLDSVKLEA
+>sp|O94913|PCF11_HUMAN Pre-mRNA cleavage complex 2 protein Pcf11 OS=Homo sapiens OX=9606 GN=PCF11 PE=1 SV=3
+MSEQTPAEAGAAGAREDACRDYQSSLEDLTFNSKPHINMLTILAEENLPFAKEIVSLIEA
+QTAKAPSSEKLPVMYLMDSIVKNVGREYLTAFTKNLVATFICVFEKVDENTRKSLFKLRS
+TWDEIFPLKKLYALDVRVNSLDPAWPIKPLPPNVNTSSIHVNPKFLNKSPEEPSTPGTVV
+SSPSISTPPIVPDIQKNLTQEQLIRQQLLAKQKQLLELQQKKLELELEQAKAQLAVSLSV
+QQETSNLGPGSAPSKLHVSQIPPMAVKAPHQVPVQSEKSRPGPSLQIQDLKGTNRDPRLN
+RISQHSHGKDQSHRKEFLMNTLNQSDTKTSKTIPSEKLNSSKQEKSKSGEKITKKELDQL
+DSKSKSKSKSPSPLKNKLSHTKDLKNQESESMRLSDMNKRDPRLKKHLQDKTDGKDDDVK
+EKRKTAEKKDKDEHMKSSEHRLAGSRNKIINGIVQKQDTITEESEKQGTKPGRSSTRKRS
+RSRSPKSRSPIIHSPKRRDRRSPKRRQRSMSPTSTPKAGKIRQSGAKQSHMEEFTPPSRE
+DRNAKRSTKQDIRDPRRMKKTEEERPQETTNQHSTKSGTEPKENVENWQSSKSAKRWKSG
+WEENKSLQQVDEHSKPPHLRHRESWSSTKGILSPRAPKQQQHRLSVDANLQIPKELTLAS
+KRELLQKTSERLASGEITQDDFLVVVHQIRQLFQYQEGVREEQRSPFNDRFPLKRPRYED
+SDKPFVDSPASRFAGLDTNQRLTALAEDRPLFDGPSRPSVARDGPTKMIFEGPNKLSPRI
+DGPPTPASLRFDGSPGQMGGGGPLRFEGPQGQLGGGCPLRFEGPPGPVGTPLRFEGPIGQ
+AGGGGFRFEGSPGLRFEGSPGGLRFEGPGGQPVGGLRFEGHRGQPVGGLRFEGPHGQPVG
+GLRFDNPRGQPVGGLRFEGGHGPSGAAIRFDGPHGQPGGGIRFEGPLLQQGVGMRFEGPH
+GQSVAGLRFEGQHNQLGGNLRFEGPHGQPGVGIRFEGPLVQQGGGMRFEGPSVPGGGLRI
+EGPLGQGGPRFEGCHALRFDGQPGQPSLLPRFDGLHGQPGPRFERTPGQPGPQRFDGPPG
+QQVQPRFDGVPQRFDGPQHQQASRFDIPLGLQGTRFDNHPSQRLESVSFNQTGPYNDPPG
+NAFNAPSQGLQFQRHEQIFDSPQGPNFNGPHGPGNQSFSNPLNRASGHYFDEKNLQSSQF
+GNFGNIPAPMTVGNIQASQQVLSGVAQPVAFGQGQQFLPVHPQNPGFVQNPSGALPKAYP
+DNHLSQVDVNELFSKLLKTGILKLSQTDSATTQVSEVTAQPPPEEEEDQNEDQDVPDLTN
+FTVEELKQRYDSVINRLYTGIQCYSCGMRFTTSQTDVYADHLDWHYRQNRTEKDVSRKVT
+HRRWYYSLTDWIEFEEIADLEERAKSQFFEKVHEEVVLKTQEAAKEKEFQSVPAGPAGAV
+ESCEICQEQFEQYWDEEEEEWHLKNAIRVDGKIYHPSCYEDYQNTSSFDCTPSPSKTPVE
+NPLNIMLNIVKNELQEPCDSPKVKEERIDTPPACTEESIATPSEIKTENDTVESV
+>sp|O95210|STBD1_HUMAN Starch-binding domain-containing protein 1 OS=Homo sapiens OX=9606 GN=STBD1 PE=1 SV=1
+MGAVWSALLVGGGLAGALFVWLLRGGPGDTGKDGDAEQEKDAPLGGAAIPGGHQSGSSGL
+SPGPSGQELVTKPEHLQESNGHLISKTKDLGKLQAASWRLQNPSREVCDNSREHVPSGQF
+PDTEAPATSETSNSRSYSEVSRNESLESPMGEWGFQKGQEISAKAATCFAEKLPSSNLLK
+NRAKEEMSLSDLNSQDRVDHEEWEMVPRHSSWGDVGVGGSLKAPVLNLNQGMDNGRSTLV
+EARGQQVHGKMERVAVMPAGSQQVSVRFQVHYVTSTDVQFIAVTGDHECLGRWNTYIPLH
+YNKDGFWSHSIFLPADTVVEWKFVLVENGGVTRWEECSNRFLETGHEDKVVHAWWGIH
+>sp|O95274|LYPD3_HUMAN Ly6/PLAUR domain-containing protein 3 OS=Homo sapiens OX=9606 GN=LYPD3 PE=1 SV=2
+MDPARKAGAQAMIWTAGWLLLLLLRGGAQALECYSCVQKADDGCSPNKMKTVKCAPGVDV
+CTEAVGAVETIHGQFSLAVRGCGSGLPGKNDRGLDLHGLLAFIQLQQCAQDRCNAKLNLT
+SRALDPAGNESAYPPNGVECYSCVGLSREACQGTSPPVVSCYNASDHVYKGCFDGNVTLT
+AANVTVSLPVRGCVQDEFCTRDGVTGPGFTLSGSCCQGSRCNSDLRNKTYFSPRIPPLVR
+LPPPEPTTVASTTSVTTSTSAPVRPTSTTKPMPAPTSQTPRQGVEHEASRDEEPRLTGGA
+AGHQDRSNSGQYPAKGGPQQPHNKGCVAPTAGLAALLLAVAAGVLL
+>sp|O95415|BRI3_HUMAN Brain protein I3 OS=Homo sapiens OX=9606 GN=BRI3 PE=1 SV=1
+MDHKPLLQERPPAYNLEAGQGDYACGPHGYGAIPAAPPPPPYPYLVTGIPTHHPRVYNIH
+SRTVTRYPANSIVVVGGCPVCRVGVLEDCFTFLGIFLAIILFPFGFICCFALRKRRCPNC
+GATFA
+>sp|P00491|PNPH_HUMAN Purine nucleoside phosphorylase OS=Homo sapiens OX=9606 GN=PNP PE=1 SV=2
+MENGYTYEDYKNTAEWLLSHTKHRPQVAIICGSGLGGLTDKLTQAQIFDYGEIPNFPRST
+VPGHAGRLVFGFLNGRACVMMQGRFHMYEGYPLWKVTFPVRVFHLLGVDTLVVTNAAGGL
+NPKFEVGDIMLIRDHINLPGFSGQNPLRGPNDERFGDRFPAMSDAYDRTMRQRALSTWKQ
+MGEQRELQEGTYVMVAGPSFETVAECRVLQKLGADAVGMSTVPEVIVARHCGLRVFGFSL
+ITNKVIMDYESLEKANHEEVLAAGKQAAQKLEQFVSILMASIPLPDKAS
+>sp|P03999|OPSB_HUMAN Short-wave-sensitive opsin 1 OS=Homo sapiens OX=9606 GN=OPN1SW PE=1 SV=1
+MRKMSEEEFYLFKNISSVGPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATL
+RYKKLRQPLNYILVNVSFGGFLLCIFSVFPVFVASCNGYFVFGRHVCALEGFLGTVAGLV
+TGWSLAFLAFERYIVICKPFGNFRFSSKHALTVVLATWTIGIGVSIPPFFGWSRFIPEGL
+QCSCGPDWYTVGTKYRSESYTWFLFIFCFIVPLSLICFSYTQLLRALKAVAAQQQESATT
+QKAEREVSRMVVVMVGSFCVCYVPYAAFAMYMVNNRNHGLDLRLVTIPSFFSKSACIYNP
+IIYCFMNKQFQACIMKMVCGKAMTDESDTCSSQKTEVSTVSSTQVGPN
+>sp|P09466|PAEP_HUMAN Glycodelin OS=Homo sapiens OX=9606 GN=PAEP PE=1 SV=2
+MLCLLLTLGVALVCGVPAMDIPQTKQDLELPKLAGTWHSMAMATNNISLMATLKAPLRVH
+ITSLLPTPEDNLEIVLHRWENNSCVEKKVLGEKTENPKKFKINYTVANEATLLDTDYDNF
+LFLCLQDTTTPIQSMMCQYLARVLVEDDEIMQGFIRAFRPLPRHLWYLLDLKQMEEPCRF
+>sp|P09544|WNT2_HUMAN Protein Wnt-2 OS=Homo sapiens OX=9606 GN=WNT2 PE=2 SV=1
+MNAPLGGIWLWLPLLLTWLTPEVNSSWWYMRATGGSSRVMCDNVPGLVSSQRQLCHRHPD
+VMRAISQGVAEWTAECQHQFRQHRWNCNTLDRDHSLFGRVLLRSSRESAFVYAISSAGVV
+FAITRACSQGEVKSCSCDPKKMGSAKDSKGIFDWGGCSDNIDYGIKFARAFVDAKERKGK
+DARALMNLHNNRAGRKAVKRFLKQECKCHGVSGSCTLRTCWLAMADFRKTGDYLWRKYNG
+AIQVVMNQDGTGFTVANERFKKPTKNDLVYFENSPDYCIRDREAGSLGTAGRVCNLTSRG
+MDSCEVMCCGRGYDTSHVTRMTKCGCKFHWCCAVRCQDCLEALDVHTCKAPKNADWTTAT
+>sp|P0C629|O10J4_HUMAN Olfactory receptor 10J4 OS=Homo sapiens OX=9606 GN=OR10J4 PE=3 SV=1
+MPRPNFMAVTEFTFEGFSIFEWHHRLILFVIFLVLYVLTLASNAIILIVIRLNHQLHTPM
+YFFLSVLSISETYYTVAINPQMLSGLLSPQQTISIPGCAAQLFFYLTFGVNKCFLLTAMG
+YDHYVAICNPLQYSVIMGKKACIQLVSGSWNIGLSTAIIQVSSVFSLPFCDANLISHFFC
+DIRPIMKLACADTTIKEIITLLISLCVLVLPMVLIFISYVLIVTTILKIASAEGRRKAFA
+TCASHLTVVIVHYGRTSFIYLKPKSQNSLQDRLISVTYTVITPLLNPVVYSLRNKEVKDA
+LLRALGRKPLS
+>sp|P0C881|R10B1_HUMAN Radial spoke head 10 homolog B OS=Homo sapiens OX=9606 GN=RSPH10B PE=2 SV=1
+MVKEKKKADKKGEKSARSPSSLSDNLDFSKQDGNTTRQEMSPAGVPLLGMQLNEVKPKKD
+RQNVQQNEDATQYEESILTKLIVESYEGEKVRGLYEGEGFAAFQGGCTYRGMFSEGLMHG
+QGTYIWADGLKYEGDFVKNVPMNHGVYTWPDGSMYEGEVVNGMRNGFGMFKCSTQPVSYI
+GHWCNGKRHGKGSIYYNQEGTCWYEGDWVQNIKKGWGIRCYKSGNIYEGQWEDNMRHGEG
+RMRWLTTNEEYTGRWERGIQNGFGTHTWFLKRIRSSQYPLRNEYIGEFVNGYRHGRGKFY
+YASGAMYDGEWVSNKKHGMGRLTFKNGRVYEGAFSNDHIAGFPDLEVEFISCLDLSSGVA
+PRLSRSAELIRKLDGSESHSVLGSSIELDLNLLLDMYPETVQPEEKKQVEYAVLRNITEL
+RRIYSFYSSLGCGHSLDNTFLMTKLHFWRFLKDCKFHHHKLTLADMDRILSANNDIPVEE
+IHSPFTTILLRTFLNYLLHLAYHIYHEEFQKRSPSLFLCFTKLMTENIRPNAFQIKGNLF
+REQQRTLYSMSYMNKCWEIYLAYCRPSAAPPHEPTMKMRHFLWMLKDFKMINKELTAATF
+MEVIAEDNRFIYDGIDSNFEPELVFLEFFEALLSFAFICVTDQMTKSYTNVPADDVSGNK
+HETIYTILNQDAQNKSPSAVMSHESDAAHSDSARSSSSKLELSPDVNKIRKSEPKIKKSV
+SHERVSKMNFKLTGKGITFFSSESKKYERPKDDREEEFNTWVNNMYVFFVNTLFHAYKRE
+EAIKEKIRADRLRSTAQAQQRKMEDDELEARLNIFILREEEAKRHDYEVDITVLKEPADV
+SSSHLILDPPKEDVTVSPSSKTITSKKKKK
+>sp|P12104|FABPI_HUMAN Fatty acid-binding protein, intestinal OS=Homo sapiens OX=9606 GN=FABP2 PE=1 SV=2
+MAFDSTWKVDRSENYDKFMEKMGVNIVKRKLAAHDNLKLTITQEGNKFTVKESSAFRNIE
+VVFELGVTFNYNLADGTELRGTWSLEGNKLIGKFKRTDNGNELNTVREIIGDELVQTYVY
+EGVEAKRIFKKD
+>sp|P19622|HME2_HUMAN Homeobox protein engrailed-2 OS=Homo sapiens OX=9606 GN=EN2 PE=2 SV=3
+MEENDPKPGEAAAAVEGQRQPESSPGGGSGGGGGSSPGEADTGRRRALMLPAVLQAPGNH
+QHPHRITNFFIDNILRPEFGRRKDAGTCCAGAGGGRGGGAGGEGGASGAEGGGGAGGSEQ
+LLGSGSREPRQNPPCAPGAGGPLPAAGSDSPGDGEGGSKTLSLHGGAKKGGDPGGPLDGS
+LKARGLGGGDLSVSSDSDSSQAGANLGAQPMLWPAWVYCTRYSDRPSSGPRSRKPKKKNP
+NKEDKRPRTAFTAEQLQRLKAEFQTNRYLTEQRRQSLAQELSLNESQIKIWFQNKRAKIK
+KATGNKNTLAVHLMAQGLYNHSTTAKEGKSDSE
+>sp|P20813|CP2B6_HUMAN Cytochrome P450 2B6 OS=Homo sapiens OX=9606 GN=CYP2B6 PE=1 SV=1
+MELSVLLFLALLTGLLLLLVQRHPNTHDRLPPGPRPLPLLGNLLQMDRRGLLKSFLRFRE
+KYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNR
+WKVLRRFSVTTMRDFGMGKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIIC
+SIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKYFPGAHRQVYKNLQE
+INAYIGHSVEKHRETLDPSAPKDLIDTYLLHMEKEKSNAHSEFSHQNLNLNTLSLFFAGT
+ETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFS
+DLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGAL
+KKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKI
+PPTYQIRFLPR
+>sp|P22626|ROA2_HUMAN Heterogeneous nuclear ribonucleoproteins A2/B1 OS=Homo sapiens OX=9606 GN=HNRNPA2B1 PE=1 SV=2
+MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKR
+SRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIK
+EDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTINGH
+NAEVRKALSRQEMQEVQSSRSGRGGNFGFGDSRGGGGNFGPGPGSNFRGGSDGYGSGRGF
+GDGYNGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQGGGYGGGYDNYGGGNYGSGNY
+NDFGNYNQQPSNYGPMKSGNFGGSRNMGGPYGGGNYGPGGSGGSGGYGGRSRY
+>sp|P25929|NPY1R_HUMAN Neuropeptide Y receptor type 1 OS=Homo sapiens OX=9606 GN=NPY1R PE=1 SV=1
+MNSTLFSQVENHSVHSNFSEKNAQLLAFENDDCHLPLAMIFTLALAYGAVIILGVSGNLA
+LIIIILKQKEMRNVTNILIVNLSFSDLLVAIMCLPFTFVYTLMDHWVFGEAMCKLNPFVQ
+CVSITVSIFSLVLIAVERHQLIINPRGWRPNNRHAYVGIAVIWVLAVASSLPFLIYQVMT
+DEPFQNVTLDAYKDKYVCFDQFPSDSHRLSYTTLLLVLQYFGPLCFIFICYFKIYIRLKR
+RNNMMDKMRDNKYRSSETKRINIMLLSIVVAFAVCWLPLTIFNTVFDWNHQIIATCNHNL
+LFLLCHLTAMISTCVNPIFYGFLNKNFQRDLQFFFNFCDFRSRDDDYETIAMSTMHTDVS
+KTSLKQASPVAFKKINNNDDNEKI
+>sp|P26599|PTBP1_HUMAN Polypyrimidine tract-binding protein 1 OS=Homo sapiens OX=9606 GN=PTBP1 PE=1 SV=1
+MDGIVPDIAVGTKRGSDELFSTCVTNGPFIMSSNSASAANGNDSKKFKGDSRSAGVPSRV
+IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPV
+LRGQPIYIQFSNHKELKTDSSPNQARAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQ
+SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLS
+LDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTMAAAFGLS
+VPNVHGALAPLAIPSAAAAAAAAGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGV
+YGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREG
+QEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGV
+VKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI
+>sp|P42224|STAT1_HUMAN Signal transducer and activator of transcription 1-alpha/beta OS=Homo sapiens OX=9606 GN=STAT1 PE=1 SV=2
+MSQWYELQQLDSKFLEQVHQLYDDSFPMEIRQYLAQWLEKQDWEHAANDVSFATIRFHDL
+LSQLDDQYSRFSLENNFLLQHNIRKSKRNLQDNFQEDPIQMSMIIYSCLKEERKILENAQ
+RFNQAQSGNIQSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNR
+EHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWK
+RRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQV
+LWDRTFSLFQQLIQSSFVVERQPCMPTHPQRPLVLKTGVQFTVKLRLLVKLQELNYNLKV
+KVLFDKDVNERNTVKGFRKFNILGTHTKVMNMEESTNGSLAAEFRHLQLKEQKNAGTRTN
+EGPLIVTEELHSLSFETQLCQPGLVIDLETTSLPVVVISNVSQLPSGWASILWYNMLVAE
+PRNLSFFLTPPCARWAQLSEVLSWQFSSVTKRGLNVDQLNMLGEKLLGPNASPDGLIPWT
+RFCKENINDKNFPFWLWIESILELIKKHLLPLWNDGCIMGFISKERERALLKDQQPGTFL
+LRFSESSREGAITFTWVERSQNGGEPDFHAVEPYTKKELSAVTFPDIIRNYKVMAAENIP
+ENPLKYLYPNIDKDHAFGKYYSRPKEAPEPMELDGPKGTGYIKTELISVSEVHPSRLQTT
+DNLLPMSPEEFDEVSRIVGSVEFDSMMNTV
+>sp|P42695|CNDD3_HUMAN Condensin-2 complex subunit D3 OS=Homo sapiens OX=9606 GN=NCAPD3 PE=1 SV=2
+MVALRGLGSGLQPWCPLDLRLEWVDTVWELDFTETEPLDPSIEAEIIETGLAAFTKLYES
+LLPFATGEHGSMESIWTFFIENNVSHSTLVALFYHFVQIVHKKNVSVQYREYGLHAAGLY
+FLLLEVPGSVANQVFHPVMFDKCIQTLKKSWPQESNLNRKRKKEQPKSSQANPGRHRKRG
+KPPRREDIEMDEIIEEQEDENICFSARDLSQIRNAIFHLLKNFLRLLPKFSLKEKPQCVQ
+NCIEVFVSLTNFEPVLHECHVTQARALNQAKYIPELAYYGLYLLCSPIHGEGDKVISCVF
+HQMLSVILMLEVGEGSHRAPLAVTSQVINCRNQAVQFISALVDELKESIFPVVRILLQHI
+CAKVVDKSEYRTFAAQSLVQLLSKLPCGEYAMFIAWLYKYSRSSKIPHRVFTLDVVLALL
+ELPEREVDNTLSLEHQKFLKHKFLVQEIMFDRCLDKAPTVRSKALSSFAHCLELTVTSAS
+ESILELLINSPTFSVIESHPGTLLRNSSAFSYQRQTSNRSEPSGEINIDSSGETVGSGER
+CVMAMLRRRIRDEKTNVRKSALQVLVSILKHCDVSGMKEDLWILQDQCRDPAVSVRKQAL
+QSLTELLMAQPRCVQIQKAWLRGVVPVVMDCESTVQEKALEFLDQLLLQNIRHHSHFHSG
+DDSQVLAWALLTLLTTESQELSRYLNKAFHIWSKKEKFSPTFINNVISHTGTEHSAPAWM
+LLSKIAGSSPRLDYSRIIQSWEKISSQQNPNSNTLGHILCVIGHIAKHLPKSTRDKVTDA
+VKCKLNGFQWSLEVISSAVDALQRLCRASAETPAEEQELLTQVCGDVLSTCEHRLSNIVL
+KENGTGNMDEDLLVKYIFTLGDIAQLCPARVEKRIFLLIQSVLASSADADHSPSSQGSSE
+APASQPPPQVRGSVMPSVIRAHAIITLGKLCLQHEDLAKKSIPALVRELEVCEDVAVRNN
+VIIVMCDLCIRYTIMVDKYIPNISMCLKDSDPFIRKQTLILLTNLLQEEFVKWKGSLFFR
+FVSTLIDSHPDIASFGEFCLAHLLLKRNPVMFFQHFIECIFHFNNYEKHEKYNKFPQSER
+EKRLFSLKGKSNKERRMKIYKFLLEHFTDEQRFNITSKICLSILACFADGILPLDLDASE
+LLSDTFEVLSSKEIKLLAMRSKPDKDLLMEEDDMALANVVMQEAQKKLISQVQKRNFIEN
+IIPIIISLKTVLEKNKIPALRELMHYLREVMQDYRDELKDFFAVDKQLASELEYDMKKYQ
+EQLVQEQELAKHADVAGTAGGAEVAPVAQVALCLETVPVPAGQENPAMSPAVSQPCTPRA
+SAGHVAVSSPTPETGPLQRLLPKARPMSLSTIAILNSVKKAVESKSRHRSRSLGVLPFTL
+NSGSPEKTCSQVSSYSLEQESNGEIEHVTKRAISTPEKSISDVTFGAGVSYIGTPRTPSS
+AKEKIEGRSQGNDILCLSLPDKPPPQPQQWNVRSPARNKDTPACSRRSLRKTPLKTAN
+>sp|P47929|LEG7_HUMAN Galectin-7 OS=Homo sapiens OX=9606 GN=LGALS7B PE=1 SV=2
+MSNVPHKSSLPEGIRPGTVLRIRGLVPPNASRFHVNLLCGEEQGSDAALHFNPRLDTSEV
+VFNSKEQGSWGREERGPGVPFQRGQPFEVLIIASDDGFKAVVGDAQYHHFRHRLPLARVR
+LVEVGGDVQLDSVRIF
+>sp|P51693|APLP1_HUMAN Amyloid beta precursor like protein 1 OS=Homo sapiens OX=9606 GN=APLP1 PE=1 SV=3
+MGPASPAARGLSRRPGQPPLPLLLPLLLLLLRAQPAIGSLAGGSPGAAEAPGSAQVAGLC
+GRLTLHRDLRTGRWEPDPQRSRRCLRDPQRVLEYCRQMYPELQIARVEQATQAIPMERWC
+GGSRSGSCAHPHHQVVPFRCLPGEFVSEALLVPEGCRFLHQERMDQCESSTRRHQEAQEA
+CSSQGLILHGSGMLLPCGSDRFRGVEYVCCPPPGTPDPSGTAVGDPSTRSWPPGSRVEGA
+EDEEEEESFPQPVDDYFVEPPQAEEEEETVPPPSSHTLAVVGKVTPTPRPTDGVDIYFGM
+PGEISEHEGFLRAKMDLEERRMRQINEVMREWAMADNQSKNLPKADRQALNEHFQSILQT
+LEEQVSGERQRLVETHATRVIALINDQRRAALEGFLAALQADPPQAERVLLALRRYLRAE
+QKEQRHTLRHYQHVAAVDPEKAQQMRFQVHTHLQVIEERVNQSLGLLDQNPHLAQELRPQ
+IQELLHSEHLGPSELEAPAPGGSSEDKGGLQPPDSKDDTPMTLPKGSTEQDAASPEKEKM
+NPLEQYERKVNASVPRGFPFHSSEIQRDELAPAGTGVSREAVSGLLIMGAGGGSLIVLSM
+LLLRRKKPYGAISHGVVEVDPMLTLEEQQLRELQRHGYENPTYRFLEERP
+>sp|P57678|GEMI4_HUMAN Gem-associated protein 4 OS=Homo sapiens OX=9606 GN=GEMIN4 PE=1 SV=2
+MDLGPLNICEEMTILHGGFLLAEQLFHPKALAELTKSDWERVGRPIVEALREISSAAAHS
+QPFAWKKKALIIIWAKVLQPHPVTPSDTETRWQEDLFFSVGNMIPTINHTILFELLKSLE
+ASGLFIQLLMALPTTICHAELERFLEHVTVDTSAEDVAFFLDVWWEVMKHKGHPQDPLLS
+QFSAMAHKYLPALDEFPHPPKRLRSDPDACPTMPLLAMLLRGLTQIQSRILGPGRKCCAL
+ANLADMLTVFALTEDDPQEVSATVYLDKLATVISVWNSDTQNPYHQQALAEKVKEAERDV
+SLTSLAKLPSETIFVGCEFLHHLLREWGEELQAVLRSSQGTSYDSYRLCDSLTSFSQNAT
+LYLNRTSLSKEDRQVVSELAECVRDFLRKTSTVLKNRALEDITASIAMAVIQQKMDRHME
+VCYIFASEKKWAFSDEWVACLGSNRALFRQPDLVLRLLETVIDVSTADRAIPESQIRQVI
+HLILECYADLSLPGKNKVLAGILRSWGRKGLSEKLLAYVEGFQEDLNTTFNQLTQSASEQ
+GLAKAVASVARLVIVHPEVTVKKMCSLAVVNLGTHKFLAQILTAFPALRFVEEQGPNSSA
+TFMVSCLKETVWMKFSTPKEEKQFLELLNCLMSPVKPQGIPVAALLEPDEVLKEFVLPFL
+RLDVEEVDLSLRIFIQTLEANACREEYWLQTCSPFPLLFSLCQLLDRFSKYWQLPKEKRC
+LSLDRKDLAIHILELLCEIVSANAETFSPDVWIKSLSWLHRKLEQLDWTVGLRLKSFFEG
+HFKCEVPATLFEICKLSEDEWTSQAHPGYGAGTGLLAWMECCCVSSGISERMLSLLVVDV
+GNPEEVRLFSKGFLVALVQVMPWCSPQEWQRLHQLTRRLLEKQLLHVPYSLEYIQFVPLL
+NLKPFAQELQLSVLFLRTFQFLCSHSCRDWLPLEGWNHVVKLLCGSLTRLLDSVRAIQAA
+GPWVQGPEQDLTQEALFVYTQVFCHALHIMAMLHPEVCEPLYVLALETLTCYETLSKTNP
+SVSSLLQRAHEQRFLKSIAEGIGPEERRQTLLQKMSSF
+>sp|P78417|GSTO1_HUMAN Glutathione S-transferase omega-1 OS=Homo sapiens OX=9606 GN=GSTO1 PE=1 SV=2
+MSGESARSLGKGSAPPGPVPEGSIRIYSMRFCPFAERTRLVLKAKGIRHEVININLKNKP
+EWFFKKNPFGLVPVLENSQGQLIYESAITCEYLDEAYPGKKLLPDDPYEKACQKMILELF
+SKVPSLVGSFIRSQNKEDYAGLKEEFRKEFTKLEEVLTNKKTTFFGGNSISMIDYLIWPW
+FERLEAMKLNECVDHTPKLKLWMAAMKEDPTVSALLTSEKDWQGFLELYLQNSPEACDYG
+L
+>sp|P80188|NGAL_HUMAN Neutrophil gelatinase-associated lipocalin OS=Homo sapiens OX=9606 GN=LCN2 PE=1 SV=2
+MPLGLLWLGLALLGALHAQAQDSTSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNA
+ILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKSY
+PGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLG
+LPENHIVFPVPIDQCIDG
+>sp|Q05195|MAD1_HUMAN Max dimerization protein 1 OS=Homo sapiens OX=9606 GN=MXD1 PE=1 SV=1
+MAAAVRMNIQMLLEAADYLERREREAEHGYASMLPYNNKDRDALKRRNKSKKNNSSSRST
+HNEMEKNRRAHLRLCLEKLKGLVPLGPESSRHTTLSLLTKAKLHIKKLEDCDRKAVHQID
+QLQREQRHLKRQLEKLGIERIRMDSIGSTVSSERSDSDREEIDVDVESTDYLTGDLDWSS
+SSVSDSDERGSMQSLGSDEGYSSTSIKRIKLQDSHKACLGL
+>sp|Q13077|TRAF1_HUMAN TNF receptor-associated factor 1 OS=Homo sapiens OX=9606 GN=TRAF1 PE=1 SV=1
+MASSSGSSPRPAPDENEFPFGCPPTVCQDPKEPRALCCAGCLSENPRNGEDQICPKCRGE
+DLQSISPGSRLRTQEKAHPEVAEAGIGCPFAGVGCSFKGSPQSVQEHEVTSQTSHLNLLL
+GFMKQWKARLGCGLESGPMALEQNLSDLQLQAAVEVAGDLEVDCYRAPCSESQEELALQH
+FMKEKLLAELEGKLRVFENIVAVLNKEVEASHLALATSIHQSQLDRERILSLEQRVVELQ
+QTLAQKDQALGKLEQSLRLMEEASFDGTFLWKITNVTRRCHESACGRTVSLFSPAFYTAK
+YGYKLCLRLYLNGDGTGKRTHLSLFIVIMRGEYDALLPWPFRNKVTFMLLDQNNREHAID
+AFRPDLSSASFQRPQSETNVASGCPLFFPLSKLQSPKHAYVKDDTMFLKCIVETST
+>sp|Q14765|STAT4_HUMAN Signal transducer and activator of transcription 4 OS=Homo sapiens OX=9606 GN=STAT4 PE=1 SV=1
+MSQWNQVQQLEIKFLEQVDQFYDDNFPMEIRHLLAQWIENQDWEAASNNETMATILLQNL
+LIQLDEQLGRVSKEKNLLLIHNLKRIRKVLQGKFHGNPMHVAVVISNCLREERRILAAAN
+MPVQGPLEKSLQSSSVSERQRNVEHKVAAIKNSVQMTEQDTKYLEDLQDEFDYRYKTIQT
+MDQSDKNSAMVNQEVLTLQEMLNSLDFKRKEALSKMTQIIHETDLLMNTMLIEELQDWKR
+RQQIACIGGPLHNGLDQLQNCFTLLAESLFQLRRQLEKLEEQSTKMTYEGDPIPMQRTHM
+LERVTFLIYNLFKNSFVVERQPCMPTHPQRPLVLKTLIQFTVKLRLLIKLPELNYQVKVK
+ASIDKNVSTLSNRRFVLCGTNVKAMSIEESSNGSLSVEFRHLQPKEMKSSAGGKGNEGCH
+MVTEELHSITFETQICLYGLTIDLETSSLPVVMISNVSQLPNAWASIIWYNVSTNDSQNL
+VFFNNPPPATLSQLLEVMSWQFSSYVGRGLNSDQLHMLAEKLTVQSSYSDGHLTWAKFCK
+EHLPGKSFTFWTWLEAILDLIKKHILPLWIDGYVMGFVSKEKERLLLKDKMPGTFLLRFS
+ESHLGGITFTWVDHSESGEVRFHSVEPYNKGRLSALPFADILRDYKVIMAENIPENPLKY
+LYPDIPKDKAFGKHYSSQPCEVSRPTERGDKGYVPSVFIPISTIRSDSTEPHSPSDLLPM
+SPSVYAVLRENLSPTTIETAMKSPYSAE
+>sp|Q15019|SEPT2_HUMAN Septin-2 OS=Homo sapiens OX=9606 GN=SEPTIN2 PE=1 SV=1
+MSKQQPTQFINPETPGYVGFANLPNQVHRKSVKKGFEFTLMVVGESGLGKSTLINSLFLT
+DLYPERVIPGAAEKIERTVQIEASTVEIEERGVKLRLTVVDTPGYGDAINCRDCFKTIIS
+YIDEQFERYLHDESGLNRRHIIDNRVHCCFYFISPFGHGLKPLDVAFMKAIHNKVNIVPV
+IAKADTLTLKERERLKKRILDEIEEHNIKIYHLPDAESDEDEDFKEQTRLLKASIPFSVV
+GSNQLIEAKGKKVRGRLYPWGVVEVENPEHNDFLKLRTMLITHMQDLQEVTQDLHYENFR
+SERLKRGGRKVENEDMNKDQILLEKEAELRRMQEMIARMQAQMQMQMQGGDGDGGALGHH
+V
+>sp|Q15468|STIL_HUMAN SCL-interrupting locus protein OS=Homo sapiens OX=9606 GN=STIL PE=1 SV=2
+MEPIYPFARPQMNTRFPSSRMVPFHFPPSKCALWNPTPTGDFIYLHLSYYRNPKLVVTEK
+TIRLAYRHAKQNKKNSSCFLLGSLTADEDEEGVTLTVDRFDPGREVPECLEITPTASLPG
+DFLIPCKVHTQELCSREMIVHSVDDFSSALKALQCHICSKDSLDCGKLLSLRVHITSRES
+LDSVEFDLHWAAVTLANNFKCTPVKPIPIIPTALARNLSSNLNISQVQGTYKYGYLTMDE
+TRKLLLLLESDPKVYSLPLVGIWLSGITHIYSPQVWACCLRYIFNSSVQERVFSESGNFI
+IVLYSMTHKEPEFYECFPCDGKIPDFRFQLLTSKETLHLFKNVEPPDKNPIRCELSAESQ
+NAETEFFSKASKNFSIKRSSQKLSSGKMPIHDHDSGVEDEDFSPRPIPSPHPVSQKISKI
+QPSVPELSLVLDGNFIESNPLPTPLEMVNNENPPLINHLEHLKPLQPQLYDEKHSPEVEA
+GEPSLRGIPNQLNQDKPALLRHCKVRQPPAYKKGNPHTRNSIKPSSHNGPSHDIFEKLQT
+VSAGNVQNEEYPIRPSTLNSRQSSLAPQSQPHDFVFSPHNSGRPMELQIPTPPLPSYCST
+NVCRCCQHHSHIQYSPLNSWQGANTVGSIQDVQSEALQKHSLFHPSGCPALYCNAFCSSS
+SPIALRPQGDMGSCSPHSNIEPSPVARPPSHMDLCNPQPCTVCMHTPKTESDNGMMGLSP
+DAYRFLTEQDRQLRLLQAQIQRLLEAQSLMPCSPKTTAVEDTVQAGRQMELVSVEAQSSP
+GLHMRKGVSIAVSTGASLFWNAAGEDQEPDSQMKQDDTKISSEDMNFSVDINNEVTSLPG
+SASSLKAVDIPSFEESNIAVEEEFNQPLSVSNSSLVVRKEPDVPVFFPSGQLAESVSMCL
+QTGPTGGASNNSETSEEPKIEHVMQPLLHQPSDNQKIYQDLLGQVNHLLNSSSKETEQPS
+TKAVIISHECTRTQNVYHTKKKTHHSRLVDKDCVLNATLKQLRSLGVKIDSPTKVKKNAH
+NVDHASVLACISPEAVISGLNCMSFANVGMSGLSPNGVDLSMEANAIALKYLNENQLSQL
+SVTRSNQNNCDPFSLLHINTDRSTVGLSLISPNNMSFATKKYMKRYGLLQSSDNSEDEEE
+PPDNADSKSEYLLNQNLRSIPEQLGGQKEPSKNDHEIINCSNCESVGTNADTPVLRNITN
+EVLQTKAKQQLTEKPAFLVKNLKPSPAVNLRTGKAEFTQHPEKENEGDITIFPESLQPSE
+TLKQMNSMNSVGTFLDVKRLRQLPKLF
+>sp|Q3BBV2|NBPF8_HUMAN Putative neuroblastoma breakpoint family member 8 OS=Homo sapiens OX=9606 GN=NBPF8 PE=5 SV=1
+MVVSAGPWSSEKAEMNILEINEKLRPQLAENKQQFVNLKEMFSNSTGRLPGQPTEEIQQY
+KVLVHSQERELTQLKEKLREGRDASRSLNEHLQALLTLDEPDKSQGQDLQEQLAEGCRLA
+QHLVQKLSPENDEDEDEDVQVEEDEKVLESSAPREVQKAEESKVPEDSLEECAITCSNSH
+GPCDSIQPHKNIKITFEEDKVNSSLVVDRESSHDGCQDALNILPVPGPTSSATNVSMVVS
+AGPLSSEKAEMNILEINEKLCPQLAEKKQQFRSLKEKCFVTQVACFLAKQQNKYKYEECK
+DLIKSMLRNERQFKEEKLAEQLKQAEELRQYKVLVHSQERELTQLREKLREGRDASRSLN
+EHLQALLTPDEPDKSQGQDLQEQLAEGCRLAQHLVQKLSPENDNDDDEDVQVEVAEKVQK
+SSSPREMQKAEEKEVPEDSLEECAITCSNSHGPYDSNQPHRKTKITFEEDKVDSTLIGSS
+SHVEWEDAVHIIPENESDDEEEEEKGPVSPRNLQESEEEEVPQESWDEGYSTLSIPPERL
+ASYQSYSSTFHSLEEQQVCMAVDIGRHRWDQVKKEDQEATGPRLSRELLDEKGPEVLQDS
+LDRCYSTPSGCLELTDSCQPYRSAFYILEQQRVGLAVDMDEIEKYQEVEEDQDPSCPRLS
+RELLDEKEPEVLQDSLDRCYSTPSGYLELPDLGQPYSSAVYSLEEQYLGLALDVDRIKKD
+QEEEEDQGPPCPRLSRELLEVVEPEVLQDSLDRCYSTPSSCLEQPDSCQPYGSSFYALEE
+KHVGFSLDVGEIEKKGKGKIGRGRRSKKKRRRGRKEGEEDQNPPCPRLNSVLMEVEEPEV
+LQDSLDRCYSTPSMYCELRDSFQHYRSVF
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/omamer.loc	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,6 @@
+# Tab separated with 4 columns:
+# - value
+# - name
+# - version
+# - /path/to/data 
+test    test	2.0.2	${__HERE__}/db/
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.omamer	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,52 @@
+!omamer-version: 2.0.2
+!query-md5: 773e472d79d92b3d6d165033accb6f52
+!date-run: 2023-11-23T14:29:15.310914
+!db-path: Primates-v2.0.0.h5
+!db-info-source: OMA / All.Jul2023
+!db-info-root_level: Primates
+!db-info-database_hash: 27645bb5ca4c995ad24f8459dae3c107
+qseqid	hogid	hoglevel	family_p	family_count	family_normcount	subfamily_score	subfamily_count	qseqlen	subfamily_medianseqlen	qseq_overlap
+tr|A0A2R8YED5|A0A2R8YED5_HUMAN	HOG:D0610483	Primates	2638.1419438166727	306	1.0	0.9999760969041518	306	312	312	1.0
+sp|A0JD32|TV382_HUMAN	HOG:D0617450.2b.4a.11a	Homo sapiens	1087.8571886143745	111	1.0	0.999999812279352	6	117	117	1.0
+sp|A5D6W6|FITM1_HUMAN	HOG:D0630383	Primates	2734.0000255164123	286	1.0	0.9999850762084821	286	293	293	1.0
+sp|A6NH00|OR2T8_HUMAN	HOG:D0615771.2e.5a.12a	Homo sapiens	2404.939866884583	307	1.0	0.9999997809925772	7	313	313	1.0
+sp|B3EWG5|FM25C_HUMAN	HOG:D0615645.1b	Hominoidea	836.2635328481995	84	1.0	0.999999812279352	6	90	90	1.0
+sp|D6RGX4|F90AP_HUMAN	HOG:D0607131.3b.4b.2h	Homo sapiens	3466.867512384198	459	1.0	0.9999980289331958	63	465	465	1.0
+sp|O00451|GFRA2_HUMAN	HOG:D0637239.1g.14a	Primates	4275.204165438652	459	1.0	0.9999703088508377	459	465	461	1.0
+sp|O14817|TSN4_HUMAN	HOG:D0639114.1b.8b	Primates	2206.494860536379	233	1.0	0.9999844504729888	233	239	239	1.0
+sp|O14901|KLF11_HUMAN	HOG:D0630531	Primates	4040.9704983680986	505	1.0	0.9999356743912775	505	513	511	1.0
+sp|O15079|SNPH_HUMAN	HOG:D0631579	Primates	4235.616199577423	489	1.0	0.9999724989250646	489	495	533	1.0
+sp|O15400|STX7_HUMAN	HOG:D0671137.5c.35d.18b.8b.4a	Primates	2525.8039622379742	256	1.0	0.999983949884594	256	262	262	1.0
+sp|O15547|P2RX6_HUMAN	HOG:D0692878.1e.7a.24a	Primates	3735.3683950810037	436	1.0	0.9999472504979056	436	442	441	1.0
+sp|O43598|DNPH1_HUMAN	HOG:D0900595.1b.1a.4b.2b.2a	Catarrhini	1400.0640249439814	169	1.0	0.9999953382705741	17	175	206	1.0
+sp|O75078|ADA11_HUMAN	HOG:D0639405.1a.1a	Primates	6459.427248727791	764	1.0	0.9999506607563446	764	770	770	1.0
+sp|O75347|TBCA_HUMAN	HOG:D0685997.6b.12a.16b.7a.3a.4e.4a	Simiiformes	1000.5425844202465	103	1.0	0.9999947438218554	9	109	109	1.0
+sp|O94913|PCF11_HUMAN	HOG:D0645798.6a	Primates	11929.968463962005	1502	1.0	0.9999100505228223	1502	1556	1658	1.0
+sp|O95210|STBD1_HUMAN	HOG:D0613610	Primates	2963.2232053752086	353	1.0	0.9999462180343415	353	359	359	1.0
+sp|O95274|LYPD3_HUMAN	HOG:D0616795	Primates	2866.7497463302734	340	1.0	0.9999594210532524	340	347	353	1.0
+sp|O95415|BRI3_HUMAN	HOG:D0674725.2a.1a.3a	Primates	1064.9029691067599	120	1.0	0.9999939929392633	120	126	126	1.0
+sp|P00491|PNPH_HUMAN	HOG:D0680682.1a.1b.3b.3a.9b.14a.10a	Primates	2692.3703255880287	284	1.0	0.9999724676382901	284	290	290	1.0
+sp|P03999|OPSB_HUMAN	HOG:D0622973	Primates	3175.263453504967	343	1.0	0.9999679310559627	343	349	350	1.0
+sp|P09466|PAEP_HUMAN	HOG:D0615657.2b.1b.1a	Catarrhini	1559.31373622314	175	1.0	0.9999865779736663	148	181	181	1.0
+sp|P09544|WNT2_HUMAN	HOG:D0658980.4g.16b.11b	Primates	3150.596993999258	355	1.0	0.9999818849574658	355	361	361	1.0
+sp|P0C629|O10J4_HUMAN	HOG:D0613697.2a	Primates	517.9354158365237	83	0.2710903805261581	0.27120240872927465	83	312	313	0.9067524115755627
+sp|P0C881|R10B1_HUMAN	HOG:D0661287.1a.2b.5a.2a.1a	Homo sapiens	6421.796319570017	865	1.0	0.999999812279352	6	871	871	1.0
+sp|P12104|FABPI_HUMAN	HOG:D0641313.1b	Primates	1273.974731265406	127	1.0	0.999978724993224	127	133	133	1.0
+sp|P19622|HME2_HUMAN	HOG:D0632442.1b	Primates	2532.2810698546	327	1.0	0.999977786389984	327	334	335	1.0
+sp|P20813|CP2B6_HUMAN	HOG:D0671285.6ah.265a.202b.82b	Hominoidea	3965.2155397202205	486	1.0	0.9999944309541087	84	492	492	1.0
+sp|P22626|ROA2_HUMAN	HOG:D0679329.10fdq.3086r.2380b.1642a.1109f.653b	Primates	3180.0277293941886	340	1.0	0.9999884551801466	340	354	342	1.0
+sp|P25929|NPY1R_HUMAN	HOG:D0635707.1a	Primates	3839.2856592128996	379	1.0	0.9999819788177898	379	385	384	1.0
+sp|P26599|PTBP1_HUMAN	HOG:D0671471.2a.1a.1d.3b.6e.3a.5b.4a	Primates	4179.095968916793	524	1.0	0.9999607038110139	524	532	532	1.0
+sp|P42224|STAT1_HUMAN	HOG:D0661771.1b	Primates	6776.242926772081	745	1.0	0.9999539145809104	745	751	744	1.0
+sp|P42695|CNDD3_HUMAN	HOG:D0671844.4b	Primates	11211.682296353	1493	1.0	0.9998243873337745	1493	1499	1499	1.0
+sp|P47929|LEG7_HUMAN	HOG:D0641111.10b	Simiiformes	1219.0569952460728	131	1.0	0.9999955259912221	14	137	137	1.0
+sp|P51693|APLP1_HUMAN	HOG:D0660679.1a	Primates	5056.8124129922835	645	1.0	0.9999476259392016	645	651	640	1.0
+sp|P57678|GEMI4_HUMAN	HOG:D0639146	Primates	8562.495763610617	1053	1.0	0.999890621435752	1053	1059	1059	1.0
+sp|P78417|GSTO1_HUMAN	HOG:D0699874.1a.3c.8a.18a.27b.15b.3b	Simiiformes	2208.5054830237655	236	1.0	0.9999911458427683	46	242	242	1.0
+sp|P80188|NGAL_HUMAN	HOG:D0615744.1a.2b	Primates	1741.721242422051	193	1.0	0.999961454693606	193	199	199	1.0
+sp|Q05195|MAD1_HUMAN	HOG:D0638507.1c	Primates	2231.948352172975	216	1.0	0.9999906139675988	216	222	222	1.0
+sp|Q13077|TRAF1_HUMAN	HOG:D0615660	Primates	3704.3470383386293	411	1.0	0.9999673678940186	411	417	417	1.0
+sp|Q14765|STAT4_HUMAN	HOG:D0632400	Primates	6767.325687112324	743	1.0	0.9999589830384069	743	749	749	1.0
+sp|Q15019|SEPT2_HUMAN	HOG:D0671290.6j.36c.7b.14b.13a.11a.6a	Primates	3489.280783000945	356	1.0	0.9999813530822964	356	362	364	1.0
+sp|Q15468|STIL_HUMAN	HOG:D0645362.3b	Primates	9834.974240963404	1282	1.0	0.9998483842899468	1282	1288	1279	1.0
+sp|Q3BBV2|NBPF8_HUMAN	HOG:D0608047.2a	Catarrhini	3950.290666607274	608	0.8373227747284284	0.420437306441702	111	870	662	1.0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.omq	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,17792 @@
+>Single
+HOG:D0900595.1b.1a.4b.2b.2a
+HOG:D0639405.1a.1a
+HOG:D0637239.1g.14a
+HOG:D0671844.4b
+HOG:D0630383
+HOG:D0671285.6ah.265a.202b.82b
+HOG:D0615657.2b.1b.1a
+HOG:D0630531
+HOG:D0613610
+HOG:D0616795
+HOG:D0639146
+HOG:D0641111.10b
+HOG:D0615744.1a.2b
+HOG:D0645362.3b
+HOG:D0660679.1a
+HOG:D0680682.1a.1b.3b.3a.9b.14a.10a
+HOG:D0615660
+HOG:D0685997.6b.12a.16b.7a.3a.4e.4a
+HOG:D0639114.1b.8b
+HOG:D0638507.1c
+HOG:D0679329.10fdq.3086r.2380b.1642a.1109f.653b
+HOG:D0622973
+HOG:D0699874.1a.3c.8a.18a.27b.15b.3b
+HOG:D0615645.1b
+HOG:D0641313.1b
+HOG:D0692878.1e.7a.24a
+HOG:D0632442.1b
+HOG:D0632400
+HOG:D0671290.6j.36c.7b.14b.13a.11a.6a
+HOG:D0645798.6a
+HOG:D0658980.4g.16b.11b
+HOG:D0661771.1b
+HOG:D0671137.5c.35d.18b.8b.4a
+HOG:D0635707.1a
+>Lost
+HOG:D0659433
+HOG:D0629714
+HOG:D0671843.2c.4a.1b
+HOG:D0682523.9a.13a.3b.3a
+HOG:D0671716.6a
+HOG:D0680844.11b.12b.26a
+HOG:D0660683.1b.5a
+HOG:D0660683.1b.5b
+HOG:D0667470.5a
+HOG:D0692362.1g.6a.4a
+HOG:D0692362.1g.6b.6b
+HOG:D0679525.7a
+HOG:D0630327.1a.2b
+HOG:D0673139.1a.2a
+HOG:D0673139.1b.3d.4c.4a
+HOG:D0673139.1c
+HOG:D0618878.3b
+HOG:D0610946
+HOG:D0629901.3b
+HOG:D0687720.7c.12b
+HOG:D0686017.2a.3b.4a
+HOG:D0610601.2c
+HOG:D0610601.2f.4a
+HOG:D0605270
+HOG:D0613984
+HOG:D0629819.1b
+HOG:D0616680
+HOG:D0658626.1a.2a.3b
+HOG:D0658626.1c.4b
+HOG:D0605460
+HOG:D0618713
+HOG:D0631532
+HOG:D0658713.4h.11b
+HOG:D0658713.4t.17b
+HOG:D0631604.3b
+HOG:D0637188
+HOG:D0667973.1b.1b.8a.3b
+HOG:D0667973.1b.1c
+HOG:D0612581.5b
+HOG:D0679870.4c.6a.7a.5b
+HOG:D0614620
+HOG:D0687764.4e
+HOG:D0687764.4k.14b.21b
+HOG:D0687764.4m.15a.23a.22a.24b
+HOG:D0687764.4m.15a.23a.22g
+HOG:D0687764.4o.18a
+HOG:D0687764.4p
+HOG:D0685981.3a.7c.6a
+HOG:D0630540
+HOG:D0621397
+HOG:D0637078.2c.5b
+HOG:D0613865
+HOG:D0679860.9a.37e.43a.14a.8b
+HOG:D0679860.9a.37e.43a.14b.9g.15a.12a.7b
+HOG:D0679860.9a.37h.44b
+HOG:D0615573
+HOG:D0620005.3a
+HOG:D0623327.11b.2b
+HOG:D0611657
+HOG:D0672525.1a.5a.1a
+HOG:D0644557.3a
+HOG:D0615989
+HOG:D0629739.3b
+HOG:D0608617
+HOG:D0660768.1a.3b
+HOG:D0679453.4b
+HOG:D0680122.9a.30b
+HOG:D0613888.2a
+HOG:D0622296.2b.7a.1b.5b
+HOG:D0622296.2b.7a.1b.5a
+HOG:D0671510.2b.11a.5b
+HOG:D0608868.1a
+HOG:D0685365.1c
+HOG:D0643268.2d
+HOG:D0620131
+HOG:D0679893.30e.9c.7a.9a.1b.1b
+HOG:D0619886
+HOG:D0644291
+HOG:D0681717.2a.5a
+HOG:D0635572
+HOG:D0607932
+HOG:D0659044.1b.1a.3a
+HOG:D0628990.4b
+HOG:D0680001.8e.4b.8e.28a.25b
+HOG:D0680001.8e.4b.8e.28a.25e.27b.18b.9b
+HOG:D0646321.2a.1y.19b.6a.1b
+HOG:D0639074.1b.2b
+HOG:D0613884
+HOG:D0631500
+HOG:D0661878
+HOG:D0629561.5b
+HOG:D0658818.1d.5a.5b
+HOG:D0658818.1d.5d.12a
+HOG:D0619253
+HOG:D0681337.23b
+HOG:D0629779.1a
+HOG:D0630236
+HOG:D0629128.1b
+HOG:D0671157.2b.6b.14a.8b.9b
+HOG:D0639149.1b
+HOG:D0658651.6b
+HOG:D0701127.4g.7d.4b.4b
+HOG:D0701127.4g.7e.6c.12b.20a.5c.1a
+HOG:D0701127.4g.7e.6c.12b.20d.9b.4c.12a.8a
+HOG:D0630789
+HOG:D0618191.1b
+HOG:D0900523.11b.61ao
+HOG:D0900523.11b.61az
+HOG:D0900523.11b.61bd.221b.209b
+HOG:D0900523.11b.61by.239b.234b.118a
+HOG:D0900523.11b.61by.239b.234b.118d.62b
+HOG:D0900523.11b.61by.239b.234b.118d.62c.30a
+HOG:D0900523.11b.61by.239c.240b
+HOG:D0900523.11b.61bz.241a.242a.121b.65b.39a
+HOG:D0900523.11b.61bz.241a.242a.121b.65b.39b
+HOG:D0900523.11b.61bz.241a.242b.123b.66b.43b.31c
+HOG:D0629259.7a
+HOG:D0634477
+HOG:D0635866.1b
+HOG:D0682920.3a.3b.7a.17b.21b
+HOG:D0618862
+HOG:D0618528.1a
+HOG:D0679603.4b.4b.9b.11a.23a.9a
+HOG:D0613632.1a
+HOG:D0686259.3b.5c.4a.8b
+HOG:D0613514
+HOG:D0680123.10d.54c.45e.53b.31b
+HOG:D0680123.10e.55b.47b
+HOG:D0680123.10e.55b.47c
+HOG:D0671678.2c.1a.2b
+HOG:D0671678.2c.1a.2c
+HOG:D0611184.2b.6d.4d
+HOG:D0611184.2b.6d.4a
+HOG:D0611184.2b.6d.4b
+HOG:D0611184.2b.6e.5b
+HOG:D0626800
+HOG:D0630070.4a
+HOG:D0614354.1c.8a
+HOG:D0606829.2e.5a
+HOG:D0672669.2a.8b.2b
+HOG:D0680445.10a.10a.7a.17b.28a
+HOG:D0637205.1a
+HOG:D0607813
+HOG:D0615998.1b.4a
+HOG:D0620069.2ad
+HOG:D0620069.2br.7b
+HOG:D0620069.2dv.10c
+HOG:D0679692.2a.1a.1b.1c.2b
+HOG:D0685743.15b
+HOG:D0637203.1b
+HOG:D0679514.2a.31b.16d.30a.7c.1d.1k.1a.5a.1b.1e.5i
+HOG:D0682965.4a.13d.12a.13b.27a.18a.4b.9a
+HOG:D0671538.1a
+HOG:D0671538.1c.9b
+HOG:D0658693.3c.2a.6a.1c.5b
+HOG:D0658693.3c.2b
+HOG:D0635616.1e.1a.7a
+HOG:D0660891
+HOG:D0679558.36c.9b.2b
+HOG:D0667585.1b
+HOG:D0667585.1c.6b.6c.4b
+HOG:D0610931
+HOG:D0634308.1b.2a
+HOG:D0635390
+HOG:D0909138.1c.3a.3e
+HOG:D0909138.1c.3a.3f
+HOG:D0642105.1a.2c
+HOG:D0613600
+HOG:D0613562.2a
+HOG:D0685736.8a.18a
+HOG:D0630038
+HOG:D0644281.1a
+HOG:D0608523
+HOG:D0629239
+HOG:D0639337.1c
+HOG:D0635437
+HOG:D0620230.2a
+HOG:D0628950
+HOG:D0667626.1c.4a
+HOG:D0660953.1a.1a
+HOG:D0660953.1a.1b.8b
+HOG:D0658255
+HOG:D0673640
+HOG:D0631517
+HOG:D0662132
+HOG:D0900556.13a.7b
+HOG:D0623401.3b.1a
+HOG:D0900036.3b.14b
+HOG:D0617137
+HOG:D0682640.4c.6a.1b.4a.12b
+HOG:D0682640.4c.6a.1b.4b.15c
+HOG:D0682640.4c.6a.1b.4c.20a
+HOG:D0689136.1b.1a.2c
+HOG:D0643128.3a
+HOG:D0635380.1b
+HOG:D0635404.1b.4b
+HOG:D0662693.1b.2a.2b.3b.9b
+HOG:D0679530.9c.24a.15a
+HOG:D0657203.1a.2c
+HOG:D0615732
+HOG:D0621317
+HOG:D0667853
+HOG:D0660924.2c.2b.7a
+HOG:D0660924.2c.2d
+HOG:D0620136
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+HOG:D0667821.1a.2b.7b
+HOG:D0625626
+HOG:D0605573
+HOG:D0662261.1b.3a
+HOG:D0679774.6c.6c.9a.2b.25b.28e.19k.5a.3a.1a.2b.2c
+HOG:D0688830.1b.1c.1a.11b
+HOG:D0619055.2a
+HOG:D0622492
+HOG:D0672154.1a.1b.4a.2b.2b
+HOG:D0672154.1e.8a.7b
+HOG:D0635850.4a.2a.1c
+HOG:D0639727
+HOG:D0612770
+HOG:D0629061
+HOG:D0661162.1c.5b.1b.2b
+HOG:D0661162.1c.5b.1b.2c.15a
+HOG:D0661162.1k
+HOG:D0620086
+HOG:D0606606
+HOG:D0603966
+HOG:D0612498
+HOG:D0629897
+HOG:D0630223.1a
+HOG:D0690057.4b.4a
+HOG:D0628773.1b
+HOG:D0603933
+HOG:D0667592.1a.2b.2b
+HOG:D0667592.1b.3a
+HOG:D0628685
+HOG:D0632166.1d
+HOG:D0635474
+HOG:D0682945.5a
+HOG:D0690992.1b
+HOG:D0672517.2b.1b
+HOG:D0672517.2d.2a
+HOG:D0679472.8b.20b.21a.22b.40b.28b.22a.7a.4c.3b.3a
+HOG:D0679472.8b.20b.21b.26c.41a.30b
+HOG:D0639082.2a.5b.1a.1a
+HOG:D0639082.2b
+HOG:D0630648
+HOG:D0612779
+HOG:D0608996
+HOG:D0668804.1a.3a.4c.6a.8b
+HOG:D0668804.1a.3a.4c.6c.11b
+HOG:D0668804.1a.3a.4e.7a.14c.17b.8d
+HOG:D0613770
+HOG:D0680920.4b.13c.28b.44c.40a
+HOG:D0680976.5a.13b.13a
+HOG:D0680976.5a.13b.13f
+HOG:D0680976.5d.24b.24c.13a.17a.13b
+HOG:D0614777
+HOG:D0681338.16b
+HOG:D0680945.3b.16a.8a.2a.1b
+HOG:D0668331.1b.2b.3d.9c
+HOG:D0637135
+HOG:D0614366
+HOG:D0668036.2d.5a.2a
+HOG:D0668036.2d.5e.6a
+HOG:D0668036.2d.5e.6c
+HOG:D0620286.1a
+HOG:D0651107.1a.1b.2a
+HOG:D0645921.5b
+HOG:D0621678
+HOG:D0616745
+HOG:D0629536.6a
+HOG:D0655462.1c
+HOG:D0621421.4a
+HOG:D0635646.1b
+HOG:D0615602
+HOG:D0630209.3a
+HOG:D0671783.1a.7b
+HOG:D0671783.1a.7c.5a
+HOG:D0671783.1c
+HOG:D0621616.4b.2b
+HOG:D0623496.1b
+HOG:D0614184.2a.2b
+HOG:D0622595.2b.3a
+HOG:D0620553.1b
+HOG:D0611011.2b.5a.5b
+HOG:D0641340.1a.1a.1a.3a
+HOG:D0641340.1b
+HOG:D0629702
+HOG:D0679551.10e.63b.79b
+HOG:D0679551.10e.63c
+HOG:D0679551.10t
+HOG:D0679551.10z.74b.104a.77a.48a
+HOG:D0679551.10z.74b.104a.77d.51a
+HOG:D0679551.10z.74d.105a
+HOG:D0679551.10z.74f.111d
+HOG:D0679551.10z.74f.111f.86a
+HOG:D0610805.1a
+>Duplicated
+>Underspecific
+HOG:D0671471.2a.1a.1d.3b.6e.3a.5b.4a.2e
+>Overspecific_S
+HOG:D0617450.2b.4a
+HOG:D0607131.3b
+HOG:D0661287.1a.2b.5a.2a
+HOG:D0615771.2e.5a
+>Overspecific_D

Binary file test-data/output.pdf has changed

Binary file test-data/output.png has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.sum	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,15 @@
+#The selected clade was Hominidae
+#Number of conserved HOGs is: 17786
+#Results on conserved HOGs is:
+#S:Single:S, D:Duplicated[U:Unexpected,E:Expected],M:Missing
+S:39,D:0[U:0,E:0],M:17747
+S:0.22%,D:0.00%[U:0.00%,E:0.00%],M:99.78%
+#On the whole proteome, there are 44 proteins
+#Of which:
+#A:Consistent (taxonomically)[P:Partial hits,F:Fragmented], I: Inconsistent (taxonomically)[P:Partial hits,F:Fragmented], C: Likely Contamination[P:Partial hits,F:Fragmented], U: Unknown 
+A:43[P:0,F:0],I:1[P:0,F:0],C:0[P:0,F:0],U:0
+A:97.73%[P:0.00%,F:0.00%],I:2.27%[P:0.00%,F:0.00%],C:0.00%[P:0.00%,F:0.00%],U:0.00%
+#From HOG placement, the detected species are:
+#Clade	NCBI taxid	Number of associated proteins	Percentage of proteome's total
+Homo sapiens	9606	44	100.00%
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tax	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,4 @@
+>Sampled
+Hominidae
+>Closest
+Homo sapiens

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.ump	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,54 @@
+>Consistent_Full
+sp|P25929|NPY1R_HUMAN
+sp|P0C629|O10J4_HUMAN
+sp|D6RGX4|F90AP_HUMAN
+sp|A0JD32|TV382_HUMAN
+sp|Q05195|MAD1_HUMAN
+sp|A5D6W6|FITM1_HUMAN
+sp|O75347|TBCA_HUMAN
+sp|O43598|DNPH1_HUMAN
+sp|P20813|CP2B6_HUMAN
+sp|P26599|PTBP1_HUMAN
+sp|Q15468|STIL_HUMAN
+sp|P80188|NGAL_HUMAN
+sp|O95274|LYPD3_HUMAN
+sp|O15547|P2RX6_HUMAN
+sp|A6NH00|OR2T8_HUMAN
+sp|P42224|STAT1_HUMAN
+sp|O75078|ADA11_HUMAN
+sp|P03999|OPSB_HUMAN
+tr|A0A2R8YED5|A0A2R8YED5_HUMAN
+sp|Q15019|SEPT2_HUMAN
+sp|O95210|STBD1_HUMAN
+sp|P0C881|R10B1_HUMAN
+sp|P57678|GEMI4_HUMAN
+sp|Q3BBV2|NBPF8_HUMAN
+sp|P78417|GSTO1_HUMAN
+sp|P42695|CNDD3_HUMAN
+sp|P51693|APLP1_HUMAN
+sp|Q14765|STAT4_HUMAN
+sp|B3EWG5|FM25C_HUMAN
+sp|P47929|LEG7_HUMAN
+sp|P00491|PNPH_HUMAN
+sp|P12104|FABPI_HUMAN
+sp|Q13077|TRAF1_HUMAN
+sp|O14901|KLF11_HUMAN
+sp|O15079|SNPH_HUMAN
+sp|O94913|PCF11_HUMAN
+sp|O15400|STX7_HUMAN
+sp|P22626|ROA2_HUMAN
+sp|P19622|HME2_HUMAN
+sp|O00451|GFRA2_HUMAN
+sp|P09544|WNT2_HUMAN
+sp|P09466|PAEP_HUMAN
+sp|O14817|TSN4_HUMAN
+>Consistent_Partial
+>Consistent_Fragment
+>Inconsistent_Full
+sp|O95415|BRI3_HUMAN
+>Inconsistent_Partial
+>Inconsistent_Fragment
+>Contamination_Full
+>Contamination_Partial
+>Contamination_Fragment
+>Unknown

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_detailed_summary.txt	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,63 @@
+COMPLETENESS ASSESSMENT
+------------
+#This benchmark gives an estimate of the completeness of the gene set based on the presence or not of conserved genes of the target lineage.
+#Conserved genes are defined using Hierarchical Orthologous Groups (HOGs) defined at a certain taxonomic clade, which is a proxy for the ancestral gene repertoire of this clade. HOGs are considered conserved if they have at least one gene in >80% of the extant species. 
+#Because representatives of these groups are expected to be present in the target species repertoire, the proportion of missing HOGs proxies the proportion of missing genes in the total gene repertoire of the target proteome.
+#Ancestral genes used for this benchmark were in single copy in the selected ancestral lineage, but no assumption is made regarding their propensity to duplicate - they are not universal single copy genes. This benchmark reports the proportion of those genes that are found in multiple copies in target proteomes, and whether it corresponds to a known duplication event in descendants of this gene family (Expected) or not (Unexpected).
+
+The clade used was: Hominidae
+Number of conserved HOGs: 17786
+
+#Results on conserved HOGs:
+Single: 39 (0.22%)
+Duplicated: 0 (0.00%)
+Duplicated, Unexpected: 0 (0.00%)
+Duplicated, Expected: 0 (0.00%)
+Missing: 17747 (99.78%)
+
+
+CONSISTENCY ASSESSMENT
+-------------------------
+#This benchmark gives the proportion of annotated protein-coding genes in the query proteome that likely correspond to an actual protein-coding gene by comparing to the known gene families of the selected ancestral lineage.
+
+##High-level categories
+#Genes in the "Consistent" category correspond to a gene family known to exist in the selected lineage. Genes in the "Inconsistent" or “Contaminants'' categories correspond to known gene families from different lineages. Such genes are deemed contaminants if more genes than expected by chance correspond to the same species. They are deemed Inconsistent if they correspond to other species seemingly at random. Genes are classified in the “Unknown” category if they do not share enough similarity with known gene families: they may be orphan genes or erroneous protein sequences.
+
+##Subcategories
+#Partial hit proteins are those that share similarity with proteins in known gene families on only part of their sequence: they can indicate poorly defined gene models, structurally divergent genes, or erroneous annotation. 
+#Fragmented proteins are those whose length is smaller than the proteins from the gene families they share similarity with (<50% median length): they are likely fragmentend sequences or erroneous annotations.
+
+Number of proteins in the whole proteome: 44
+
+#Consistent lineage placements
+Total Consistent: 43 (97.73%)
+Consistent, partial hits: 0 (0.00%)
+Consistent, fragmented: 0 (0.00%)
+
+#Inconsistent lineage placements
+Total Inconsistent: 1 (2.27%)
+Inconsistent, partial hits: 0 (0.00%)
+Inconsistent, fragmented: 0 (0.00%)
+
+#Contaminants
+Total Contaminants: 0 (0.00%)
+Contaminants, partial hits: 0 (0.00%)
+Contaminants, fragmented: 0 (0.00%)
+
+#Unknown
+Total Unknown: 0 (0.00%)
+
+
+SPECIES COMPOSITION
+-------------------
+#This benchmark gives an estimate of the species composition of the dataset, according to HOGs placement. It reports the clades most consistent with the taxonomic distribution of gene families where coding-genes for the query proteomes were placed. The species to which most of the proteins in the query proteome are consistent with is called "Main species." The others are potential contaminants.
+#This section also lists the numbers of proteins that can be associated to each of these clades, based on the taxonomic placement of the gene families they share similarity with.
+
+
+##Detected species
+
+#Main species
+Clade: Homo sapiens
+Number of associated query proteins: 44 (100.00%)
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.fasta	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,22 @@
+>sp|Q8IYX0|ZN679_HUMAN Zinc finger protein 679 OS=Homo sapiens OX=9606 GN=ZNF679 PE=1 SV=2
+MAKRPGSPGSREMGLLTFRDVVIEFSLEEWQCLDHAQQNLYRDVMLENYRNLVSLGIAVS
+KPDLITCLEQNKEPWNIKRNEMVTKHPVMCSHFTQDLPPELGIKDSLQKVIPRRYGKSGH
+DNLQVKTCKSMGECEVQKGGCNEVNQCLSTTQNKIFQTHKCVKVFGKFSNSNRHKTRHTG
+KKHFKCKKYGKSFCMVSQLHQHQIIHTRENSYQCEECGKPFNCSSTLSKHKRIHTGEKPY
+RCEECGKAFTWSSTLTKHRRIHTGEKPYTCEECGQAFSRSSTLANHKRIHTGEKPYTCEE
+CGKAFSLSSSLTYHKRIHTGEKPYTCEECGKAFNCSSTLKKHKIIHTGEKPYKCKECGKA
+FAFSSTLNTHKRIHTGEEPYKCEECDKAFKWSSSLANHKSMHTGEKPYKCE
+>sp|Q8IZE3|PACE1_HUMAN Protein-associating with the carboxyl-terminal domain of ezrin OS=Homo sapiens OX=9606 GN=SCYL3 PE=1 SV=3
+MGSENSALKSYTLREPPFTLPSGLAVYPAVLQDGKFASVFVYKRENEDKVNKAAKHLKTL
+RHPCLLRFLSCTVEADGIHLVTERVQPLEVALETLSSAEVCAGIYDILLALIFLHDRGHL
+THNNVCLSSVFVSEDGHWKLGGMETVCKVSQATPEFLRSIQSIRDPASIPPEEMSPEFTT
+LPECHGHARDAFSFGTLVESLLTILNEQVSADVLSSFQQTLHSTLLNPIPKCRPALCTLL
+SHDFFRNDFLEVVNFLKSLTLKSEEEKTEFFKFLLDRVSCLSEELIASRLVPLLLNQLVF
+AEPVAVKSFLPYLLGPKKDHAQGETPCLLSPALFQSRVIPVLLQLFEVHEEHVRMVLLSH
+IEAYVEHFTQEQLKKVILPQVLLGLRDTSDSIVAITLHSLAVLVSLLGPEVVVGGERTKI
+FKRTAPSFTKNTDLSLEDSPMCVVCSHHSQISPILENPFSSIFPKCFFSGSTPINSKKHI
+QRDYYNTLLQTGDPFSQPIKFPINGLSDVKNTSEDSENFPSSSKKSEEWPDWSEPEEPEN
+QTVNIQIWPREPCDDVKSQCTTLDVEESSWDDCEPSSLDTKVNPGGGITATKPVTSGEQK
+PIPALLSLTEESMPWKSSLPQKISLVQRGDDADQIEPPKVSSQERPLKVPSELGLGEEFT
+IQVKKKPVKDPEMDWFADMIPEIKPSAAFLILPELRTEMVPKKDDVSPVMQFSSKFAAAE
+ITEGEAEGWEEEGELNWEDNNW
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/omamer.loc.sample	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,9 @@
+
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of OMAMer databases. 
+#
+# the columns are:
+#value  description version /path/to/data
+#
+#for example
+#Primates-v2.0    Primates	2.0.2	/path/to/data

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="omamer" comment_char="#">
+        <columns>value, name, version, path</columns>
+        <file path="tool-data/omamer.loc"/>
+    </table>
+</tables>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Wed Feb 21 19:27:16 2024 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="omamer" comment_char="#">
+        <columns>value, name, version, path</columns>
+        <file path="${__HERE__}/test-data/omamer.loc"/>
+    </table>
+</tables>
\ No newline at end of file