| Previous changeset 58:07ff622ec007 (2021-04-10) Next changeset 60:a6ff76e057fd (2021-07-20) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588" |
|
modified:
fasta_cli.xml ident_params.xml macros_basic.xml peptide_shaker.xml searchgui.xml |
|
added:
test-data/searchgui_smallCalibratible_Yeast.mzML test-data/searchgui_smallYeast.fasta |
| b |
| diff -r 07ff622ec007 -r 943a34df6047 fasta_cli.xml --- a/fasta_cli.xml Sat Apr 10 15:57:17 2021 +0000 +++ b/fasta_cli.xml Fri May 21 19:13:14 2021 +0000 |
| b |
| @@ -28,7 +28,15 @@ ########################################### echo 'Creating decoy database.' && - searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag && + searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI + --exec_dir="./bin/" + -use_log_folder 0 + -temp_folder `pwd` + -in '${input_database.display_name}' + -decoy + -decoy_flag $database_processing_options.decoy_tag + -suffix $database_processing_options.decoy_type + -decoy_suffix $database_processing_options.decoy_file_tag && mv '${output_db_name}' output ]]> </command> |
| b |
| diff -r 07ff622ec007 -r 943a34df6047 ident_params.xml --- a/ident_params.xml Sat Apr 10 15:57:17 2021 +0000 +++ b/ident_params.xml Fri May 21 19:13:14 2021 +0000 |
| b |
| @@ -30,8 +30,8 @@ ##################################################### searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="./bin/" + -use_log_folder 0 -out './IdentificationParametersOutput.par' - ## SPECTRUM MATCHING PARAMETERS -frag_tol '${spectrum_matching_options.fragment_tol}' |
| b |
| diff -r 07ff622ec007 -r 943a34df6047 macros_basic.xml --- a/macros_basic.xml Sat Apr 10 15:57:17 2021 +0000 +++ b/macros_basic.xml Fri May 21 19:13:14 2021 +0000 |
| b |
| @@ -11,9 +11,9 @@ </stdio> </xml> <token name="@SEARCHGUI_MAJOR_VERSION@">4</token> - <token name="@SEARCHGUI_VERSION@">4.0.25</token> + <token name="@SEARCHGUI_VERSION@">4.0.33</token> <token name="@SEARCHGUI_VERSION_SUFFIX@">0</token> - <token name="@PEPTIDESHAKER_VERSION@">2.0.18</token> + <token name="@PEPTIDESHAKER_VERSION@">2.0.25</token> <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">0</token> <xml name="citations"> <citations> |
| b |
| diff -r 07ff622ec007 -r 943a34df6047 peptide_shaker.xml --- a/peptide_shaker.xml Sat Apr 10 15:57:17 2021 +0000 +++ b/peptide_shaker.xml Fri May 21 19:13:14 2021 +0000 |
| b |
| @@ -26,8 +26,6 @@ #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") #set $bin_dir = "bin" #set $exporting_followup_boolean = False - ## TODO: Re-enable again when solving writing paths.txt to user-related folders and non-existing exportFactory.json file. - ## trap ">&2 cat resources/*.log" EXIT; mkdir output_reports && cwd=`pwd` && @@ -70,10 +68,13 @@ ###################### ## PeptideShakerCLI ## ###################### + + ## TODO: --exec_dir may not be needed anymore. To be tested further (and maybe removed from the Conda package). + peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI -gui 0 -temp_folder \$cwd/PeptideShakerCLI - -log \$cwd/resources + -use_log_folder 0 -reference '$exp_str' -identification_files \$cwd/searchgui_input.zip -id_params \$cwd/SEARCHGUI_IdentificationParameters.par @@ -187,7 +188,12 @@ #end if #end if #end if - + + ## Whilst non-blocking exception " /usr/local/share/peptide-shaker-2.0.25-0/resources/conf/paths.txt (Permission denied)" + ## is fixed , we can avoid the process to be stopped by removing that message from the output + + | grep -v "resources/conf/paths.txt (Permission denied)" + ## If the user chose to zip the results but also export reports out of the zip, we have to unzip them #if $exporting_options.zip_conditional.zip_output_boolean == 'zip' and $exporting_options.zip_conditional.export_reports_when_zip and (len(output_reports_list)>0 or $exporting_followup_boolean): ## This unzipping command creates a reports folder into the current folder! |
| b |
| diff -r 07ff622ec007 -r 943a34df6047 searchgui.xml --- a/searchgui.xml Sat Apr 10 15:57:17 2021 +0000 +++ b/searchgui.xml Fri May 21 19:13:14 2021 +0000 |
| b |
| @@ -65,6 +65,7 @@ echo 'running search gui' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="\$cwd/${bin_dir}" + -use_log_folder 0 -spectrum_files \$cwd -fasta_file "\$cwd/input_fasta_file.fasta" -output_folder \$cwd/output @@ -173,12 +174,14 @@ <param format="fasta" name="input_fasta_file" type="data" label="Fasta file" help="For postprocessing with PeptideShaker the sequences must have UniProt style headers and contain decoy sequences (see help)."/> <param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists" - help="Select appropriate MGF/MZML dataset(s) from history" /> + help="Select appropriate MGF/MZML dataset(s) from history. + Remember to choose only .mzML files when using MetaMorpheus." /> <!-- Search Engine Selection --> <section name="search_engines_options" expanded="true" title="Search Engine Options"> <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> - <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA may not work into isolated environments like containers.</help> + <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA may not work into isolated environments like containers. + MetaMorpheus only produce results when using mzML format.</help> <option value="X!Tandem" selected="True">X!Tandem</option> <option value="MSGF" selected="True">MS-GF+</option> <option value="OMSSA">OMSSA</option> @@ -186,8 +189,7 @@ <option value="Tide">Tide</option> <option value="MyriMatch">MyriMatch</option> <option value="MS_Amanda">MS_Amanda</option> - <!-- TODO: MetaMorpheus Waiting for support for dotnet in bioconda package --> - <!-- <option value="MetaMorpheus">MetaMorpheus</option> --> + <option value="MetaMorpheus">MetaMorpheus</option> <!-- Windows only <option value="Andromeda">Andromeda</option> --> @@ -239,6 +241,21 @@ <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/> <output name="searchgui_results" file="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> </test> + + + <!-- Test that search works with MetaMorpheus with default parameters works--> + <!-- Test data has been taken from metamorpheus galaxy tool --> + <test> + <param name="peak_lists_files" value="searchgui_smallCalibratible_Yeast.mzML"/> + <param name="input_parameters_file" value="Identification_Parameters_default.par"/> + <param name="input_fasta_file" value="searchgui_smallYeast.fasta" ftype="fasta" /> + <param name="engines" value="MetaMorpheus"/> + <output name="searchgui_results" ftype="searchgui_archive"> + <assert_contents> + <has_size value="798597" delta="10000"/> + </assert_contents> + </output> + </test> <!-- Test that search works with MSAmanda with default parameters works--> <test> @@ -324,7 +341,7 @@ Default: X! Tandem and MS-GF+ are executed. -Optional: MyriMatch, MS-Amanda, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed. +Optional: MyriMatch, MS-Amanda, MetaMorpheus, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed. **Input FASTA** |
| b |
| diff -r 07ff622ec007 -r 943a34df6047 test-data/searchgui_smallCalibratible_Yeast.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/searchgui_smallCalibratible_Yeast.mzML Fri May 21 19:13:14 2021 +0000 |
| b |
| b'@@ -0,0 +1,8555 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">\n+ <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="SmallCalibratible_Yeast" version="1.1.0">\n+ <cvList count="2">\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ </cvList>\n+ <fileDescription>\n+ <fileContent>\n+ <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>\n+ </fileContent>\n+ <sourceFileList count="1">\n+ <sourceFile id="RAW1" name="SmallCalibratible_Yeast.raw" location="file:///C:\\Data\\SlicedYeastRawFiles">\n+ <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4ede32545182c06b031abc46e29802452427783d"/>\n+ </sourceFile>\n+ </sourceFileList>\n+ </fileDescription>\n+ <referenceableParamGroupList count="1">\n+ <referenceableParamGroup id="CommonInstrumentParams">\n+ <cvParam cvRef="MS" accession="MS:1001742" name="LTQ Orbitrap Velos" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN03001B"/>\n+ </referenceableParamGroup>\n+ </referenceableParamGroupList>\n+ <softwareList count="2">\n+ <software id="Xcalibur" version="2.6.0">\n+ <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n+ </software>\n+ <software id="pwiz" version="3.0.10875">\n+ <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n+ </software>\n+ </softwareList>\n+ <instrumentConfigurationList count="2">\n+ <instrumentConfiguration id="IC1">\n+ <referenceableParamGroupRef ref="CommonInstrumentParams"/>\n+ <componentList count="3">\n+ <source order="1">\n+ <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>\n+ </source>\n+ <analyzer order="2">\n+ <cvParam cvRef="MS" accession="MS:1000484" name="orbitrap" value=""/>\n+ </analyzer>\n+ <detector order="3">\n+ <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>\n+ </detector>\n+ </componentList>\n+ <softwareRef ref="Xcalibur"/>\n+ </instrumentConfiguration>\n+ <instrumentConfiguration id="IC2">\n+ <referenceableParamGroupRef ref="CommonInstrumentParams"/>\n+ <componentList count="3">\n+ <source order="1">\n+ <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>\n+ </source>\n+ <analyzer order="2">\n+ <cvParam cvRef="MS" accession="MS:1000083" name="radial ejection linear ion trap" value=""/>\n+ </analyzer>\n+ <detector order="3">\n+ <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>\n+ </detector>\n+ </componentList>\n+ <softwareRef ref="Xcalibur"/>\n+ </instrumentConfiguration>\n+ </inst'..b'ffset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=99">981886</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=100">989172</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=101">997002</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=102">1004254</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=103">1011747</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=104">1035932</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=105">1043307</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=106">1050803</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=107">1058878</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=108">1066221</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=109">1073686</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=110">1080747</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=111">1087865</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=112">1111119</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=113">1118742</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=114">1125916</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=115">1134143</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=116">1141957</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=117">1149219</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=118">1174954</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=119">1182714</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=120">1191272</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=121">1198515</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=122">1206044</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=123">1213062</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=124">1236825</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=125">1243912</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=126">1252320</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=127">1259232</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=128">1266337</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=129">1274020</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=130">1281279</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=131">1288376</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=132">1312740</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=133">1320191</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=134">1328041</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=135">1335964</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=136">1342797</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=137">1350824</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=138">1374937</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=139">1382080</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=140">1404145</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=141">1411929</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=142">1419044</offset>\n+ </index>\n+ <index name="chromatogram">\n+ <offset idRef="TIC">1441766</offset>\n+ </index>\n+ </indexList>\n+ <indexListOffset>1445342</indexListOffset>\n+ <fileChecksum>9193c5186ed5d828310b72d8c3f2233a88a2afc4</fileChecksum>\n+</indexedmzML>\n' |
| b |
| diff -r 07ff622ec007 -r 943a34df6047 test-data/searchgui_smallYeast.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/searchgui_smallYeast.fasta Fri May 21 19:13:14 2021 +0000 |
| b |
| b'@@ -0,0 +1,1187 @@\n+>sp|P38013|AHP1_YEAST Peroxiredoxin type-2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=AHP1 PE=1 SV=4\n+MSDLVNKKFPAGDYKFQYIAISQSDADSESCKMPQTVEWSKLISENKKVIITGAPAAFSP\n+TCTVSHIPGYINYLDELVKEKEVDQVIVVTVDNPFANQAWAKSLGVKDTTHIKFASDPGC\n+AFTKSIGFELAVGDGVYWSGRWAMVVENGIVTYAAKETNPGTDVTVSSVESVLAHL\n+\n+>sp|P46672|ARC1_YEAST tRNA-aminoacylation cofactor ARC1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ARC1 PE=1 SV=2\n+MSDLVTKFESLIISKYPVSFTKEQSAQAAQWESVLKSGQIQPHLDQLNLVLRDNTFIVST\n+LYPTSTDVHVFEVALPLIKDLVASSKDVKSTYTTYRHILRWIDYMQNLLEVSSTDKLEIN\n+HDLDLPHEVIEKKKKAPAGGAADAAAKADEDVSKKAKKQDHPRGKPDEETLKKLREEAKA\n+KKAAKKAANAKQQQEQQNKAPEKPKPSAIDFRVGFIQKAIKHPDADSLYVSTIDVGDEEG\n+PRTVCSGLVKHFPLDAMQERYVVVVCNLKPVNMRGIKSTAMVLCGSNDDKVEFVEPPKDS\n+KAGDKVFFEGFGDEAPMKQLNPKKKIWEHLQPHFTTNDGLEVIFKDEEEKDHPVRKLTNA\n+KGESFKVASIANAQVR\n+\n+>sp|Q01389|BCK1_YEAST Serine/threonine-protein kinase BCK1/SLK1/SSP31 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=BCK1 PE=1 SV=1\n+MPFLRKIAGTAHTHSRSDSNSSVKFGHQPTSSVASTKSSSKSPRATSRKSIYDDIRSQFP\n+NLTPNSTSSQFYESTPVIEQSFNWTTDDHISAGTLENPTSFTNSSYKNDNGPSSLSDSRK\n+SSGGNSVNSLSFDKLILSWDPTDPDEWTMHRVTSWFKFHDFPESWILFFKKHQLFGHRFI\n+KLLAYDNFAVYEKYLPQTKTASYTRFQQLLKKTMTKNVTNSHIRQKSASKLKSSRSSSES\n+IKSKLKNSKSQEDISNSRSTSESALSPTKSGPSKTDEKNFLHSTSTHQKTKSASSLYRRS\n+FISLRGSSSSNASSAKSPSNIKLSIPARPHSIIESNSTLTKSASPPASPSYPSIFRRHHK\n+SSSSESSLLNSLFGSGIGEEAPTKPNPQGHSLSSENLAKGKSKHYETNVSSPLKQSSLPT\n+SDDKGNLWNKFKRKSQIGVPSPNTVAYVTSQETPSLKSNSSTATLTVQTADVNIPSPSSS\n+PPPIPKTANRSLEVISTEDTPKISSTTASFKETYPDCINPDKTVPVPVNNQKYSVKNFLL\n+DQKFYPLKKTGLNDSENKYILVTKDNVSFVPLNLKSVAKLSSFKESALTKLGINHKNVTF\n+HMTDFDCDIGAAIPDDTLEFLKKSLFLNTSGKIYIKDQMKLQQKPKPAPLTSENNVPLKS\n+VKSKSSMRSGTSSLIASTDDVSIVTSSSDITSFDEHASGSGRRYPQTPSYYYDRVSNTNP\n+TEELNYWNIKEVLSHEENAPKMVFKTSPKLELNLPDKGSKLNIPTPITENESKSSFQVLR\n+KDEGTEIDFNHRRESPYTKPELAPKREAPKPPANTSPQRTLSTSKQNKPIRLVRASTKIS\n+RSKRSKPLPPQLLSSPIEASSSSPDSLTSSYTPASTHVLIPQPYKGANDVMRRLKTDQDS\n+TSTSPSLKMKQKVNRSNSTVSTSNSIFYSPSPLLKRGNSKRVVSSTSAADIFEENDITFA\n+DAPPMFDSDDSDDDSSSSDDIIWSKKKTAPETNNENKKDEKSDNSSTHSDEIFYDSQTQD\n+KMERKMTFRPSPEVVYQNLEKFFPRANLDKPITEGIASPTSPKSLDSLLSPKNVASSRTE\n+PSTPSRPVPPDSSYEFIQDGLNGKNKPLNQAKTPKRTKTIRTIAHEASLARKNSVKLKRQ\n+NTKMWGTRMVEVTENHMVSINKAKNSKGEYKEFAWMKGEMIGKGSFGAVYLCLNVTTGEM\n+MAVKQVEVPKYSSQNEAILSTVEALRSEVSTLKDLDHLNIVQYLGFENKNNIYSLFLEYV\n+AGGSVGSLIRMYGRFDEPLIKHLTTQVLKGLAYLHSKGILHRDMKADNLLLDQDGICKIS\n+DFGISRKSKDIYSNSDMTMRGTVFWMAPEMVDTKQGYSAKVDIWSLGCIVLEMFAGKRPW\n+SNLEVVAAMFKIGKSKSAPPIPEDTLPLISQIGRNFLDACFEINPEKRPTANELLSHPFS\n+EVNETFNFKSTRLAKFIKSNDKLNSSKLRITSQENKTE\n+\n+>sp|P07267|CARP_YEAST Saccharopepsin OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PEP4 PE=1 SV=1\n+MFSLKALLPLALLLVSANQVAAKVHKAKIYKHELSDEMKEVTFEQHLAHLGQKYLTQFEK\n+ANPEVVFSREHPFFTEGGHDVPLTNYLNAQYYTDITLGTPPQNFKVILDTGSSNLWVPSN\n+ECGSLACFLHSKYDHEASSSYKANGTEFAIQYGTGSLEGYISQDTLSIGDLTIPKQDFAE\n+ATSEPGLTFAFGKFDGILGLGYDTISVDKVVPPFYNAIQQDLLDEKRFAFYLGDTSKDTE\n+NGGEATFGGIDESKFKGDITWLPVRRKAYWEVKFEGIGLGDEYAELESHGAAIDTGTSLI\n+TLPSGLAEMINAEIGAKKGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPYDYTLEVSGS\n+CISAITPMDFPEPVGPLAIVGDAFLRKYYSIYDLGNNAVGLAKAI\n+\n+>sp|P29547|EF1G1_YEAST Elongation factor 1-gamma 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CAM1 PE=1 SV=2\n+MSQGTLYANFRIRTWVPRGLVKALKLDVKVVTPDAAAEQFARDFPLKKVPAFVGPKGYKL\n+TEAMAINYYLVKLSQDDKMKTQLLGADDDLNAQAQIIRWQSLANSDLCIQIANTIVPLKG\n+GAPYNKKSVDSAMDAVDKIVDIFENRLKNYTYLATENISLADLVAASIFTRYFESLFGTE\n+WRAQHPAIVRWFNTVRASPFLKDEYKDFKFADKPLSPPQKKKEKKAPAAAPAASKKKEEA\n+KPAATETETSSKKPKHPLELLGKSTFVLDDWKRKYSNEDTRPVALPWFWEHYNPEEYSLW\n+KVTYKYNDELTLTFMSNNLVGGFFNRLSASTKYMFGCLVVYGENNNNGIVGAVMVRGQDY\n+VPAFDVAPDWESYDYAKLDPTNDDDKEFINNMWAWDKPVSVNGEPKEIVDGKVLK\n+\n+>sp|P43616|DUG1_YEAST Cys-Gly metallodipeptidase DUG1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=DUG1 PE=1 SV=1\n+MSHSLTSVFQKIDSLKPQFFSRLTKAIQIPAVSSDESLRSKVFDKAKFISEQLSQSGFHD\n+IKMVDLGIQPPPISTPNLSLPPVILSRFGSDPSKKTVLVYGHYDVQPAQLEDGWDTEPFK\n+LVIDEAKGIMKGRGVTDDTGPLLSWINVVDAFKASGQEFPVNLVTCFEGMEESGSLKLDE\n+LIKKEANGYFKGVDAVCISDNYWLGTKKPVLTYGLRGCNYYQTIIEGPSADLHSGIFGGV\n+VAEPMI'..b'NSQQTTTPAS\n+SAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGWSFYGHPSMIPYTPYQMSPM\n+YFPPGPQSQFPQYPSSVGTPLSTPSPESGNTFTDSSSADSDMTSTKKYVRPPPMLTSPND\n+FPNWVKTYIKFLQNSNLGGIIPTVNGKPVRQITDDELTFLYNTFQIFAPSQFLPTWVKDI\n+LSVDYTDIMKILSKSIEKMQSDTQEANDIVTLANLQYNGSTPADAFETKVTNIINRLNNN\n+GIHINNKVACQLIMRGLSGEYKFLRYTRHRHLNMTVAELFLDIHAIYEEQQGSRNSKPNY\n+RRNLSDEKNDSRSYTNTTKPKVIARNPQKTNNSKSKTARAHNVSTSNNSPSTDNDSISKS\n+TTEPIQLNNKHDLHLRPGTY\n+\n+>sp|Q12414|YP11B_YEAST Transposon Ty1-PL Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TY1B-PL PE=3 SV=1\n+MESQQLSQHSPISHGSACASVTSKEVHTNQDPLDVSASKTEECEKASTKANSQQTTTPAS\n+SAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGWSFYGHPSMIPYTPYQMSPM\n+YFPPGPQSQFPQYPSSVGTPLSTPSPESGNTFTDSSSADSDMTSTKKYVRPPPMLTSPND\n+FPNWVKTYIKFLQNSNLGGIIPTVNGKPVRQITDDELTFLYNTFQIFAPSQFLPTWVKDI\n+LSVDYTDIMKILSKSIEKMQSDTQEANDIVTLANLQYNGSTPADAFETKVTNIIDRLNNN\n+GIHINNKVACQLIMRGLSGEYKFLRYTRHRHLNMTVAELFLDIHAIYEEQQGSRNSKPNY\n+RRNLSDEKNDSRSYTNTTKPKVIARNPQKTNNSKSKTARAHNVSTSNNSPSTDNDSISKS\n+TTEPIQLNNKHDLHLGQELTESTVNHTNHSDDELPGHLLLDSGASRTLIRSAHHIHSASS\n+NPDINVVDAQKRNIPINAIGDLQFHFQDNTKTSIKVLHTPNIAYDLLSLNELAAVDITAC\n+FTKNVLERSDGTVLAPIVKYGDFYWVSKKYLLPSNISVPTINNVHTSESTRKYPYPFIHR\n+MLAHANAQTIRYSLKNNTITYFNESDVDWSSAIDYQCPDCLIGKSTKHRHIKGSRLKYQN\n+SYEPFQYLHTDIFGPVHNLPNSAPSYFISFTDETTKFRWVYPLHDRREDSILDVFTTILA\n+FIKNQFQASVLVIQMDRGSEYTNRTLHKFLEKNGITPCYTTTADSRAHGVAERLNRTLLD\n+DCRTQLQCSGLPNHLWFSAIEFSTIVRNSLASPKSKKSARQHAGLAGLDISTLLPFGQPV\n+IVNDHNPNSKIHPRGIPGYALHPSRNSYGYIIYLPSLKKTVDTTNYVILQGKESRLDQFN\n+YDALTFDEDLNRLTASYHSFIASNEIQESNDLNIESDHDFQSDIELHPEQPRNVLSKAVS\n+PTDSTPPSTHTEDSKRVSKTNIRAPREVDPNISESNILPSKKRSSTPQISNIESTGSGGM\n+HKLNVPLLAPMSQSNTHESSHASKSKDFRHSDSYSENETNHTNVPISSTGGTNNKTVPQI\n+SDQETEKRIIHRSPSIDASPPENNSSHNIVPIKTPTTVSEQNTEESIIADLPLPDLPPES\n+PTEFPDPFKELPPINSRQTNSSLGGIGDSNAYTTINSKKRSLEDNETEIKVSRDTWNTKN\n+MRSLEPPRSKKRIHLIAAVKAVKSIKPIRTTLRYDEAITYNKDIKEKEKYIEAYHKEVNQ\n+LLKMKTWDTDEYYDRKEIDPKRVINSMFIFNKKRDGTHKARFVARGDIQHPDTYDSGMQS\n+NTVHHYALMTSLSLALDNNYYITQLDISSAYLYADIKEELYIRPPPHLGMNDKLIRLKKS\n+LYGLKQSGANWYETIKSYLIKQCGMEEVRGWSCVFKNSQVTICLFVDDMILFSKDLNANK\n+KIITTLKKQYDTKIINLGESDNEIQYDILGLEIKYQRGKYMKLGMENSLTEKIPKLNVPL\n+NPKGRKLSAPGQPGLYIDQDELEIDEDEYKEKVHEMQKLIGLASYVGYKFRFDLLYYINT\n+LAQHILFPSRQVLDMTYELIQFMWDTRDKQLIWHKNKPTEPDNKLVAISDASYGNQPYYK\n+SQIGNIYLLNGKVIGGKSTKASLTCTSTTEAEIHAISESVPLLNNLSYLIQELNKKPIIK\n+GLLTDSRSTISIIKSTNEEKFRNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKP\n+LPIKTFKLLTNKWIH\n+\n+>sp|P31111|ZIP1_YEAST Synaptonemal complex protein ZIP1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ZIP1 PE=1 SV=2\n+MSNFFRDSSMGFKPRPNIFAKLRVRDVDSDSSANTVVENSSNCLDVGSSIEGDDTFKKPH\n+KTSTEQELITSMSLSQRNHGYSDDMEIGSPKKTTSTDQYNRILKNDVAAIENDTDEDFEI\n+TEVREVSEGVAKETKESHGDPNDSETTLKDSKMHEYTMTNGKAPLHTSINNSSTSSNDVL\n+LEAFTNTQRICSNLKQELQKQQQDNAKLKVRLQSYASNSDKINEKVGKYKSCLETLQERI\n+ATLTSHKNNQETKLKDLRQNHQLYQRRISGFKTSIENLNKTINDLGKNKKEADAELMKKG\n+KEIEYLKRELDDCSGQLSEEKIKNSSLIQEMGKNREEMIKSIENFFSEDKAHHLLQFNKF\n+EERVHDLFEKKLQKHFDVAKDTLNVGLRNTTVELSSNTETMLKQQYEDIKENLEQKMSSS\n+KDEMAKTINELSVTQKGLIMGVQEELLTSSGNIQTALVSEMNNTRQELLDDASQTAKNYA\n+SLENLVKAYKAEIVQSNEYEERIKHLESERSTLSSQKNQIISSLGTKEAQYEDLVKKLEA\n+KNIEISQISGKEQSLTEKNENLSNELKKVQDQLEKLNNLNITTKSNYENKISSQNEIVKA\n+LVSENDTLKQRIQQLVEIKENEQKDHTTKLEAFQKNNEQLQKLNVEVVQLKAHELELEEQ\n+NRHLKNCLEKKETGVEESLSDVKTLKQQVIVLKSEKQDITAEKLELQDNLESLEEVTKNL\n+QQKVQSQKRELEQKIKELEEIKNHKRNEPSKKGTQNFTKPSDSPKKNATTSNLFPNNSAA\n+IHSPMKKCPKVDHISKSRINSSKETSKFNDEFDLSSSSNDDLELTNPSPIQIKPVRGKIK\n+KGSNCMKPPISSRKKLLLVEDEDQSLKISKKRRRK\n+\n+>sp|P0CX75|YL13A_YEAST Transposon Ty1-LR3 Gag polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TY1A-LR3 PE=2 SV=1\n+MESQQLSQHSHISHGSACASVTSKEVHTNQDPLDVSASKTEECEKASTKANSQQTTTPAS\n+SAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGWSFYGHPSMIPYTPYQMSPM\n+YFPPGPQSQFPQYPSSVGTPLSTPSPESGNTFTDSSSADSDMTSTKKYVRPPPMLTSPND\n+FPNWVKTYIKFLQNSNLGGIIPTVNGKPVRQITDDELTFLYNTFQIFAPSQFLPTWVKDI\n+LSVDYTDIMKILSKSIEKMQSDTQEANDIVTLANLQYNGSTPADAFETKVTNIIDRLNNN\n+GIHINNKVACQLIMRGLSGEYKFLRYTRHRHLNMTVAELFLDIHAIYEEQQGSRNSKPNY\n+RRNLSDEKNDSRSYTNTTKPKVIARNPQKTNNSKSKTARAHNVSTSNNSPSTDNDSISKS\n+TTEPIQLNNKHDLHLRPGTY\n+\n' |