| Previous changeset 1:dde913004c8a (2018-03-20) Next changeset 3:23af1883f977 (2019-05-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5 |
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modified:
OpenPepXL.xml macros.xml test-data/MetaProSIP_1_output_1.csv test-data/MetaProSIP_1_output_2.csv |
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added:
test-data/OpenPepXL_input.fasta test-data/SequenceCoverageCalculator.fasta test-data/SequenceCoverageCalculator.idXML test-data/SequenceCoverageCalculator.tsv |
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| diff -r dde913004c8a -r ec2524b5a07a OpenPepXL.xml --- a/OpenPepXL.xml Tue Mar 20 15:18:56 2018 -0400 +++ b/OpenPepXL.xml Fri May 17 05:01:49 2019 -0400 |
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| @@ -10,7 +10,7 @@ <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> - <command>OpenPepXL + <command detect_errors="aggressive"><![CDATA[OpenPepXL #if $param_in: -in $param_in @@ -162,7 +162,7 @@ -precursor:max_charge $adv_opts.param_precursor_max_charge #end if #end if -</command> +]]></command> <inputs> <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing the spectra" help="(-in) "/> <param name="param_consensus" type="data" format="consensusxml" optional="False" label="Input file containing the linked mass peaks" help="(-consensus) "/> @@ -5340,5 +5340,5 @@ <help>Tool for protein-protein cross-linking identification using labeled linkers. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenPepXL.html</help> +For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_OpenPepXL.html</help> </tool> |
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| diff -r dde913004c8a -r ec2524b5a07a macros.xml --- a/macros.xml Tue Mar 20 15:18:56 2018 -0400 +++ b/macros.xml Fri May 17 05:01:49 2019 -0400 |
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| @@ -11,9 +11,9 @@ </xml> <xml name="stdio"> <stdio> - <exit_code range="1:"/> - <exit_code range=":-1"/> - <regex match="Exception:"/> + <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> + <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> + <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/> </stdio> </xml> <xml name="references"> |
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| diff -r dde913004c8a -r ec2524b5a07a test-data/MetaProSIP_1_output_1.csv --- a/test-data/MetaProSIP_1_output_1.csv Tue Mar 20 15:18:56 2018 -0400 +++ b/test-data/MetaProSIP_1_output_1.csv Fri May 17 05:01:49 2019 -0400 |
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| @@ -3,5 +3,5 @@ Protein Accession Description # Unique Peptides Median Global LR median RIA 1 median RIA 2 CONTIG23640_802236 length=2326 numreads=28 strand:-1 frame:0 orf_location:136:990 1 0.269627132474428 0.603333333333335 36.4733333333347 Peptide Sequence RT Exp. m/z Theo. m/z Charge Score TIC fraction #non-natural weights RIA 1 INT 1 Cor. 1 RIA 2 INT 2 Cor. 2 Peak intensities Global LR - YGGAVDPTVLGGVK 80.52 666.8623 666.861538013921 2 0.174659044235501 0.831887919884233 7 0.6 1432379 1.00 36.5 146376 0.87 659720 461384 165174 49177 14782 11728 6541 7410 10868 8404 9437 9556 10203 12619 12159 15831 16288 19847 19258 22222 21275 21576 21294 22006 24019 19046 17493 19060 17884 15631 15769 13964 14131 10090 9445 9216 7297 6670 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.269627132474428 + YGGAVDPTVLGGVK 80.52 666.8623 666.861538013921 2 0.174659044235501 0.831887919884232 7 0.6 1432379 1.00 36.5 146376 0.87 659720 461384 165174 49177 14782 11728 6541 7410 10868 8404 9437 9556 10203 12619 12159 15831 16288 19847 19258 22222 21275 21576 21294 22006 24019 19046 17493 19060 17884 15631 15769 13964 14131 10090 9445 9216 7297 6670 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.269627132474428 Non-Unique Peptides Accessions Peptide Sequence Descriptions Score RT Exp. m/z Theo. m/z Charge #non-natural weights Peak intensities Global LR |
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| diff -r dde913004c8a -r ec2524b5a07a test-data/MetaProSIP_1_output_2.csv --- a/test-data/MetaProSIP_1_output_2.csv Tue Mar 20 15:18:56 2018 -0400 +++ b/test-data/MetaProSIP_1_output_2.csv Fri May 17 05:01:49 2019 -0400 |
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| @@ -1,3 +1,2 @@ -Peptide Sequence Feature Quality Report Spectrum Quality report scores Sample Name Protein Accessions Description Unique #Ambiguity members Score RT Exp. m/z Theo. m/z Charge TIC fraction #non-natural weights Peak intensities Group Global Peptide LR RIA 1 LR of RIA 1 INT 1 Cor. 1 RIA 2 LR of RIA 2 INT 2 Cor. 2 RIA 3 LR of RIA 3 INT 3 Cor. 3 RIA 4 LR of RIA 4 INT 4 Cor. 4 RIA 5 LR of RIA 5 INT 5 Cor. 5 RIA 6 LR of RIA 6 INT 6 Cor. 6 RIA 7 LR of RIA 7 INT 7 Cor. 7 RIA 8 LR of RIA 8 INT 8 Cor. 8 RIA 9 LR of RIA 9 INT 9 Cor. 9 RIA 10 LR of RIA 10 INT 10 Cor. 10 -YGGAVDPTVLGGVK feature test_mode_enabled.mzML CONTIG23640_802236 length=2326 numreads=28 strand:-1 frame:0 orf_location:136:990 1 1 0.174659044235501 80.52 666.8623 666.8615 2 0.831887919884232 7 659720 461384 165174 49177 14782 11728 6541 7410 10868 8404 9437 9556 10203 12619 12159 15831 16288 19847 19258 22222 21275 21576 21294 22006 24019 19046 17493 19060 17884 15631 15769 13964 14131 10090 9445 9216 7297 6670 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.269627132474428 0.6 1.0 1432378.6 1.0 36.5 0.0 146375.7 0.9 - +#Peptide_Sequence Feature Quality_Report_Spectrum Quality_report_scores Sample_Name Protein_Accessions Description Unique #Ambiguity_members Score RT Exp._m/z Theo._m/z Charge TIC_fraction #non-natural_weights Peak_intensities Group Global_Peptide_LR RIA_1 LR_of_RIA_1 INT_1 Cor._1 RIA_2 LR_of_RIA_2 INT_2 Cor._2 RIA_3 LR_of_RIA_3 INT_3 Cor._3 RIA_4 LR_of_RIA_4 INT_4 Cor._4 RIA_5 LR_of_RIA_5 INT_5 Cor._5 RIA_6 LR_of_RIA_6 INT_6 Cor._6 RIA_7 LR_of_RIA_7 INT_7 Cor._7 RIA_8 LR_of_RIA_8 INT_8 Cor._8 RIA_9 LR_of_RIA_9 INT_9 Cor._9 RIA_10 LR_of_RIA_10 INT_10 Cor._10 +YGGAVDPTVLGGVK feature spectrum_dataset_1_575Z_rt_4831.43346884947.png scores_dataset_1_575Z_rt_4831.43346884947.png dataset_1.dat CONTIG23640_802236 length=2326__numreads=28_strand:-1_frame:0_orf_location:136:990 1 1 0.174659044235501 80.52 666.8623 666.8615 2 0.831887919884232 7 659720_461384_165174_49177_14782_11728_6541_7410_10868_8404_9437_9556_10203_12619_12159_15831_16288_19847_19258_22222_21275_21576_21294_22006_24019_19046_17493_19060_17884_15631_15769_13964_14131_10090_9445_9216_7297_6670_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0_0 0 0.269627132474428 0.6 1.0 1432378.6 1.0 36.5 0.0 146375.7 0.9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 |
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| diff -r dde913004c8a -r ec2524b5a07a test-data/OpenPepXL_input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OpenPepXL_input.fasta Fri May 17 05:01:49 2019 -0400 |
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| @@ -0,0 +1,39 @@ +>Protein1 +MSERDTALEKYKSYLLQHREWDSKLKDLRFGNRDLVKKYDKTEDDIKSLQSVGQIIGEVL +KQLDSERFIVKASSGPRYVVGCRNNVDQSHLVQGVRVSLDMTTLTIMRILPREVDPLVYN +MSIEDPGDISFAGVGGLNEQIRELREVIELPLKNPELFLRVGIKPPKGVLLYGPPGTGKT +LLARAVAASLGVNFLKVVSSAIVDKYIGESARIIREMFGYAKEHEPCVIFMDEIDAIGGR +RFSEGTSADREIQRTLMELLNQMDGFDYLGQTKIIMATNRPDTLDPALLRPGRLDRKIEI +PLPNEVGRMEILKIHLEKVSKQGEIDYEALVKLTDGTNGADLRNVVTEAGFIAIKEDRDY +VIQSDLMSAARKVADLKKLEGTIDYQKL +>Protein2 +MSTLEELDALDQSQQGGSSNNEGLDGIEQEILAAGIDELNSRTRLLENDIKVMKSEFQRL +THEKSTMLEKIKENQEKISNNKMLPYLVGNVVEILDMQPDEVDVQESANQNSEATRVGKS +AVIKTSTRQTIFLPLIGLVEPEELHPGDLIGVNKDSYLIIDKLPSEYDSRVKAMEVDEKP +TERYSDIGGLSKQIEELFEAIVLPMQQADKFRKLGVKPPKGCLMFGPPGTGKTLLARACA +AQSNATFLKLAAPQLVQMFIGDGAKLVRDAFALAKEKSPAIIFIDELDAIGTKRFDSEKA +GDREVQRTMLELLNQLDGFSSDDRVKVIAATNRVDTLDPALLRSGRLDRKLEFPLPNEEA +RVGILRIHSRKMAIDDDINWEELARSTDEYNGAMLKSVCVEAGMIALRQGDTKINHEHFM +DGILEVQMRKSKTLQYFA +>Protein3 +MPFGNTHNKFKLNYKPEEEYPDLSKHNNHMAKVLTLELYKKLRDKETPSGFTVDDVIQTG +VDNPGHPFIMTVGCVAGDEESYEVFKELFDPIISDRHGGYKPTDKHKTDLNHENLKGGDD +LDPNYVLSSRVRTGRSIKGYTLPPHCSRGERRAVEKLSVEALNSLTGEFKGKYYPLKSMT +EKEQQQLIDDHFLFDKPVSPLLLASGMARDWPDARGIWHNDNKSFLVWVNEEDHLRVISM +EKGGNMKEVFRRFCVGLQKIEEIFKKAGHPFMWNQHLGYVLTCPSNLGTGLRGGVHVKLA +HLSKHPKFEEILTRLRLQKRGTGGVDTAAVGSVFDVSNADRLGSSEVEQVQLVVDGVKLM +VEMEKKLEKGQSIDDMIPAQK +>Protein4 +MSTLDLNHLADLYDRKDWNACKKELLKLKVELAKQNLFVPTSDKEKASFARNVFEYGVLV +SIQTCDIESFARYASQVIPFYHDSLVPSSRMGLVTGLNLLYLLSENRIAEFHTALESVPD +KSLFERDPYVEWVISLEQNVMEGAFDKVASMIRSCNFPEFSYFMKIVMSMVRNEIATCAE +KVYSEIPLSNATSLLYLENTKETEKLAEERGWDIRDGVIYFPKEANALETEDGMLIDEED +ELELPPTASKHTISSIRQLLSYTSELEQIV +>Protein5 +MCSPSATLTHRTMTEKARTVSDLTISQAIFELSSPFLENKSQKALDTLFSAIRDHDLAPL +YKYLSENPKTSASIDFDSNFLNSMIKKNEEKLAEFDKAIEDAQELNGEHEILEAMKNKAD +YYTNICDRERGVQLCDETFERATLTGMKIDVLFSKIRLAYVYADMRVVGQLLEKLKPLIE +KGGDWERKNRLKAYQGIYLMSIRNFSGAADLLLDCMSTFSSTELLPYYDVVRYAVISGAI +SLDRVDVKTKIVDSPEVLAVLPQNESMSSLEACINSLYLCDYSGFFRTLADVEVNHLKCD +QFLVAHYRYYVREMRRRAYAQLLESYRALSIDSMAASFGVSVDYIDRDLASFIPDNKLNC +VIDRVNGVVFTNRPDEKNRQYQEVVKQGDVLLNKLQKYQATVMRGAFKV \ No newline at end of file |
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| diff -r dde913004c8a -r ec2524b5a07a test-data/SequenceCoverageCalculator.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SequenceCoverageCalculator.fasta Fri May 17 05:01:49 2019 -0400 |
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| b'@@ -0,0 +1,149508 @@\n+>sp|Q16827|PTPRO_HUMAN Receptor-type tyrosine-protein phosphatase O OS=Homo sapiens OX=9606 GN=PTPRO PE=1 SV=2\n+MGHLPTGIHGARRLLPLLWLFVLFKNATAFHVTVQDDNNIVVSLEASDVISPASVYVVKITGESKNYFFEFEEFNSTLPPPVIFKASYHGLYYIITLVVVNGNVVTKPSRSITVLTKPLPVTSVSIYDYKPSPETGVLFEIHYPEKYNVFTRVNISYWEGKDFRTMLYKDFFKGKTVFNHWLPGMCYSNITFQLVSEATFNKSTLVEYSGVSHEPKQHRTAPYPPQNISVRIVNLNKNNWEEQSGNFPEESFMRSQDTIGKEKLFHFTEETPEIPSGNISSGWPDFNSSDYETTSQPYWWDSASAAPESEDEFVSVLPMEYENNSTLSETEKSTSGSFSFFPVQMILTWLPPKPPTAFDGFHIHIEREENFTEYLMVDEEAHEFVAELKEPGKYKLSVTTFSSSGSCETRKSQSAKSLSFYISPSGEWIEELTEKPQHVSVHVLSSTTALMSWTSSQENYNSTIVSVVSLTCQKQKESQRLEKQYCTQVNSSKPIIENLVPGAQYQVVIYLRKGPLIGPPSDPVTFAIVPTGIKDLMLYPLGPTAVVLSWTRPYLGVFRKYVVEMFYFNPATMTSEWTTYYEIAATVSLTASVRIANLLPAWYYNFRVTMVTWGDPELSCCDSSTISFITAPVAPEITSVEYFNSLLYISWTYGDDTTDLSHSRMLHWMVVAEGKKKIKKSVTRNVMTAILSLPPGDIYNLSVTACTERGSNTSMLRLVKLEPAPPKSLFAVNKTQTSVTLLWVEEGVADFFEVFCQQVGSSQKTKLQEPVAVSSHVVTISSLLPATAYNCSVTSFSHDSPSVPTFIAVSTMVTEMNPNVVVISVLAILSTLLIGLLLVTLIILRKKHLQMARECGAGTFVNFASLERDGKLPYNWRRSIFAFLTLLPSCLWTDYLLAFYINPWSKNGLKKRKLTNPVQLDDFDAYIKDMAKDSDYKFSLQFEELKLIGLDIPHFAADLPLNRCKNRYTNILPYDFSRVRLVSMNEEEGADYINANYIPGYNSPQEYIATQGPLPETRNDFWKMVLQQKSQIIVMLTQCNEKRRVKCDHYWPFTEEPIAYGDITVEMISEEEQDDWACRHFRINYADEMQDVMHFNYTAWPDHGVPTANAAESILQFVHMVRQQATKSKGPMIIHCSAGVGRTGTFIALDRLLQHIRDHEFVDILGLVSEMRSYRMSMVQTEEQYIFIHQCVQLMWMKKKQQFCISDVIYENVSKS\n+>DECOY_sp|Q16827|PTPRO_HUMAN Receptor-type tyrosine-protein phosphatase O OS=Homo sapiens OX=9606 GN=PTPRO PE=1 SV=2\n+SKSVNEYIVDSICFQQKKKMWMLQVCQHIFIYQEETQVMSMRYSRMESVLGLIDVFEHDRIHQLLRDLAIFTGTRGVGASCHIIMPGKSKTAQQRVMHVFQLISEAANATPVGHDPWATYNFHMVDQMEDAYNIRFHRCAWDDQEEESIMEVTIDGYAIPEETFPWYHDCKVRRKENCQTLMVIIQSKQQLVMKWFDNRTEPLPGQTAIYEQPSNYGPIYNANIYDAGEEENMSVLRVRSFDYPLINTYRNKCRNLPLDAAFHPIDLGILKLEEFQLSFKYDSDKAMDKIYADFDDLQVPNTLKRKKLGNKSWPNIYFALLYDTWLCSPLLTLFAFISRRWNYPLKGDRELSAFNVFTGAGCERAMQLHKKRLIILTVLLLGILLTSLIALVSIVVVNPNMETVMTSVAIFTPVSPSDHSFSTVSCNYATAPLLSSITVVHSSVAVPEQLKTKQSSGVQQCFVEFFDAVGEEVWLLTVSTQTKNVAFLSKPPAPELKVLRLMSTNSGRETCATVSLNYIDGPPLSLIATMVNRTVSKKIKKKGEAVVMWHLMRSHSLDTTDDGYTWSIYLLSNFYEVSTIEPAVPATIFSITSSDCCSLEPDGWTVMTVRFNYYWAPLLNAIRVSATLSVTAAIEYYTTWESTMTAPNFYFMEVVYKRFVGLYPRTWSLVVATPGLPYLMLDKIGTPVIAFTVPDSPPGILPGKRLYIVVQYQAGPVLNEIIPKSSNVQTCYQKELRQSEKQKQCTLSVVSVITSNYNEQSSTWSMLATTSSLVHVSVHQPKETLEEIWEGSPSIYFSLSKASQSKRTECSGSSSFTTVSLKYKGPEKLEAVFEHAEEDVMLYETFNEEREIHIHFGDFATPPKPPLWTLIMQVPFFSFSGSTSKETESLTSNNEYEMPLVSVFEDESEPAASASDWWYPQSTTEYDSSNFDPWGSSINGSPIEPTEETFHFLKEKGITDQSRMFSEEPFNGSQEEWNNKNLNVIRVSINQPPYPATRHQKPEHSVGSYEVLTSKNFTAESVLQFTINSYCMGPLWHNFVTKGKFFDKYLMTRFDKGEWYSINVRTFVNYKEPYHIEFLVGTEPSPKYDYISVSTVPLPKTLVTISRSPKTVVNGNVVVLTIIYYLGHYSAKFIVPPPLTSNFEEFEFFYNKSEGTIKVVYVSAPSIVDSAELSVVINNDDQVTVHFATANKFLVFLWLLPLLRRAGHIGTPLHGM\n+>sp|Q15256|PTPRR_HUMAN Receptor-type tyrosine-protein phosphatase R OS=Homo sapiens OX=9606 GN=PTPRR PE=1 SV=2\n+MRRAVCFPALCLLLNLHAAGCFSGNNDHFLAINQKKSGKPVFIYKHSQDIEKSLDIAPQKIYRHSYHSSSEAQVSKRHQIVNSAFPRPAYDPSLNLLAMDGQDLEVENLPIPAANVIVVTLQMDVNKLNITLLRIFRQGVAAALGLLPQQVHINRLIGKKNSIELFVSPINRKTGISDALPSEEVLRSLNINVLHQSLSQFGITEVSPEKNVLQGQHEADKIWSKEGFYAVVIFLSIFVIIVTCLMILYRLKERFQLSLRQDKEKNQEIHLSPITLQPALSEAKTVHSMVQPEQAPKVLNVVVDPQGRGAPEIKATTATSVCPSPFKMKPIGLQERRGSNVSLTLDMSSLGNIEPFVSIPTPREKVAMEYLQSASRILTRSQLRDVVASSHLLQSEFMEIPMNFVDPKEIDIPRHGTKNRYKTILPNPLSRVCLRPKNVTDSLSTYINANYIRGYSGKEKAFIATQGPMINTVDDFWQMVWQEDSPVIVMITKLKEKNEKCVLYWPEKRGIYGKVEVLVISVNECDNYTIRNLVLKQGSHTQHVKHYWYTSWPDHKTPDSAQPLLQLMLDVEEDRLASQGRGPVVVHCSAGIGRTGCFIATSIGCQQLKEEGVVDALSIVCQLRMDRGGMVQTSEQYEFVHHALCLYESRLSAETVQ\n+>DECOY_sp|Q15256|PTPRR_HUMAN Receptor-type tyrosine-protein phosphatase R OS=Homo sapiens OX=9606 GN=PTPRR PE=1 SV=2\n+QVTEASLRSEYLCLAHHVFEYQESTQVMGGRDMRLQCVISLADVVGEEKLQQCGISTAIFCGTRGIGASCHVVVPGRGQSALRDEEVDLMLQLLPQASDPTKHDPWSTYWYHKVHQTHSGQKLVLNRITYNDCENVSIVLVEVKGYIGRKEPWYLVCKENKEKLKTIMVIVPSDEQWVMQWFDDVTNIMPGQTAIFAKEKGSYGRIYNANIYTSLSDTVNKPRLCVRSLPNPLITKYRNKTGHRPIDIEKPDVFNMPIEMFESQLLHSSAVVDRLQSRTLIRSASQLYEMAVKERPTPISVFPEINGLSSMDLTLSVNSGRREQLGIPKMKFPSPCVSTATTAKIEPAGRGQPDVVVNLVKPAQEPQVMSHVTKAESLAPQLTIPSLHIEQNKEKDQRLSLQFREKLRYLIMLCTVIIVFIS'..b'STVFAM\n+>NM_000106|744367_2_460_548\n+MGPRGASRGASPSPPCATWAWARSRWSSG\n+>DECOY_NM_000106|744367_2_460_548\n+GSSWRSRAWAWTACPPSPSAGRSAGRPGM\n+>NM_002543|744389_2_565_653\n+MEKTVTYFPRAHLTGKRAKRSACLWMPSC\n+>DECOY_NM_002543|744389_2_565_653\n+CSPMWLCASRKARKGTLHARPFYTVTKEM\n+>NM_000690|744529_2_820_1010\n+MASPMSSPTWWIWTWSSNVSGIMPAGLISTTGKPSPLTETSSATHAMNLWGCAGRSFRGISRS\n+>DECOY_NM_000690|744529_2_820_1010\n+SRSIGRFSRGACGWLNMAHTASSTETLPSPKGTTSILGAPMIGSVNSSWTWIWWTPSSMPSAM\n+>NM_000761|744570_3_198_391\n+MGLALARACADPGEEPAPGTVKDEPALRGRPADPHWLHARAGAEPPGHHPAGPGAAGRRFQGPA\n+>DECOY_NM_000761|744570_3_198_391\n+APGQFRRGAAGPGAPHHGPPEAGARAHLWHPDAPRGRLAPEDKVTGPAPEEGPDACARALALGM\n+>NM_006018|744640_2_288_367\n+MALPCGFSVSTSSPGNPAGFSCSTWQ\n+>DECOY_NM_006018|744640_2_288_367\n+QWTSCSFGAPNGPSSTSVSFGCPLAM\n+>NM_006018|744641_2_666_1009\n+MALQMCASASASAIPSGGTKLCSSWSSSCPWASSCSAQPELSGACGRDKWTGMPRSREPSPSSWWWPSSLSSASFPAWLCGSTSSGSCTLRARRIVKCTARWTWRSLSLSASPT\n+>DECOY_NM_006018|744641_2_666_1009\n+TPSASLSLSRWTWRATCKVIRRARLTCSGSSTSGCLWAPFSASSLSSPWWWSSPSPERSRPMGTWKDRGCAGSLEPQASCSSAWPCSSSWSSCLKTGGSPIASASASACMQLAM\n+>NM_000578|744661_2_383_456\n+MVPSPARPARPAQGHSKHLPERPT\n+>DECOY_NM_000578|744661_2_383_456\n+TPREPLHKSHGQAPRAPRAPSPVM\n+>NM_000578|744669_3_513_730\n+MGLHGAWLPHEHCFPGPRKHRVRSSGWRRGGIQTSLGAALGHRVGLALPATGCTSGRGDRQGLGRGLPSLLP\n+>DECOY_NM_000578|744669_3_513_730\n+PLLSPLGRGLGQRDGRGSTCGTAPLALGVRHGLAAGLSTQIGGRRWGSSRVRHKRPGPFCHEHPLWAGHLGM\n+>NM_021245|744690_2_744_1078\n+MALISSTIWALGLELGVQVVPRARLAEEELLAQQGLVRQDQETRQAEKENISLCSRPIFPHGSEPWGLTPSKKWNLALTCWPMGPKLNFPNISPSTGRQCPMVDMRRPPNA\n+>DECOY_NM_021245|744690_2_744_1078\n+ANPPRRMDVMPCQRGTSPSINPFNLKPGMPWCTLALNWKKSPTLGWPESGHPFIPRSCLSINEKEAQRTEQDQRVLGQQALLEEEALRARPVVQVGLELGLAWITSSILAM\n+>NM_015088|744804_2_1547_1716\n+MGTMEKRERTPGKELLFRNQLGQKMTLGTTITGLRVGPGTLAPRTLMTTNGVKGTK\n+>DECOY_NM_015088|744804_2_1547_1716\n+KTGKVGNTTMLTRPALTGPGVRLGTITTGLTMKQGLQNRFLLEKGPTRERKEMTGM\n+>NM_015088|744805_2_1556_1716\n+MEKRERTPGKELLFRNQLGQKMTLGTTITGLRVGPGTLAPRTLMTTNGVKGTK\n+>DECOY_NM_015088|744805_2_1556_1716\n+KTGKVGNTTMLTRPALTGPGVRLGTITTGLTMKQGLQNRFLLEKGPTRERKEM\n+>NM_015088|744811_2_2450_2583\n+MVGGRKSIRQKTAIGKVLQVNLCLGGVKEGRMKSGLGVMVAMQA\n+>DECOY_NM_015088|744811_2_2450_2583\n+AQMAVMVGLGSKMRGEKVGGLCLNVQLVKGIATKQRISKRGGVM\n+>NM_015088|744838_3_2433_2509\n+MVFWKEWLGGGSRSDKKQQLGKFCK\n+>DECOY_NM_015088|744838_3_2433_2509\n+KCFKGLQQKKDSRSGGGLWEKWFVM\n+>NM_000958|744871_2_1811_1884\n+MALEAGICFQVCLAWAWPRKTPPH\n+>DECOY_NM_000958|744871_2_1811_1884\n+HPPTKRPWAWALCVQFCIGAELAM\n+>NM_004958|744986_2_4253_4359\n+MALFCWVRELPSAEHMPKHYTTKNWSSRKAPPLPF\n+>DECOY_NM_004958|744986_2_4253_4359\n+FPLPPAKRSSWNKTTYHKPMHEASPLERVWCFLAM\n+>NM_004958|744989_2_4745_4845\n+MGHFIELCWHCIRTSSPWHNSALTRPGTCWMLN\n+>DECOY_NM_004958|744989_2_4745_4845\n+NLMWCTGPRTLASNHWPSSTRICHWCLEIFHGM\n+>NM_004958|745002_3_3966_4102\n+MAETAEPGAAEGLIIALPALLLGPGTGLQPDGQGSLQCCICVLLV\n+>DECOY_NM_004958|745002_3_3966_4102\n+VLLVCICCQLSGQGDPQLGTGPGLLLAPLAIILGEAAGPEATEAM\n+>NM_006725|745106_2_758_906\n+MASGDQCAMTLGTWRTPTWCAGNWAAAGQSRPCPACTSRPAAGLSTGTR\n+>DECOY_NM_006725|745106_2_758_906\n+RTGTSLGAAPRSTCAPCPRSQGAAAWNGACWTPTRWTGLTMACQDGSAM\n+>NM_006725|745108_2_1214_1371\n+MGRSSPSPTAPGGSTTPTSAASRWQPGSSAQLPGVCTICPLPKSLQVFRQSL\n+>DECOY_NM_006725|745108_2_1214_1371\n+LSQRFVQLSKPLPCITCVGPLQASSGPQWRSAASTPTTSGGPATPSPSSRGM\n+>NM_001470|745249_3_2930_3024\n+MAVGGAGHHEDRVIDQQQRGGEVPAVGEGEP\n+>DECOY_NM_001470|745249_3_2930_3024\n+PEGEGVAPVEGGRQQQDIVRDEHHGAGGVAM\n+>NM_001042594|745506_2_1677_1771\n+MVQLKPQMSSYKIHHYMIQKSGPLKIKKDEK\n+>DECOY_NM_001042594|745506_2_1677_1771\n+KEDKKIKLPGSKQIMYHHIKYSSMQPKLQVM\n+>NM_007335|745575_2_2872_3071\n+MVPGATFLCMLRYRSPMCTYRAARWRLEISTWVCPRRQPSHLSMARSCLPSSTGASSSDTKQNSAW\n+>DECOY_NM_007335|745575_2_2872_3071\n+WASNQKTDSSSAGTSSPLCSRAMSLHSPQRRPCVWTSIELRWRAARYTCMPSRYRLMCLFTAGPVM\n+>NM_007335|745583_2_4612_4727\n+MGRARTTELLALARSRSVRRRQPQRTSSWCSKHRRTCW\n+>DECOY_NM_007335|745583_2_4612_4727\n+WCTRRHKSCWSSTRQPQRRRVSRSRALALLETTRARGM\n+>NM_007337|745641_3_5066_5163\n+MVVEGVLGEKSCTLRLRGQGSYDERYMLPHQP\n+>DECOY_NM_007337|745641_3_5066_5163\n+PQHPLMYREDYSGQGRLRLTCSKEGLVGEVVM\n' |
| b |
| diff -r dde913004c8a -r ec2524b5a07a test-data/SequenceCoverageCalculator.idXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SequenceCoverageCalculator.idXML Fri May 17 05:01:49 2019 -0400 |
| [ |
| b'@@ -0,0 +1,161 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<?xml-stylesheet type="text/xsl" href="https://www.openms.de/xml-stylesheet/IdXML.xsl" ?>\n+<IdXML version="1.5" xsi:noNamespaceSchemaLocation="https://www.openms.de/xml-schema/IdXML_1_5.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">\n+\t<SearchParameters id="SP_0" db="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="3,4,5,6,7" enzyme="trypsin" missed_cleavages="2" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="0.2" peak_mass_tolerance_ppm="false" >\n+\t\t\t\t<UserParam type="string" name="input_consensusXML" value="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.consensusXML"/>\n+\t\t\t\t<UserParam type="string" name="input_mzML" value="/home/eugen/Development/OpenMS/src/tests/topp/OpenPepXL_input.mzML"/>\n+\t\t\t\t<UserParam type="string" name="input_decoys" value=""/>\n+\t\t\t\t<UserParam type="int" name="decoy_prefix" value="0"/>\n+\t\t\t\t<UserParam type="string" name="decoy_string" value="decoy"/>\n+\t\t\t\t<UserParam type="string" name="out_xquest_specxml" value="OpenPepXL_output.spec.xml.tmp"/>\n+\t\t\t\t<UserParam type="int" name="precursor:min_charge" value="3"/>\n+\t\t\t\t<UserParam type="int" name="precursor:max_charge" value="7"/>\n+\t\t\t\t<UserParam type="float" name="fragment:mass_tolerance_xlinks" value="0.3"/>\n+\t\t\t\t<UserParam type="int" name="peptide:min_size" value="5"/>\n+\t\t\t\t<UserParam type="stringList" name="cross_link:residue1" value="[K]"/>\n+\t\t\t\t<UserParam type="stringList" name="cross_link:residue2" value="[K]"/>\n+\t\t\t\t<UserParam type="float" name="cross_link:mass" value="138.0680796"/>\n+\t\t\t\t<UserParam type="float" name="cross_link:mass_isoshift" value="12.075321"/>\n+\t\t\t\t<UserParam type="floatList" name="cross_link:mass_monolink" value="[156.07864431, 155.094628715]"/>\n+\t\t\t\t<UserParam type="string" name="cross_link:name" value="DSS"/>\n+\t\t\t\t<UserParam type="int" name="modifications:variable_max_per_peptide" value="2"/>\n+\t\t\t\t<UserParam type="int" name="MS:1001029" value="329"/>\n+\t</SearchParameters>\n+\t<IdentificationRun date="2018-03-06T13:21:04" search_engine="OpenXQuest" search_engine_version="2.3.0" search_parameters_ref="SP_0" >\n+\t\t<ProteinIdentification score_type="" higher_score_better="true" significance_threshold="0" >\n+\t\t\t<ProteinHit id="PH_0" accession="Protein3" score="0" sequence="" >\n+\t\t\t\t<UserParam type="string" name="target_decoy" value="target"/>\n+\t\t\t</ProteinHit>\n+\t\t\t<ProteinHit id="PH_1" accession="Protein2" score="0" sequence="" >\n+\t\t\t\t<UserParam type="string" name="target_decoy" value="target"/>\n+\t\t\t</ProteinHit>\n+\t\t\t<ProteinHit id="PH_2" accession="Protein1" score="0" sequence="" >\n+\t\t\t\t<UserParam type="string" name="target_decoy" value="target"/>\n+\t\t\t</ProteinHit>\n+\t\t\t<UserParam type="string" name="SpectrumIdentificationProtocol" value="MS:1002494"/>\n+\t\t</ProteinIdentification>\n+\t\t<PeptideIdentification score_type="OpenXQuest:combined score" higher_score_better="true" significance_threshold="0" MZ="728.411010742188" RT="2120.05249023438" spectrum_reference="spectrum=99,spectrum=48" >\n+\t\t\t<PeptideHit score="0.936605209529642" sequence="LAAPQLVQMFIGDGAK(Xlink:DSS)LVR" charge="3" aa_before="K" aa_after="D" start="249" end="267" protein_refs="PH_1" >\n+\t\t\t\t<UserParam type="string" name="fragment_annotation" value="1004.99096679688,0.334201395511627,2,"[alpha|xi$b18]""/>\n+\t\t\t\t<UserParam type="string" name="spectrum_reference" value="spectrum=99"/>\n+\t\t\t\t<UserParam type="string" name="target_decoy" value="target"/>\n+\t\t\t\t<UserParam type="int" name="spectrum_index" value="81"/>\n+\t\t\t\t<UserParam type="float" name="xl_mass" value="156.07864431"/>\n+\t\t\t\t<UserParam type="string" name="xl_chain" value="MS:1002509"/>\n+\t\t\t\t<UserParam type="int" name="xl_pos" value="15"/>\n+\t\t\t\t<UserParam type="string" name="xl_type" value="mono-link"/>\n+\t\t\t\t<UserParam type="int" name="xl_rank" value="2"/>\n+\t\t\t\t<UserParam type="string" name="xl_term_spec" '..b'="unique"/>\n+\t\t\t</PeptideHit>\n+\t\t</PeptideIdentification>\n+\t\t<PeptideIdentification score_type="OpenXQuest:combined score" higher_score_better="true" significance_threshold="0" MZ="656.050903320313" RT="2228.50292963107" spectrum_reference="spectrum=238,spectrum=219" >\n+\t\t\t<PeptideHit score="30.0056519661123" sequence="EVIELPLK(Xlink:DSS)NPELFLR" charge="3" aa_before="R" aa_after="V" start="145" end="159" protein_refs="PH_2" >\n+\t\t\t\t<UserParam type="string" name="fragment_annotation" value="387.815673828125,0.215708956122398,2,"[alpha|ci$y6]"|435.218322753906,0.0836383178830147,1,"[alpha|ci$y3]"|444.946411132812,0.119465403258801,2,"[alpha|ci$y7]"|471.207763671875,0.061412189155817,1,"[alpha|ci$b4]"|584.244018554688,0.203754380345345,1,"[alpha|ci$b5]"|692.068786621094,1,2,"[alpha|xi$y10]"|748.578674316406,0.292433172464371,2,"[alpha|xi$y11]"|774.424987792969,0.361789405345917,1,"[alpha|ci$y6]"|812.867004394531,0.152033895254135,2,"[alpha|xi$y12]"|839.981567382812,0.125570505857468,2,"[alpha|xi$b13]"|888.39013671875,0.356793075799942,1,"[alpha|ci$y7]"|896.316162109375,0.0581442341208458,2,"[alpha|xi$b14]""/>\n+\t\t\t\t<UserParam type="string" name="spectrum_reference" value="spectrum=238"/>\n+\t\t\t\t<UserParam type="string" name="target_decoy" value="target"/>\n+\t\t\t\t<UserParam type="int" name="spectrum_index" value="195"/>\n+\t\t\t\t<UserParam type="float" name="xl_mass" value="156.07864431"/>\n+\t\t\t\t<UserParam type="string" name="xl_chain" value="MS:1002509"/>\n+\t\t\t\t<UserParam type="int" name="xl_pos" value="7"/>\n+\t\t\t\t<UserParam type="string" name="xl_type" value="mono-link"/>\n+\t\t\t\t<UserParam type="int" name="xl_rank" value="1"/>\n+\t\t\t\t<UserParam type="string" name="xl_term_spec" value="ANYWHERE"/>\n+\t\t\t\t<UserParam type="float" name="spec_heavy_RT" value="2221.23388666232"/>\n+\t\t\t\t<UserParam type="float" name="spec_heavy_MZ" value="660.072448730469"/>\n+\t\t\t\t<UserParam type="string" name="spectrum_reference_heavy" value="spectrum=219"/>\n+\t\t\t\t<UserParam type="int" name="spectrum_index_heavy" value="180"/>\n+\t\t\t\t<UserParam type="float" name="OMS:precursor_mz_error_ppm" value="6.2016465793789"/>\n+\t\t\t\t<UserParam type="float" name="OpenXQuest:xcorr xlink" value="0.389891893192958"/>\n+\t\t\t\t<UserParam type="float" name="OpenXQuest:xcorr common" value="0.462351176037813"/>\n+\t\t\t\t<UserParam type="float" name="OpenXQuest:match-odds" value="2.59304858228082"/>\n+\t\t\t\t<UserParam type="float" name="OpenXQuest:intsum" value="3.03074353560805"/>\n+\t\t\t\t<UserParam type="float" name="OpenXQuest:wTIC" value="0.672367841921044"/>\n+\t\t\t\t<UserParam type="float" name="OpenXQuest:TIC" value="0.672367841921044"/>\n+\t\t\t\t<UserParam type="float" name="OpenXQuest:prescore" value="0.107142858207226"/>\n+\t\t\t\t<UserParam type="float" name="OpenXQuest:log_occupancy" value="5.62904796479063"/>\n+\t\t\t\t<UserParam type="float" name="OpenXQuest:log_occupancy_alpha" value="5.62904796479063"/>\n+\t\t\t\t<UserParam type="float" name="OpenXQuest:log_occupancy_beta" value="0"/>\n+\t\t\t\t<UserParam type="float" name="OpenXQuest:log_occupancy_full_spec" value="5.33167976719043"/>\n+\t\t\t\t<UserParam type="float" name="HyperCommon" value="8.15707933298946"/>\n+\t\t\t\t<UserParam type="float" name="HyperXlink" value="4.59543196178458"/>\n+\t\t\t\t<UserParam type="float" name="HyperAlpha" value="17.3945020752073"/>\n+\t\t\t\t<UserParam type="float" name="HyperBeta" value="0"/>\n+\t\t\t\t<UserParam type="float" name="HyperBoth" value="17.3945020752073"/>\n+\t\t\t\t<UserParam type="int" name="matched_xlink_alpha" value="5"/>\n+\t\t\t\t<UserParam type="int" name="matched_xlink_beta" value="0"/>\n+\t\t\t\t<UserParam type="int" name="matched_common_alpha" value="7"/>\n+\t\t\t\t<UserParam type="int" name="matched_common_beta" value="0"/>\n+\t\t\t\t<UserParam type="string" name="selected" value="false"/>\n+\t\t\t\t<UserParam type="string" name="protein_references" value="unique"/>\n+\t\t\t</PeptideHit>\n+\t\t</PeptideIdentification>\n+\t</IdentificationRun>\n+</IdXML>\n' |
| b |
| diff -r dde913004c8a -r ec2524b5a07a test-data/SequenceCoverageCalculator.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SequenceCoverageCalculator.tsv Fri May 17 05:01:49 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +#protein coverage% #unique hits +Protein1 3.86598 1 +Protein2 4.3379 1 +Protein3 3.14961 1 |