Repository 'openms_qcshrinker'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/openms_qcshrinker

Changeset 8:fd4184a9016b (2019-05-17)
Previous changeset 7:52720a19f8f1 (2019-05-15) Next changeset 9:ccfc3e189087 (2020-09-09)
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty
removed:
test-data/DecoyDatabase_input.fasta
test-data/DecoyDatabase_output.fasta
test-data/FileFilter_1_input.mzML
test-data/MetaProSIP_1_input.fasta
test-data/MetaProSIP_1_input.featureXML
test-data/MetaProSIP_1_input.mzML
test-data/MetaProSIP_1_output_1.csv
test-data/MetaProSIP_1_output_2.csv
test-data/MzMLSplitter_output_part1.mzML
test-data/MzMLSplitter_output_part2.mzML
test-data/OpenPepXL_input.fasta
test-data/SequenceCoverageCalculator.fasta
test-data/SequenceCoverageCalculator.idXML
test-data/SequenceCoverageCalculator.tsv
b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/DecoyDatabase_input.fasta
--- a/test-data/DecoyDatabase_input.fasta Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,146 +0,0 @@\n->12 \n-MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI\n-STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL\n-YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM\n-VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR\n-DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL\n-MIIVPTDTQNIFFMSKVTNPKQA\n->18\n-MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMK\n-QLNIIQNAEAVHFFCNYEESRGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQ\n-NASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLITMACGSCSNENALKTIFMWYR\n-SKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS\n-FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGG\n-DNHASDDFFRKLRDIARKHGCAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMM\n-TGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIKREDLLNNAAHAGKALLTGLL\n-DLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF\n-RDHHAHLFLNIFSDILADFK\n->88\n-MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIE\n-NIEEDFRNGLKLMLLLEVISGERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAE\n-EIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNIQNFHTSW\n-KDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP\n-DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRT\n-IPWLENRTPEKTMQAMQKKLEDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAF\n-MPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLEHLAEKFRQKASTHETWAYGK\n-EQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN\n-DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQ\n-DMFIVHSIEEIQSLITAHEQFKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYS\n-TVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRRQFAAQANAIGPWIQNKMEEI\n-ARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI\n-RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRA\n-CLISMGYDLGEAEFARIMTLVDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILAS\n-DKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALDYAAFSSALYGESDL\n->112\n-MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGP\n-PRCPWQDDAFIRRGGPGKGKELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWR\n-RLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLVLLTAVLLAFHAAPARPQPAY\n-VALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW\n-CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTN\n-VIGICTHYPAEVSQRQAFQETRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINT\n-KKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHC\n-LRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV\n-HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNA\n-YLKEQHIETFLILGASQKRKEEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFR\n-QMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQLRKDHVRRFLLTFQREDLEKK\n-YSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC\n-GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLT\n-PADITACHLQQLNYSLGLDAPLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLA\n-MIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNETFDGLDCPAAGRVALKYMTPV\n-ILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF\n-LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIIS\n-EERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNN\n-FQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVLAAKG\n-YQLECRGVVKVKGKGEMTTYFLNGGPSS\n->114\n-MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGS\n-GSGGSGKASDPAGGGPNHHAPQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASG\n-SGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNSFKSRDLERLYQRYFLGQRRK\n-SEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT\n-YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTS\n-LLQVILQVVIPRLAVISINQVVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEAR\n-LRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQHQFHRIYIHRYENVSILFADV\n-KGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH\n-CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKL\n-ESGGIPGRIHISKATLDCLNGDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPED\n-IVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLAALTRNSINLLPNHLAQALHV\n-QSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF\n-IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINE\n-TYLARNVIIFASILINFLGAILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTG\n'..b'VPEETYLIL\n-KDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV\n-QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP\n->143\n-MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQ\n-LNSIQKNHVHIANPDFIWKSIREKRLLDVKNYDPYKPLDITPPPDQKASSSEVKTEGLCP\n-DSATEEEDTVELTEFGMQNVEIPHLPQDFEVAKYNTLEKVGMEGGQEAVVVELQCSRDSR\n-DCPFLISSHFLLDDGMETRRQFAIKKTSEDASEYFENYIEELKKQGFLLREHFTPEATQL\n-ASEQLQALLLEEVMNSSTLSQEVSDLVEMIWAEALGHLEHMLLKPVNRISLNDVSKAEGI\n-LLLVKAALKNGETAEQLQKMMTEFYRLIPHKGTMPKEVNLGLLAKKADLCQLIRDMVNVC\n-ETNLSKPNPPSLAKYRALRCKIEHVEQNTEEFLRVRKEVLQNHHSKSPVDVLQIFRVGRV\n-NETTEFLSKLGNVRPLLHGSPVQNIVGILCRGLLLPKVVEDRGVQRTDVGNLGSGIYFSD\n-SLSTSIKYSHPGETDGTRLLLICDVALGKCMDLHEKDFSLTEAPPGYDSVHGVSQTASVT\n-TDFEDDEFVVYKTNQVKMKYIIKFSMPGDQIKDFHPSDHTELEEYRPEFSNFSKVEDYQL\n-PDAKTSSSTKAGLQDASGNLVPLEDVHIKGRIIDTVAQVIVFQTYTNKSHVPIEAKYIFP\n-LDDKAAVCGFEAFINGKHIVGEIKEKEEAQQEYLEAVTQGHGAYLMSQDAPDVFTVSVGN\n-LPPKAKVLIKITYITELSILGTVGVFFMPATVAPWQQDKALNENLQDTVEKICIKEIGTK\n-QSFSLTMSIEMPYVIEFIFSDTHELKQKRTDCKAVISTMEGSSLDSSGFSLHIGLSAAYL\n-PRMWVEKHPEKESEACMLVFQPDLDVDLPDLASESEVIICLDCSSSMEGVTFLQAKQIAL\n-HALSLVGEKQKVNIIQFGTGYKELFSYPKHITSNTMAAEFIMSATPTMGNTDFWKTLRYL\n-SLLYPARGSRNILLVSDGHLQDESLTLQLVKRSRPHTRLFACGIGSTANRHVLRILSQCG\n-AGVFEYFNAKSKHSWRKQIEDQMTRLCSPSCHSVSVKWQQLNPDVPEALQAPAQVPSLFL\n-NDRLLVYGFIPHCTQATLCALIQEKEFRTMVSTTELQKTTGTMIHKLAARALIRDYEDGI\n-LHENETSHEMKKQTLKSLIIKLSKENSLITQFTSFVAVEKRDENESPFPDIPKVSELIAK\n-EDVDFLPYMSWQGEPQEAVRNQSLLASSEWPELRLSKRKHRKIPFSKRKMELSQPEVSED\n-FEEDGLGVLPAFTSNLERGGVEKLLDLSWTESCKPTATEPLFKKVSPWETSTSSFFPILA\n-PAVGSYLPPTARAHSPASLSFASYRQVASFGSAAPPRQFDASQFSQGPVPGTCADWIPQS\n-ASCPTGPPQNPPSSPYCGIVFSGSSLSSAQSAPLQHPGGFTTRPSAGTFPELDSPQLHFS\n-LPTDPDPIRGFGSYHPSASSPFHFQPSAASLTANLRLPMASALPEALCSQSRTTPVDLCL\n-LEESVGSLEGSRCPVFAFQSSDTESDELSEVLQDSCFLQIKCDTKDDSILCFLEVKEEDE\n-IVCIQHWQDAVPWTELLSLQTEDGFWKLTPELGLILNLNTNGLHSFLKQKGIQSLGVKGR\n-ECLLDLIATMLVLQFIRTRLEKEGIVFKSLMKMDDASISRNIPWAFEAIKQASEWVRRTE\n-GQYPSICPRLELGNDWDSATKQLLGLQPISTVSPLHRVLHYSQG\n->213\n-MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF\n-EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP\n-ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF\n-FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV\n-ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK\n-ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR\n-RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE\n-QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV\n-LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL\n-SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV\n-AASQAALGL\n->230\n-MPHSYPALSAEQKKELSDIALRIVAPGKGILAADESVGSMAKRLSQIGVENTEENRRLYR\n-QVLFSADDRVKKCIGGVIFFHETLYQKDDNGVPFVRTIQDKGIVVGIKVDKGVVPLAGTD\n-GETTTQGLDGLSERCAQYKKDGADFAKWRCVLKISERTPSALAILENANVLARYASICQQ\n-NGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHVYLEGTLLKPNMVTPGHAC\n-PIKYTPEEIAMATVTALRRTVPPAVPGVTFLSGGQSEEEASFNLNAINRCPLPRPWALTF\n-SYGRALQASALNAWRGQRDNAGAATEEFIKRAEVNGLAAQGKYEGSGEDGGAAAQSLYIA\n-NHAY\n->231\n-MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQ\n-EKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGK\n-EFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKP\n-AVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAK\n-HNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCA\n-LLSCTSHKDYPFHEEF\n->242\n-MATYKVRVATGTDLLSGTRDSISLTIVGTQGESHKQLLNHFGRDFATGAVGQYTVQCPQD\n-LGELIIIRLHKERYAFFPKDPWYCNYVQICAPNGRIYHFPAYQWMDGYETLALREATGKT\n-TADDSLPVLLEHRKEEIRAKQDFYHWRVFLPGLPSYVHIPSYRPPVRRHRNPNRPEWNGY\n-IPGFPILINFKATKFLNLNLRYSFLKTASFFVRLGPMALAFKVRGLLDCKHSWKRLKDIR\n-KIFPGKKSVVSEYVAEHWAEDTFFGYQYLNGVNPGLIRRCTRIPDKFPVTDDMVAPFLGE\n-GTCLQAELEKGNIYLADYRIMEGIPTVELSGRKQHHCAPLCLLHFGPEGKMMPIAIQLSQ\n-TPGPDCPIFLPSDSEWDWLLAKTWVRYAEFYSHEAIAHLLETHLIAEAFCLALLRNLPMC\n-HPLYKLLIPHTRYTVQINSIGRAVLLNEGGLSAKGMSLGVEGFAGVMVRALSELTYDSLY\n-LPNDFVERGVQDLPGYYYRDDSLAVWNALEKYVTEIITYYYPSDAAVEGDPELQSWVQEI\n-FKECLLGRESSGFPRCLRTVPELIRYVTIVIYTCSAKHAAVNTGQMEFTAWMPNFPASMR\n-NPPIQTKGLTTLETFMDTLPDVKTTCITLLVLWTLSREPDDRRPLGHFPDIHFVEEAPRR\n-SIEAFRQRLNQISHDIRQRNKCLPIPYYYLDPVLIENSISI\n'
b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/DecoyDatabase_output.fasta
--- a/test-data/DecoyDatabase_output.fasta Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,228 +0,0 @@\n->12 \n-MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI\n-STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL\n-YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM\n-VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR\n-DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL\n-MIIVPTDTQNIFFMSKVTNPKQA\n->18 \n-MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMKQLNIIQNAEAVHFFCNYEES\n-RGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQNASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLIT\n-MACGSCSNENALKTIFMWYRSKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS\n-FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGGDNHASDDFFRKLRDIARKHG\n-CAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMMTGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIK\n-REDLLNNAAHAGKALLTGLLDLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF\n-RDHHAHLFLNIFSDILADFK\n->88 \n-MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVIS\n-GERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLW\n-CQRKTAPYRNVNIQNFHTSWKDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP\n-DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRTIPWLENRTPEKTMQAMQKKL\n-EDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAFMPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLE\n-HLAEKFRQKASTHETWAYGKEQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN\n-DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQDMFIVHSIEEIQSLITAHEQ\n-FKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYSTVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRR\n-QFAAQANAIGPWIQNKMEEIARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI\n-RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRACLISMGYDLGEAEFARIMTL\n-VDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILASDKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALD\n-YAAFSSALYGESDL\n->112 \n-MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGPPRCPWQDDAFIRRGGPGKGK\n-ELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWRRLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLV\n-LLTAVLLAFHAAPARPQPAYVALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW\n-CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTNVIGICTHYPAEVSQRQAFQE\n-TRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINTKKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQEL\n-VMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV\n-HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNAYLKEQHIETFLILGASQKRK\n-EEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFRQMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQL\n-RKDHVRRFLLTFQREDLEKKYSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC\n-GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLTPADITACHLQQLNYSLGLDA\n-PLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLAMIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNET\n-FDGLDCPAAGRVALKYMTPVILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF\n-LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAA\n-SGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDST\n-GVPDRIQVTTDLYQVLAAKGYQLECRGVVKVKGKGEMTTYFLNGGPSS\n->114 \n-MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGSGSGGSGKASDPAGGGPNHHA\n-PQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASGSGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNS\n-FKSRDLERLYQRYFLGQRRKSEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT\n-YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTSLLQVILQVVIPRLAVISINQ\n-VVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEARLRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQH\n-QFHRIYIHRYENVSILFADVKGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH\n-CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKLESGGIPGRIHISKATLDCLN\n-GDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPEDIVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLA\n-ALTRNSINLLPNHLAQALHVQSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF\n-IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINETYLARNVIIFASILINFLGA\n-ILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTGVLAMVTCAVFLRLNSVLKLAVLL'..b'SGSASGSGSREPFVKTGCTSHAREGPGLSYLPLASDGSLQPAHHNPGGGAPDSAKGSGGSGSGSGGRHGH\n-IFRQETIHRVATQWLLRQPRSASRGDGAPPTPHITYLEESGTLCRVDSLEM\n->DECOY_143 \n-GQSYHLVRHLPSVTSIPQLGLLQKTASDWDNGLELRPCISPYQGETRRVWESAQKIAEFAWPINRSISADDMKMLSKFVI\n-GEKELRTRIFQLVLMTAILDLLCERGKVGLSQIGKQKLFSHLGNTNLNLILGLEPTLKWFGDETQLSLLETWPVADQWHQ\n-ICVIEDEEKVELFCLISDDKTDCKIQLFCSDQLVESLEDSETDSSQFAFVPCRSGELSGVSEELLCLDVPTTRSQSCLAE\n-PLASAMPLRLNATLSAASPQFHFPSSASPHYSGFGRIPDPDTPLSFHLQPSDLEPFTGASPRTTFGGPHQLPASQASSLS\n-SGSFVIGCYPSSPPNQPPGTPCSASQPIWDACTGPVPGQSFQSADFQRPPAASGFSAVQRYSAFSLSAPSHARATPPLYS\n-GVAPALIPFFSSTSTEWPSVKKFLPETATPKCSETWSLDLLKEVGGRELNSTFAPLVGLGDEEFDESVEPQSLEMKRKSF\n-PIKRHKRKSLRLEPWESSALLSQNRVAEQPEGQWSMYPLFDVDEKAILESVKPIDPFPSENEDRKEVAVFSTFQTILSNE\n-KSLKIILSKLTQKKMEHSTENEHLIGDEYDRILARAALKHIMTGTTKQLETTSVMTRFEKEQILACLTAQTCHPIFGYVL\n-LRDNLFLSPVQAPAQLAEPVDPNLQQWKVSVSHCSPSCLRTMQDEIQKRWSHKSKANFYEFVGAGCQSLIRLVHRNATSG\n-IGCAFLRTHPRSRKVLQLTLSEDQLHGDSVLLINRSGRAPYLLSLYRLTKWFDTNGMTPTASMIFEAAMTNSTIHKPYSF\n-LEKYGTGFQIINVKQKEGVLSLAHLAIQKAQLFTVGEMSSSCDLCIIVESESALDPLDVDLDPQFVLMCAESEKEPHKEV\n-WMRPLYAASLGIHLSFGSSDLSSGEMTSIVAKCDTRKQKLEHTDSFIFEIVYPMEISMTLSFSQKTGIEKICIKEVTDQL\n-NENLAKDQQWPAVTAPMFFVGVTGLISLETIYTIKILVKAKPPLNGVSVTFVDPADQSMLYAGHGQTVAELYEQQAEEKE\n-KIEGVIHKGNIFAEFGCVAAKDDLPFIYKAEIPVHSKNTYTQFVIVQAVTDIIRGKIHVDELPVLNGSADQLGAKTSSST\n-KADPLQYDEVKSFNSFEPRYEELETHDSPHFDKIQDGPMSFKIIYKMKVQNTKYVVFEDDEFDTTVSATQSVGHVSDYGP\n-PAETLSFDKEHLDMCKGLAVDCILLLRTGDTEGPHSYKISTSLSDSFYIGSGLNGVDTRQVGRDEVVKPLLLGRCLIGVI\n-NQVPSGHLLPRVNGLKSLFETTENVRGVRFIQLVDVPSKSHHNQLVEKRVRLFEETNQEVHEIKCRLARYKALSPPNPKS\n-LNTECVNVMDRILQCLDAKKALLGLNVEKPMTGKHPILRYFETMMKQLQEATEGNKLAAKVLLLIGEAKSVDNLSIRNVP\n-KLLMHELHGLAEAWIMEVLDSVEQSLTSSNMVEELLLAQLQESALQTAEPTFHERLLFGQKKLEEIYNEFYESADESTKK\n-IAFQRRTEMGDDLLFHSSILFPCDRSDRSCQLEVVVAEQGGEMGVKELTNYKAVEFDQPLHPIEVNQMGFETLEVTDEEE\n-TASDPCLGETKVESSSAKQDPPPTIDLPKYPDYNKVDLLRKERISKWIFDPNAIHVHNKQISNLQYQSLVDANDLIIHTC\n-QPNLSFSFKGGNEKIDTQLKKKQQQPLYKVKLCFICNAFIGMVM\n->DECOY_213 \n-LGLAAQSAAVLKKGEEAFCTEKDDAKCCKEVFAAFDDMVAKLQEKTAKPKHKVLEVLATQKKIQREKESLTCIDAHFTFT\n-EANFEKPVYTEDVELASFCPRRNVLSETCCKTVRDSVPTKEHLVCLQNLVVSLYDEACPMRKAEPHKCCKSGVKGLNRSV\n-EVLTPTSVQPVKKTYRVLLANQFKYEGLQEFLECNQKILNQPEEVLPKFEDFVKAYCEHPDAAACCKELTTEYTKALRLL\n-LVVSYDPHRRAYEYLFMGLFVDKAEAYNKCVDKSEVFDAALSPLDAPMEDNEVEAICHSKELLPKECCEKLKSSISDQNE\n-CIYKALDARDDACELLDGHCCETHVKTLDTVLKSVEAFEAKPFRQSLRAVAWAKFAREGFKQLSACKLRQKASSAKGEDR\n-LEDLKPLLCAAKDAAQCCETFAAKYRKAFFLLEPAYFYPHRRAIEYLYKKLFTEENDHFATCMVDVEPRVLRPLNPNDDK\n-HQLFCENREPEQKACCDAMEGYTERLTAVTCLKDGFLTHLSKDCNEASEDAVCTKAFETVENVLKVHDEFPCQQLYQAFA\n-ILVLAKFNEEGLDKFRHAVESKHADRRFVGRSYASSFLFLLSIFTVWKM\n->DECOY_230 \n-YAHNAIYLSQAAAGGDEGSGEYKGQAALGNVEARKIFEETAAGANDRQGRWANLASAQLARGYSFTLAWPRPLPCRNIAN\n-LNFSAEEESQGGSLFTVGPVAPPVTRRLATVTAMAIEEPTYKIPCAHGPTVMNPKLLTGELYVHHDSLAKYVAALVKETV\n-YQCRKLDHDGDPLIEPEVIPVIGNQQCISAYRALVNANELIALASPTRESIKLVCRWKAFDAGDKKYQACRESLGDLGQT\n-TTEGDTGALPVVGKDVKIGVVIGKDQITRVFPVGNDDKQYLTEHFFIVGGICKKVRDDASFLVQRYLRRNEETNEVGIQS\n-LRKAMSGVSEDAALIGKGPAVIRLAIDSLEKKQEASLAPYSHPM\n->DECOY_231 \n-FEEHFPYDKHSTCSLLACVRWNRNYSLLTTMDQSSLEFDFVKFNEAIREPTVSKPIVVLNRQMPFRILVQATTKNHKAAI\n-AKIRPDELLSPDEPKAWPRDPSGLPSYATVVIGKSQCYQILKEQTLYPHCEIQNVAPKYKLGPKNLIMEVQLHNFNSIGI\n-AKVLGEDVLEEMAAWTDLINTDSPVVNGSEDLPFFEKGPKFGTPWHILYLDLYDLKLDSLTKQCAGKVLGKEHYTCWLKS\n-VIFLEERKVVQERLKEQIAVGVENENQYVHACDIHRYGVDIAVKVAETVQGPPSKWTGLGLIPMKAGNNLLLRSAM\n->DECOY_242 \n-ISISNEILVPDLYYYPIPLCKNRQRIDHSIQNLRQRFAEISRRPAEEVFHIDPFHGLPRRDDPERSLTWLVLLTICTTKV\n-DPLTDMFTELTTLGKTQIPPNRMSAPFNPMWATFEMQGTNVAAHKASCTYIVITVYRILEPVTRLCRPFGSSERGLLCEK\n-FIEQVWSQLEPDGEVAADSPYYYTIIETVYKELANWVALSDDRYYYGPLDQVGREVFDNPLYLSDYTLESLARVMVGAFG\n-EVGLSMGKASLGGENLLVARGISNIQVTYRTHPILLKYLPHCMPLNRLLALCFAEAILHTELLHAIAEHSYFEAYRVWTK\n-ALLWDWESDSPLFIPCDPGPTQSLQIAIPMMKGEPGFHLLCLPACHHQKRGSLEVTPIGEMIRYDALYINGKELEAQLCT\n-GEGLFPAVMDDTVPFKDPIRTCRRILGPNVGNLYQYGFFTDEAWHEAVYESVVSKKGPFIKRIDKLRKWSHKCDLLGRVK\n-FALAMPGLRVFFSATKLFSYRLNLNLFKTAKFNILIPFGPIYGNWEPRNPNRHRRVPPRYSPIHVYSPLGPLFVRWHYFD\n-QKARIEEKRHELLVPLSDDATTKGTAERLALTEYGDMWQYAPFHYIRGNPACIQVYNCYWPDKPFFAYREKHLRIIILEG\n-LDQPCQVTYQGVAGTAFDRGFHNLLQKHSEGQTGVITLSISDRTGSLLDTGTAVRVKYTAM\n'
b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/FileFilter_1_input.mzML
--- a/test-data/FileFilter_1_input.mzML Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,336 +0,0 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\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" accession="" version="1.1.0">\n-\t<cvList count="2">\n-\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n-\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n-\t</cvList>\n-\t<fileDescription>\n-\t\t<fileContent>\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n-\t\t</fileContent>\n-\t\t<contact>\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=", " />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="" />\n-\t\t</contact>\n-\t</fileDescription>\n-\t<sampleList count="1">\n-\t\t<sample id="sa_0" name="">\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0"  unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />\n-\t\t</sample>\n-\t</sampleList>\n-\t<softwareList count="12">\n-\t\t<software id="so_in_0" version="" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n-\t\t</software>\n-\t\t<software id="so_default" version="" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n-\t\t</software>\n-\t\t<software id="so_dp_sp_0_pm_0" version="" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n-\t\t</software>\n-\t\t<software id="so_dp_sp_0_pm_1" version="version_string" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000756" name="FileConverter" />\n-\t\t</software>\n-\t</softwareList>\n-\t<instrumentConfigurationList count="1">\n-\t\t<instrumentConfiguration id="ic_0">\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n-\t\t\t<componentList count="3">\n-\t\t\t\t<source order="0">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />\n-\t\t\t\t</source>\n-\t\t\t\t<analyzer order="0">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />\n-\t\t\t\t</analyzer>\n-\t\t\t\t<detector order="0">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000026" name="detector type" />\n-\t\t\t\t</detector>\n-\t\t\t</componentList>\n-\t\t\t<softwareRef ref="so_in_0" />\n-\t\t</instrumentConfiguration>\n-\t</instrumentConfigurationList>\n-\t<dataProcessingList count="10">\n-\t\t<dataProcessing id="dp_sp_0">\n-\t\t\t<processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000543" name="data processing action" />\n-\t\t\t</processingMethod>\n-\t\t\t<processingMethod order="0" softwareRef="so_dp_sp_0_pm_1">\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:10'..b'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b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/MetaProSIP_1_input.fasta
--- a/test-data/MetaProSIP_1_input.fasta Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,6 +0,0 @@
->contig23640_802236  length=2326  numreads=28 strand:-1 frame:0 orf_location:136:990
-GGIPNEENWNFGSSDGSGLPVRGSGQRRDVLGRLCRRNFTSSIGQSVNVRDVEASGFAGG
-MSRYHFKYGGAVDPTVLGGVKLGTWFVKEGFAGWSGYPDWCKYFGFYTDFSYHRFYTRDN
-RISGTDFFAAYGGGSAALGDVGFMKTEGMVATWAFMLAARYGFFQDSEVPFGRLQPYVAV
-GPAIMFSSMKPKIWTQFNEPNVGFPNPDLVYSPGNQSSTDLGLAVDTGIRYMCLKNVSLD
-ISFKYRYAQPHYNFSGQDGSVMVPAHMSLSPALNLYSFQAGVAYHF
b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/MetaProSIP_1_input.featureXML
--- a/test-data/MetaProSIP_1_input.featureXML Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,129 +0,0 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\n-<featureMap version="1.9" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/FeatureXML_1_9.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">\n-\t<dataProcessing completion_time="2017-12-08T12:44:40">\n-\t\t<software name="FileFilter" version="2.3.0" />\n-\t\t<processingAction name="Data filtering" />\n-\t\t<UserParam type="string" name="parameter: in" value="MetaProSIP_1_input.featureXML"/>\n-\t\t<UserParam type="string" name="parameter: in_type" value=""/>\n-\t\t<UserParam type="string" name="parameter: out" value="MetaProSIP_1_input.featureXML"/>\n-\t\t<UserParam type="string" name="parameter: out_type" value=""/>\n-\t\t<UserParam type="string" name="parameter: rt" value=":"/>\n-\t\t<UserParam type="string" name="parameter: mz" value=":"/>\n-\t\t<UserParam type="string" name="parameter: int" value=":"/>\n-\t\t<UserParam type="string" name="parameter: sort" value="false"/>\n-\t\t<UserParam type="string" name="parameter: log" value=""/>\n-\t\t<UserParam type="int" name="parameter: debug" value="0"/>\n-\t\t<UserParam type="int" name="parameter: threads" value="1"/>\n-\t\t<UserParam type="string" name="parameter: no_progress" value="false"/>\n-\t\t<UserParam type="string" name="parameter: force" value="false"/>\n-\t\t<UserParam type="string" name="parameter: test" value="false"/>\n-\t\t<UserParam type="float" name="parameter: peak_options:sn" value="0"/>\n-\t\t<UserParam type="intList" name="parameter: peak_options:rm_pc_charge" value="[]"/>\n-\t\t<UserParam type="string" name="parameter: peak_options:pc_mz_range" value=":"/>\n-\t\t<UserParam type="floatList" name="parameter: peak_options:pc_mz_list" value="[]"/>\n-\t\t<UserParam type="intList" name="parameter: peak_options:level" value="[1, 2, 3]"/>\n-\t\t<UserParam type="string" name="parameter: peak_options:sort_peaks" value="false"/>\n-\t\t<UserParam type="string" name="parameter: peak_options:no_chromatograms" value="false"/>\n-\t\t<UserParam type="string" name="parameter: peak_options:remove_chromatograms" value="false"/>\n-\t\t<UserParam type="string" name="parameter: peak_options:mz_precision" value="64"/>\n-\t\t<UserParam type="string" name="parameter: peak_options:int_precision" value="32"/>\n-\t\t<UserParam type="string" name="parameter: peak_options:indexed_file" value="false"/>\n-\t\t<UserParam type="string" name="parameter: peak_options:zlib_compression" value="false"/>\n-\t\t<UserParam type="string" name="parameter: peak_options:numpress:masstime" value="none"/>\n-\t\t<UserParam type="float" name="parameter: peak_options:numpress:masstime_error" value="0.0001"/>\n-\t\t<UserParam type="string" name="parameter: peak_options:numpress:intensity" value="none"/>\n-\t\t<UserParam type="float" name="parameter: peak_options:numpress:intensity_error" value="0.0001"/>\n-\t\t<UserParam type="string" name="parameter: spectra:remove_zoom" value="false"/>\n-\t\t<UserParam type="string" name="parameter: spectra:remove_mode" value=""/>\n-\t\t<UserParam type="string" name="parameter: spectra:remove_activation" value=""/>\n-\t\t<UserParam type="string" name="parameter: spectra:remove_collision_energy" value=":"/>\n-\t\t<UserParam type="string" name="parameter: spectra:remove_isolation_window_width" value=":"/>\n-\t\t<UserParam type="string" name="parameter: spectra:select_zoom" value="false"/>\n-\t\t<UserParam type="string" name="parameter: spectra:select_mode" value=""/>\n-\t\t<UserParam type="string" name="parameter: spectra:select_activation" value=""/>\n-\t\t<UserParam type="string" name="parameter: spectra:select_collision_energy" value=":"/>\n-\t\t<UserParam type="string" name="parameter: spectra:select_isolation_window_width" value=":"/>\n-\t\t<UserParam type="string" name="parameter: spectra:select_polarity" value=""/>\n-\t\t<UserParam type="string" name="parameter: feature:q" value=":"/>\n-\t\t<UserParam type="intList" name="parameter: consensus:map" value="[]"/>\n-\t\t<UserParam type="string" name="parameter: consensus:map_and" value="false"/>\n-\t\t<UserParam type="string" name="parameter: consensus:blackorwhitelist:bl'..b'id:remove_unannotated_features" value="true"/>\n-\t\t<UserParam type="string" name="parameter: id:remove_unassigned_ids" value="false"/>\n-\t\t<UserParam type="string" name="parameter: id:blacklist" value=""/>\n-\t\t<UserParam type="float" name="parameter: id:rt" value="0.1"/>\n-\t\t<UserParam type="float" name="parameter: id:mz" value="0.001"/>\n-\t\t<UserParam type="string" name="parameter: id:blacklist_imperfect" value="false"/>\n-\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:max_intensity" value="-1"/>\n-\t\t<UserParam type="float" name="parameter: algorithm:SignalToNoise:auto_max_stdev_factor" value="3"/>\n-\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_max_percentile" value="95"/>\n-\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_mode" value="0"/>\n-\t\t<UserParam type="float" name="parameter: algorithm:SignalToNoise:win_len" value="200"/>\n-\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:bin_count" value="30"/>\n-\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:min_required_elements" value="10"/>\n-\t\t<UserParam type="float" name="parameter: algorithm:SignalToNoise:noise_for_empty_window" value="1e+20"/>\n-\t\t<UserParam type="string" name="parameter: algorithm:SignalToNoise:write_log_messages" value="true"/>\n-\t</dataProcessing>\n-\t<IdentificationRun id="PI_0" date="2011-03-11T14:53:29" search_engine="OMSSA" search_engine_version="2.1.8">\n-\t\t<SearchParameters db="/raid/sachsenb/Jana/fasta/Zeitz_1and2_454AllContigs_HEX.fasta.psq" db_version="" taxonomy="0" mass_type="monoisotopic" charges="+2-+3" enzyme="trypsin" missed_cleavages="2" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="false" peak_mass_tolerance="0.5" peak_mass_tolerance_ppm="false" >\n-\t\t\t<FixedModification name="Carbamidomethyl (C)" />\n-\t\t\t<VariableModification name="Oxidation (M)" />\n-\t\t</SearchParameters>\n-\t\t<ProteinIdentification score_type="OMSSA" higher_score_better="false" significance_threshold="0">\n-\t\t\t<ProteinHit id="PH_0" accession="contig23640_802236" score="0" sequence="">\n-\t\t\t</ProteinHit>\n-\t\t</ProteinIdentification>\n-\t</IdentificationRun>\n-\t<featureList count="1">\n-\t\t<feature id="f_988449706551050085">\n-\t\t\t<position dim="0">4831.43346884947</position>\n-\t\t\t<position dim="1">666.862287171363</position>\n-\t\t\t<intensity>3.25608e+06</intensity>\n-\t\t\t<quality dim="0">0</quality>\n-\t\t\t<quality dim="1">0</quality>\n-\t\t\t<overallquality>0.882314</overallquality>\n-\t\t\t<charge>2</charge>\n-\t\t\t<convexhull nr="0">\n-\t\t\t\t<pt x="4803.8473" y="666.862043575291" />\n-\t\t\t\t<pt x="4805.8211" y="666.862135109963" />\n-\t\t\t</convexhull>\n-\t\t\t<convexhull nr="1">\n-\t\t\t\t<pt x="4803.8473" y="667.364150217852" />\n-\t\t\t\t<pt x="4805.8211" y="667.363529666672" />\n-\t\t\t</convexhull>\n-\t\t\t<convexhull nr="2">\n-\t\t\t\t<pt x="4805.8211" y="667.865608520739" />\n-\t\t\t\t<pt x="4807.3928" y="667.864992849711" />\n-\t\t\t</convexhull>\n-\t\t\t<convexhull nr="3">\n-\t\t\t\t<pt x="4810.5312" y="668.364801015548" />\n-\t\t\t\t<pt x="4812.1021" y="668.365292284748" />\n-\t\t\t</convexhull>\n-\t\t\t<PeptideIdentification identification_run_ref="PI_0" score_type="OMSSA" higher_score_better="false" significance_threshold="0" MZ="666.861999511719" RT="4808.4946" >\n-\t\t\t\t<PeptideHit score="0.174659044235501" sequence="YGGAVDPTVLGGVK" charge="2" aa_before="K" aa_after="L" protein_refs="PH_0">\n-\t\t\t\t\t<UserParam type="string" name="target_decoy" value="target"/>\n-\t\t\t\t\t<UserParam type="string" name="protein_references" value="unique"/>\n-\t\t\t\t</PeptideHit>\n-\t\t\t</PeptideIdentification>\n-\t\t\t<UserParam type="int" name="label" value="453"/>\n-\t\t\t<UserParam type="float" name="score_fit" value="0.783165906030983"/>\n-\t\t\t<UserParam type="float" name="score_correlation" value="0.994014816652796"/>\n-\t\t\t<UserParam type="float" name="FWHM" value="23.5379981994629"/>\n-\t\t\t<UserParam type="int" name="spectrum_index" value="1569"/>\n-\t\t\t<UserParam type="string" name="spectrum_native_id" value="controllerType=0 controllerNumber=1 scan=6112"/>\n-\t\t</feature>\n-\t</featureList>\n-</featureMap>\n'
b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/MetaProSIP_1_input.mzML
--- a/test-data/MetaProSIP_1_input.mzML Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,2621 +0,0 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\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/mzML1.1.0_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" accession="" version="1.1.0">\n-\t<cvList count="5">\n-\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n-\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n-\t\t<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>\n-\t\t<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>\n-\t\t<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>\n-\t</cvList>\n-\t<fileDescription>\n-\t\t<fileContent>\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n-\t\t</fileContent>\n-\t\t<sourceFileList count="1">\n-\t\t\t<sourceFile id="sf_ru_0" name="Zeitz_SIP_13-II_020_picked.mzML" location="file:///nfs/wsi/abi/old-data/sachsenb/OpenMS_IDE/MetaProSIP/Zeitz">\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="cda64713a3466f7bf74af2a42da97351aaff691b" />\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000584" name="mzML format" />\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />\n-\t\t\t</sourceFile>\n-\t\t</sourceFileList>\n-\t</fileDescription>\n-\t<sampleList count="1">\n-\t\t<sample id="sa_0" name="">\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />\n-\t\t</sample>\n-\t</sampleList>\n-\t<softwareList count="5">\n-\t\t<software id="so_in_0" version="2.5.5" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" />\n-\t\t</software>\n-\t\t<software id="so_default" version="" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n-\t\t</software>\n-\t\t<software id="so_dp_sp_0_pm_0" version="2.0.1885" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" />\n-\t\t</software>\n-\t\t<software id="so_dp_sp_0_pm_1" version="1.8.0" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000763" name="PeakPicker" />\n-\t\t</software>\n-\t\t<software id="so_dp_sp_0_pm_2" version="2.3.0" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="SpectrumCanvas" />\n-\t\t</software>\n-\t</softwareList>\n-\t<instrumentConfigurationList count="1">\n-\t\t<instrumentConfiguration id="ic_0">\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000556" name="LTQ Orbitrap XL" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN01757B"/>\n-\t\t\t<componentList count="3">\n-\t\t\t\t<source order="1">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" />\n-\t\t\t\t</source>\n-\t\t\t\t<analyzer order="2">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unit'..b'ntrollerType=0 controllerNumber=1 scan=6072">32939</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6074">35910</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6075">50741</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6077">53845</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6078">56980</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6079">72151</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6081">75306</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6083">78505</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6086">81862</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6089">85432</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6093">89366</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6095">93424</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6097">97550</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6100">101763</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6104">106419</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6107">111284</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6112">116083</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6114">121096</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6116">125835</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6117">141040</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6118">145957</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6119">150825</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6123">166221</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6125">171358</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6128">176225</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6130">181237</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6131">197169</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6132">201908</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6135">217825</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6138">222882</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6140">227623</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6144">231990</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6145">247361</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6147">252112</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6150">256418</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6155">260869</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6157">275807</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6163">280291</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6165">284708</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6169">300162</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6170">304804</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6173">320528</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6179">325158</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6182">329574</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6184">333979</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6188">338637</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6191">343073</offset>\n-\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6194">357613</offset>\n-\t</index>\n-</indexList>\n-<indexListOffset>362032</indexListOffset>\n-<fileChecksum>0</fileChecksum>\n-</indexedmzML>\n\\ No newline at end of file\n'
b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/MetaProSIP_1_output_1.csv
--- a/test-data/MetaProSIP_1_output_1.csv Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,7 +0,0 @@
-Group 1 # Distinct Peptides # Unambigous Proteins Median Global LR median RIA 1 median RIA 2
- 1 1 0.269627132474428 0.603333333333335 36.4733333333347
- 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 0.831887919884232 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
b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/MetaProSIP_1_output_2.csv
--- a/test-data/MetaProSIP_1_output_2.csv Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,2 +0,0 @@
-#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
b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/MzMLSplitter_output_part1.mzML
--- a/test-data/MzMLSplitter_output_part1.mzML Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,222 +0,0 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\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/mzML1.1.0_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" accession="" version="1.1.0">\n-\t<cvList count="5">\n-\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n-\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n-\t\t<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>\n-\t\t<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>\n-\t\t<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>\n-\t</cvList>\n-\t<fileDescription>\n-\t\t<fileContent>\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n-\t\t</fileContent>\n-\t\t<contact>\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=", " />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="" />\n-\t\t</contact>\n-\t</fileDescription>\n-\t<sampleList count="1">\n-\t\t<sample id="sa_0" name="">\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />\n-\t\t</sample>\n-\t</sampleList>\n-\t<softwareList count="4">\n-\t\t<software id="so_in_0" version="" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n-\t\t</software>\n-\t\t<software id="so_default" version="" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n-\t\t</software>\n-\t\t<software id="so_dp_sp_0_pm_0" version="" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n-\t\t</software>\n-\t\t<software id="so_dp_sp_0_pm_1" version="version_string" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000756" name="FileConverter" />\n-\t\t</software>\n-\t</softwareList>\n-\t<instrumentConfigurationList count="1">\n-\t\t<instrumentConfiguration id="ic_0">\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n-\t\t\t<componentList count="3">\n-\t\t\t\t<source order="0">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />\n-\t\t\t\t</source>\n-\t\t\t\t<analyzer order="0">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />\n-\t\t\t\t</analyzer>\n-\t\t\t\t<detector order="0">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName='..b'" unitName="number of detector counts" unitCvRef="MS"/>\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />\n-\t\t\t\t\t\t<binary>Q1AYQ2XIvEL9I51D</binary>\n-\t\t\t\t\t</binaryDataArray>\n-\t\t\t\t</binaryDataArrayList>\n-\t\t\t</spectrum>\n-\t\t\t<spectrum id="spectrum=4" index="3" defaultArrayLength="5">\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />\n-\t\t\t\t<scanList count="1">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />\n-\t\t\t\t\t<scan >\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="27.8168" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />\n-\t\t\t\t\t</scan>\n-\t\t\t\t</scanList>\n-\t\t\t\t<binaryDataArrayList count="2">\n-\t\t\t\t\t<binaryDataArray encodedLength="56">\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />\n-\t\t\t\t\t\t<binary>AAAAAAA4gEAAAACg76CHQAAAAGByuIdAAAAAAADIh0AAAABg+26IQA==</binary>\n-\t\t\t\t\t</binaryDataArray>\n-\t\t\t\t\t<binaryDataArray encodedLength="28">\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />\n-\t\t\t\t\t\t<binary>cnq9QXJQmEPn4JFCfnq9QY1f/0E=</binary>\n-\t\t\t\t\t</binaryDataArray>\n-\t\t\t\t</binaryDataArrayList>\n-\t\t\t</spectrum>\n-\t\t\t<spectrum id="spectrum=5" index="4" defaultArrayLength="8">\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n-\t\t\t\t<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />\n-\t\t\t\t<scanList count="1">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />\n-\t\t\t\t\t<scan >\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="25.3972" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />\n-\t\t\t\t\t</scan>\n-\t\t\t\t</scanList>\n-\t\t\t\t<binaryDataArrayList count="2">\n-\t\t\t\t\t<binaryDataArray encodedLength="88">\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />\n-\t\t\t\t\t\t<binary>AAAAgGlaf0AAAAAAxmp/QAAAAKAOin9AAAAAQKXDf0AAAABAsjOAQAAAAAAfeoBAAAAAAJQigUAAAAAg0/aJQA==</binary>\n-\t\t\t\t\t</binaryDataArray>\n-\t\t\t\t\t<binaryDataArray encodedLength="44">\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />\n-\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />\n-\t\t\t\t\t\t<binary>dFNiQxQQLkIcK5ZCCBdQQ2L91UOKGBVDhPZcQ0KtHUM=</binary>\n-\t\t\t\t\t</binaryDataArray>\n-\t\t\t\t</binaryDataArrayList>\n-\t\t\t</spectrum>\n-\t\t</spectrumList>\n-\t</run>\n-</mzML>\n-<indexList count="1">\n-\t<index name="spectrum">\n-\t\t<offset idRef="spectrum=1">4899</offset>\n-\t\t<offset idRef="spectrum=2">19011</offset>\n-\t\t<offset idRef="spectrum=3">31431</offset>\n-\t\t<offset idRef="spectrum=4">32961</offset>\n-\t\t<offset idRef="spectrum=5">34527</offset>\n-\t</index>\n-</indexList>\n-<indexListOffset>36171</indexListOffset>\n-<fileChecksum>0</fileChecksum>\n-</indexedmzML>\n\\ No newline at end of file\n'
b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/MzMLSplitter_output_part2.mzML
--- a/test-data/MzMLSplitter_output_part2.mzML Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,222 +0,0 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\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/mzML1.1.0_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" accession="" version="1.1.0">\n-\t<cvList count="5">\n-\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n-\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n-\t\t<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>\n-\t\t<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>\n-\t\t<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>\n-\t</cvList>\n-\t<fileDescription>\n-\t\t<fileContent>\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n-\t\t</fileContent>\n-\t\t<contact>\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=", " />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="" />\n-\t\t</contact>\n-\t</fileDescription>\n-\t<sampleList count="1">\n-\t\t<sample id="sa_0" name="">\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />\n-\t\t</sample>\n-\t</sampleList>\n-\t<softwareList count="4">\n-\t\t<software id="so_in_0" version="" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n-\t\t</software>\n-\t\t<software id="so_default" version="" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n-\t\t</software>\n-\t\t<software id="so_dp_sp_0_pm_0" version="" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n-\t\t</software>\n-\t\t<software id="so_dp_sp_0_pm_1" version="version_string" >\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000756" name="FileConverter" />\n-\t\t</software>\n-\t</softwareList>\n-\t<instrumentConfigurationList count="1">\n-\t\t<instrumentConfiguration id="ic_0">\n-\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n-\t\t\t<componentList count="3">\n-\t\t\t\t<source order="0">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />\n-\t\t\t\t</source>\n-\t\t\t\t<analyzer order="0">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />\n-\t\t\t\t</analyzer>\n-\t\t\t\t<detector order="0">\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />\n-\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName='..b'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</binary>\n-\t\t\t\t\t</binaryDataArray>\n-\t\t\t\t</binaryDataArrayList>\n-\t\t\t</spectrum>\n-\t\t</spectrumList>\n-\t</run>\n-</mzML>\n-<indexList count="1">\n-\t<index name="spectrum">\n-\t\t<offset idRef="spectrum=6">4899</offset>\n-\t\t<offset idRef="spectrum=7">20575</offset>\n-\t\t<offset idRef="spectrum=8">22141</offset>\n-\t\t<offset idRef="spectrum=9">23739</offset>\n-\t\t<offset idRef="spectrum=10">25269</offset>\n-\t</index>\n-</indexList>\n-<indexListOffset>39000</indexListOffset>\n-<fileChecksum>0</fileChecksum>\n-</indexedmzML>\n\\ No newline at end of file\n'
b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/OpenPepXL_input.fasta
--- a/test-data/OpenPepXL_input.fasta Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,39 +0,0 @@
->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
b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/SequenceCoverageCalculator.fasta
--- a/test-data/SequenceCoverageCalculator.fasta Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,149508 +0,0 @@\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 52720a19f8f1 -r fd4184a9016b test-data/SequenceCoverageCalculator.idXML
--- a/test-data/SequenceCoverageCalculator.idXML Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,161 +0,0 @@\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,&quot;[alpha|xi$b18]&quot;"/>\n-\t\t\t\t<UserParam type="string" name="spectrum_reference" value="spectrum=99"/>\n-\t\t\t\t<UserParam type="string" name="target_decoy" value="target"/>\n-\t\t\t\t<UserParam type="int" name="spectrum_index" value="81"/>\n-\t\t\t\t<UserParam type="float" name="xl_mass" value="156.07864431"/>\n-\t\t\t\t<UserParam type="string" name="xl_chain" value="MS:1002509"/>\n-\t\t\t\t<UserParam type="int" name="xl_pos" value="15"/>\n-\t\t\t\t<UserParam type="string" name="xl_type" value="mono-link"/>\n-\t\t\t\t<UserParam type="int" name="xl_rank" value="2"/>\n-\t\t\t\t<UserParam type="string" name="xl_term_spec" '..b'="unique"/>\n-\t\t\t</PeptideHit>\n-\t\t</PeptideIdentification>\n-\t\t<PeptideIdentification score_type="OpenXQuest:combined score" higher_score_better="true" significance_threshold="0" MZ="656.050903320313" RT="2228.50292963107" spectrum_reference="spectrum=238,spectrum=219" >\n-\t\t\t<PeptideHit score="30.0056519661123" sequence="EVIELPLK(Xlink:DSS)NPELFLR" charge="3" aa_before="R" aa_after="V" start="145" end="159" protein_refs="PH_2" >\n-\t\t\t\t<UserParam type="string" name="fragment_annotation" value="387.815673828125,0.215708956122398,2,&quot;[alpha|ci$y6]&quot;|435.218322753906,0.0836383178830147,1,&quot;[alpha|ci$y3]&quot;|444.946411132812,0.119465403258801,2,&quot;[alpha|ci$y7]&quot;|471.207763671875,0.061412189155817,1,&quot;[alpha|ci$b4]&quot;|584.244018554688,0.203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b
diff -r 52720a19f8f1 -r fd4184a9016b test-data/SequenceCoverageCalculator.tsv
--- a/test-data/SequenceCoverageCalculator.tsv Wed May 15 08:06:32 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,4 +0,0 @@
-#protein coverage% #unique hits
-Protein1 3.86598 1
-Protein2 4.3379 1
-Protein3 3.14961 1