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

Changeset 4:e86e83ac0cd3 (2019-05-15)
Previous changeset 3:7f1786e1c462 (2018-03-20) Next changeset 5:3c5ffd6de67a (2019-05-17)
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
modified:
MapAlignerPoseClustering.xml
macros.xml
test-data/MetaProSIP_1_output_1.csv
test-data/MetaProSIP_1_output_2.csv
added:
test-data/OpenPepXL_input.fasta
test-data/SequenceCoverageCalculator.fasta
test-data/SequenceCoverageCalculator.idXML
test-data/SequenceCoverageCalculator.tsv
b
diff -r 7f1786e1c462 -r e86e83ac0cd3 MapAlignerPoseClustering.xml
--- a/MapAlignerPoseClustering.xml Tue Mar 20 14:42:51 2018 -0400
+++ b/MapAlignerPoseClustering.xml Wed May 15 08:10:13 2019 -0400
[
@@ -10,7 +10,9 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command><![CDATA[
+  <command detect_errors="aggressive"><![CDATA[
+
+  #import re
 
   mkdir -p ./results_trafoxml ./results_out &&
   MapAlignerPoseClustering
@@ -21,13 +23,15 @@
 #end for
 
 -out
-#for $counter,$infile in enumerate($param_in):
-    ./results_out/${infile.element_identifier}.${infile.extension}
+#for $infile in $param_in:
+  #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($infile.element_identifier))
+  './results_out/${escaped_element_identifier}.${infile.extension}'
 #end for
 
 -trafo_out
-#for $counter,$infile in enumerate($param_in):
-    ./results_trafoxml/${infile.element_identifier}.trafoxml
+#for $infile in $param_in:
+  #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($infile.element_identifier))
+  './results_trafoxml/${escaped_element_identifier}.trafoxml'
 #end for
 
 #if $param_reference_file:
@@ -184,5 +188,5 @@
     </outputs>
     <help>Corrects retention time distortions between maps using a pose clustering approach.
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MapAlignerPoseClustering.html</help>
 </tool>
b
diff -r 7f1786e1c462 -r e86e83ac0cd3 macros.xml
--- a/macros.xml Tue Mar 20 14:42:51 2018 -0400
+++ b/macros.xml Wed May 15 08:10:13 2019 -0400
b
@@ -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">
b
diff -r 7f1786e1c462 -r e86e83ac0cd3 test-data/MetaProSIP_1_output_1.csv
--- a/test-data/MetaProSIP_1_output_1.csv Tue Mar 20 14:42:51 2018 -0400
+++ b/test-data/MetaProSIP_1_output_1.csv Wed May 15 08:10:13 2019 -0400
b
@@ -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
b
diff -r 7f1786e1c462 -r e86e83ac0cd3 test-data/MetaProSIP_1_output_2.csv
--- a/test-data/MetaProSIP_1_output_2.csv Tue Mar 20 14:42:51 2018 -0400
+++ b/test-data/MetaProSIP_1_output_2.csv Wed May 15 08:10:13 2019 -0400
b
@@ -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
b
diff -r 7f1786e1c462 -r e86e83ac0cd3 test-data/OpenPepXL_input.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OpenPepXL_input.fasta Wed May 15 08:10:13 2019 -0400
b
@@ -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
b
diff -r 7f1786e1c462 -r e86e83ac0cd3 test-data/SequenceCoverageCalculator.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SequenceCoverageCalculator.fasta Wed May 15 08:10:13 2019 -0400
b
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 7f1786e1c462 -r e86e83ac0cd3 test-data/SequenceCoverageCalculator.idXML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SequenceCoverageCalculator.idXML Wed May 15 08:10:13 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,&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 7f1786e1c462 -r e86e83ac0cd3 test-data/SequenceCoverageCalculator.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SequenceCoverageCalculator.tsv Wed May 15 08:10:13 2019 -0400
b
@@ -0,0 +1,4 @@
+#protein coverage% #unique hits
+Protein1 3.86598 1
+Protein2 4.3379 1
+Protein3 3.14961 1