| Previous changeset 0:b4098353ee73 (2018-01-05) Next changeset 2:28b65ce1a091 (2018-02-14) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 |
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modified:
moff.xml test-data/input/mbr_output/mbr_test1_match.txt test-data/input/mbr_output/mbr_test2_match.txt test-data/make_test_data.sh |
|
removed:
test-data/output1/mbr_test1_match_moff_result.txt test-data/output1/mbr_test2_match_moff_result.txt test-data/output2/test_moff_result.txt |
| b |
| diff -r b4098353ee73 -r 8f0e76ad46ef moff.xml --- a/moff.xml Fri Jan 05 12:47:36 2018 -0500 +++ b/moff.xml Thu Jan 18 00:51:56 2018 -0500 |
| b |
| @@ -1,7 +1,7 @@ <tool id="proteomics_moff" name="moFF" version="@VERSION@"> <description>extracts MS1 intensities from spectrum files</description> <macros> - <token name="@VERSION@">1.2</token> + <token name="@VERSION@">1.2.1</token> <!-- xml macros, used for shared Galaxy parameter inputs --> <xml name="ident_input_macro" token_allow_multiple="true" token_input_type="data"> <!-- this is exactly the same across all three, except for allowing multiple in MBR and all but not in moff --> @@ -176,15 +176,13 @@ --rt_p $task.rt_p --rt_p_match $task.rt_p_match --output_folder ./out - --ext txt #if $task.peptide_summary: --peptide_summary 1 #end if && #if $task.peptide_summary: - mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary' && + mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary' #end if - echo -ne #end if ]]></command> <inputs> @@ -250,13 +248,14 @@ <!-- test moff_all --> <test> <param name="task_selector" value="all"/> - <param name="input_type_selector" value="ps"/> + <param name="ident_input|input_type_selector" value="ps"/> <param name="ident_input_file"> <collection type="list"> <element name="mbr_test1" value="input/mbr_test1.tabular"/> <element name="mbr_test2" value="input/mbr_test2.tabular"/> </collection> </param> + <param name="msms_input|input_type_selector" value="mzml"/> <param name="inputraw"> <collection type="list"> <element name="mbr_test1" value="input/mbr_test1.mzml"/> @@ -271,8 +270,16 @@ </assert_contents> </output> <output_collection name="ident_output" type="list"> - <element name="mbr_test1_match_moff_result" value="output1/mbr_test1_match_moff_result.txt"/> - <element name="mbr_test2_match_moff_result" value="output1/mbr_test2_match_moff_result.txt"/> + <element name="mbr_test1_match_moff_result"> + <assert_contents> + <has_text text="NH2-QVEEAVQSDDK-COOH"/> + </assert_contents> + </element> + <element name="mbr_test2_match_moff_result"> + <assert_contents> + <has_text text="NH2-RDVGINNTVK-COOH"/> + </assert_contents> + </element> </output_collection> <output_collection name="log_output" type="list"> <element name="mbr_test1_match__moff"> @@ -290,9 +297,9 @@ <!-- test moff alone --> <test> <param name="task_selector" value="moff"/> - <param name="input_type_selector" value="ps"/> + <param name="ident_input|input_type_selector" value="ps"/> <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/> - <param name="msms_input" value="mzml"/> + <param name="msms_input|input_type_selector" value="mzml"/> <param name="inputraw" value="input/test.mzml" ftype="mzml"/> <param name="peptide_summary" value="true"/> <output name="output_peptide_summary" ftype="tabular" file="output2/moff_test_pepsum.tab"/> @@ -305,10 +312,10 @@ <!-- test the generic input --> <test> <param name="task_selector" value="moff"/> - <param name="input_type_selector" value="generic"/> + <param name="ident_input|input_type_selector" value="generic"/> <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/> <param name="remove_header" value="true"/> - <param name="msms_input" value="mzml"/> + <param name="msms_input|input_type_selector" value="mzml"/> <param name="inputraw" value="input/test.mzml" ftype="mzml"/> <param name="peptide" value="3"/> <param name="prot" value="2"/> @@ -328,7 +335,7 @@ <!-- test mbr --> <test> <param name="task_selector" value="mbr"/> - <param name="input_type_selector" value="ps"/> + <param name="ident_input|input_type_selector" value="ps"/> <param name="ident_input_file"> <collection type="list"> <element name="mbr_test1" value="input/mbr_test1.tabular"/> @@ -337,8 +344,16 @@ </param> <param name="ext" value="tabular"/> <output_collection name="ident_output" type="list" count="2"> - <element name="mbr_test1_match" file="input/mbr_output/mbr_test1_match.txt"/> - <element name="mbr_test2_match" file="input/mbr_output/mbr_test2_match.txt"/> + <element name="mbr_test1_match"> + <assert_contents> + <has_text text="NH2-QVEEAVQSDDK-COOH"/> + </assert_contents> + </element> + <element name="mbr_test2_match"> + <assert_contents> + <has_text text="NH2-RDVGINNTVK-COOH"/> + </assert_contents> + </element> </output_collection> </test> </tests> |
| b |
| diff -r b4098353ee73 -r 8f0e76ad46ef test-data/input/mbr_output/mbr_test1_match.txt --- a/test-data/input/mbr_output/mbr_test1_match.txt Fri Jan 05 12:47:36 2018 -0500 +++ b/test-data/input/mbr_output/mbr_test1_match.txt Thu Jan 18 00:51:56 2018 -0500 |
| [ |
| b'@@ -1,265 +1,265 @@\n aas after\taas before\tcharge\tcode_unique\tconfidence [%]\td-score\tfixed modifications\tidentification charge\tisotope number\tlocalization confidence\tmass\tmatched\tmod_peptide\tmz\tpeptide\tposition\tprecursor m/z error [ppm]\tprobabilistic ptm score\tprot\trt\tspectrum file\tspectrum scan number\tspectrum title\tvalidation\tvariable modifications\n-DA; ; DA\tIK; ; ; IK; IK\t2+\tNH2-QVEEAVQSDDK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1246.5677\t0\tNH2-QVEEAVQSDDK-COOH\t624.292668193\tQVEEAVQSDDK\t15; 1; 1; 9; 9\t2.44958264245\t\tASDEEKVAIEAGIKQVEEAVQSDDK, QVEEAVQSDDK, QVEEAVQSDDKDAIDEAAK, VAIEAGIKQVEEAVQSDDK, VAIEAGIKQVEEAVQSDDKDAIDEAAK\t2125.86\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.10613.10613.2\tDoubtful\t\n-FT; FT; FT\t\t2+\tNH2-GTTNGTSTDFNGK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1298.5739\t0\tNH2-GTTNGTSTDFNGK-COOH\t650.293779699\tGTTNGTSTDFNGK\t1; 1; 1; 1\t-0.666230198055\t\tGTTNGTSTDFNGK, GTTNGTSTDFNGKFTLQAK, GTTNGTSTDFNGKFTLQAKSDSGR, GTTNGTSTDFNGKFTLQSK\t2274.86\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.12577.12577.2\tDoubtful\t\n-\t\t2+\tNH2-ADAHITSNVEANK-COOH\t99.8278829604\t\t\t2+\t1.0\t\t1368.6634\t0\tNH2-ADAHITSNVEANK-COOH\t685.84\tADAHITSNVEANK\t1\t-0.922491400517\t\tADAHITSNVEANK\t2338.13\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.13537.13537.2\tDoubtful\t\n-\tEK\t2+\tNH2-AGATANDSLDDGNAGK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1475.6488\t0\tNH2-AGATANDSLDDGNAGK-COOH\t738.832041435\tAGATANDSLDDGNAGK\t5\t0.474488705639\t\tAREKAGATANDSLDDGNAGK\t2344.0\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.13631.13631.2\tDoubtful\t\n-\tEK\t2+\tNH2-AGATANDSLDDGNAGK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1475.6488\t0\tNH2-AGATANDSLDDGNAGK-COOH\t738.833460428\tAGATANDSLDDGNAGK\t5\t2.39507898017\t\tAREKAGATANDSLDDGNAGK\t2349.33\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.13710.13710.2\tDoubtful\t\n-KG; ; K; KG; KD; KG; KG; KD; KG\tVR; VR; VR; VR; VR; VR; VR; ; \t2+\tNH2-NPATGESFK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t949.4505\t0\tNH2-NPATGESFK-COOH\t475.732747603\tNPATGESFK\t9; 13; 13; 13; 4; 4; 4; 1; 1\t0.453938376043\t\tERPERMVRNPATGESFKKGADKVVK, IYCRERPERMVRNPATGESFK, IYCRERPERMVRNPATGESFKK, IYCRERPERMVRNPATGESFKKGADK, MVRNPATGESFKKDADKVVKMTIAKALK, MVRNPATGESFKKGADKVVKMTIAK, MVRNPATGESFKKGADKVVKMTIAKALK, NPATGESFKKDADRVVKMTIAKALK, NPATGESFKKGADKVVKMTIAKALK\t2475.54\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.15623.15623.2\tDoubtful\t\n-YI; YI; ; ; YI; ; ; ; ; ; YI; YI\tLR; LR; LR; LR; ; ; LR; LR; LR; LA; LR; LR; LR\t2+\tNH2-EM<ox>TSTEGLAGSAK-COOH\t99.8278829604\tOxidation of M (2: 100.0)\t\t2+\t0.0\tOxidation of M (2: Very Confident)\t1296.5867\t0\tNH2-EM<ox>TSTEGLAGSAK-COOH\t649.301568419\tEMTSTEGLAGSAK\t7; 7; 7; 16; 1; 1; 16; 16; 16; 4; 4; 4; 4\t1.41518840069\tOxidation of M (2: 100.0)\tAMKVLREMTSTEGLAGSAK, AMKVLREMTSTEGLAGSAKYIAYAPWR, AMKVLREMTSTEGLAGSAKYIAYAPWRK, DGPGYADGSAMKVLREMTSTEGLAGSAK, EMTSTEGLAGSAK, EMTSTEGLAGSAKYIAYAPWRK, GGPNDANGEAMKVLREMTSTEGLAGSAK, GGPNDANGKAMKVLREMTSTEGLAGSAK, GGPNDANGNAMKVLREMTSTEGLAGSAK, VLAEMTSTEGLAGSAK, VLREMTSTEGLAGSAK, VLREMTSTEGLAGSAKYIAYAPWR, VLREMTSTEGLAGSAKYIAYAPWRK\t2482.71\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.15737.15737.2\tDoubtful\tOxidation of M(2)\n-YI; YI; ; ; YI; ; ; ; ; ; YI; YI\tLR; LR; LR; LR; ; ; LR; LR; LR; LA; LR; LR; LR\t2+\tNH2-EM<ox>TSTEGLAGSAK-COOH\t99.8278829604\tOxidation of M (2: 100.0)\t\t2+\t0.0\tOxidation of M (2: Very Confident)\t1296.5867\t0\tNH2-EM<ox>TSTEGLAGSAK-COOH\t649.3\tEMTSTEGLAGSAK\t7; 7; 7; 16; 1; 1; 16; 16; 16; 4; 4; 4; 4\t-1.00036313327\tOxidation of M (2: 100.0)\tAMKVLREMTSTEGLAGSAK, AMKVLREMTSTEGLAGSAKYIAYAPWR, AMKVLREMTSTEGLAGSAKYIAYAPWRK, DGPGYADGSAMKVLREMTSTEGLAGSAK, EMTSTEGLAGSAK, EMTSTEGLAGSAKYIAYAPWRK, GGPNDANGEAMKVLREMTSTEGLAGSAK, GGPNDANGKAMKVLREMTSTEGLAGSAK, GGPNDANGNAMKVLREMTSTEGLAGSAK, VLAEMTSTEGLAGSAK, VLREMTSTEGLAGSAK, VLREMTSTEGLAGSAKYIAYAPWR, VLREMTSTEGLAGSAKYIAYAPWRK\t2494.56\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.15923.15923.2\tDoubtful\tOxidation of M(2)\n-SA; SA; SA; ; ; \tVK; ; ; ; VK; VK; VK\t2+\tNH2-EVTTDEYR-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1011.4509\t0\tNH2-EVTTDEYR-COOH\t506.732862123\tEVTTDEYR\t10; 1; 1; 1; 20; 20; 20\t0.263474422335\t\tDVGINNTV'..b'SSEQVK, GTMEVLMDAKGVSNSFFKSTTELTSSEQVK, GVDNSFFKSTTELTSSEQVK, GVDNSFFKSTTELTSSEQVKALCDGK, GVKNSFFKSTTELTSSEQVK, GVKNSFFKSTTELTSSEQVKALCDGK, GVNNNFFKSTTELTSSEQVK, GVNNNFFKSTTELTSSEQVKALCDGK, GVNNSFFKSTTELTSSEQVK, GVNNSFFKSTTELTSSEQVKALCDGK, GVNNSFFKSTTELTSSEQVKALCDGKR, GVSNSFFKSTTELTSSEQVK, GVSNSFFKSTTELTSSEQVKALCDGK, NSFFKSTTELTSSEQVKALCDGK, SAKGVNNSFFKSTTELTSSEQVK, SDAKGVSNSFFKSTTELTSSEQVK, SNSFFKSTTELTSSEQVKALCDGK, SSDLFKSTTELTSSEQVKALCDGK, STTELTSSEQVK, STTELTSSEQVKADRK, STTELTSSEQVKALCDGK, STTELTSSEQVKALCDGKIDAFGR, STTELTSSEQVKALCDGKIDAFGYR, STTELTSSEQVKALCDGKIDAFGYSEIGR, STTELTSSEQVKALCDGKIDAFGYSVR, STTELTSSEQVKALCDGKIDAFRSEER, SVLMDAKGVNNSFFKSTTELTSSEQVK\t2821.273148176294\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1952.0215\t1\t\t977.52\tTAGGIIIPDTAQEKPQEGK\t\t\t\tSSEKTAGGIIIPDTAQEKPQEGK, SSSEKTAGGIIIPDTAQEKPQEGK, TAGGIIIPDTAQEKPQEGK, TAGGIIIPDTAQEKPQEGKVIAVEIGR, TAGGIIIPDTAQEKPQEGKVIAVGGGAK, TAGGIIIPDTAQEKPQEGKVIAVGR, TAGGIIIPDTAQEKPQEGKVVAVGDRK, VLIEVLDSSEKTAGGIIIPDTAQEKPQEGK, VLIEVLNSSEKTAGGIIIPDTAQEKPQEGK, VLIQVLDSSEKTAGGIIIPDTAQEKPQEGK\t4102.460286150489\t\t\t\t\t\n+\t\t3+\t\t\t\t\t\t\t\t1952.0215\t1\t\t651.68405652463\tTAGGIIIPDTAQEKPQEGK\t\t\t\tSSEKTAGGIIIPDTAQEKPQEGK, SSSEKTAGGIIIPDTAQEKPQEGK, TAGGIIIPDTAQEKPQEGK, TAGGIIIPDTAQEKPQEGKVIAVEIGR, TAGGIIIPDTAQEKPQEGKVIAVGGGAK, TAGGIIIPDTAQEKPQEGKVIAVGR, TAGGIIIPDTAQEKPQEGKVVAVGDRK, VLIEVLDSSEKTAGGIIIPDTAQEKPQEGK, VLIEVLNSSEKTAGGIIIPDTAQEKPQEGK, VLIQVLDSSEKTAGGIIIPDTAQEKPQEGK\t4097.895676171116\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t951.5025\t1\t\t476.76\tTAGTFASVAK\t\t\t\tDLDKSFGSMPGSMNKKTAGTFASVAK, DLNKSFGSIPGSMNEKTAGTFASVAK, DLNKSFGSIPGSMNKKTAGTFASVAK, DLNKSFGSMPGSMNEKTAGTFASVAK, DLNKSFGSMPGSMNKKTAGTFASVAK, KTAGTFASVAK, SFGSIPGSMNKKTAGTFASVAK, SFGSLPGSMNEKTAGTFASVAK, SFGSMPGSMNEKTAGTFASVAK, SFGSMPGSMNKKTAGTFASVAK, SGSMNKKTAGTFASVAK, TAGTFASVAK\t3093.8812448218832\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t2089.0539\t1\t\t1046.03\tTNDEAGDGTTTATILAQAIVK\t\t\t\tEVASRTNDEAGDGTTTATILAQAIVK, TNDEAGDGTTTATILAQAIVK, TNDEAGDGTTTATILAQAIVKEGMK\t6407.897960108952\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1074.5306\t1\t\t538.27156638424\tTTGDIQVEGR\t\t\t\tTTGDIQVEGR, TTGDIQVEGRVDGDIR, TTGDIQVEGRVEGDIR\t2772.7903979796247\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1436.7147\t1\t\t719.37\tTTPSIVAFTESER\t\t\t\tTTPSIVAFTESER, TTPSIVAFTESERLVGQPAK, TTPSIVAFTESERLVGQPAKR, VIENAEGARTTPSIVAFTESER, VIENAEGARTTPSIVAFTESERLVGQPAK\t5425.877557588121\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1479.7093\t1\t\t740.86\tTTPSVVAFTEDGEK\t\t\t\tSENAEGARTTPSVVAFTEDGEK, SGARTTPSVVAFTEDGEK, TTPSVVAFTEDGEK, TTPSVVAFTEDGEKLEIGRAVQQECRDR, TTPSVVAFTEDGEKLVGQPAK, TTPSVVAFTEDGEKLVGQPAKR, TTPSVVAFTEDGEKLVGQPAKRQDRK, TTPSVVAFTEDGEKLVGQPDRK, TTPSVVAFTEDGEKLVGQSAKR, VLENAEGARTTPSVVAFTEDGEK, VLENAEGARTTPSVVAFTEDGEKLVGQPAK, VLENAEGTRTTPSVVAFTEDGEK, VLENTEGARTTPSVVAFTEDGEK\t4801.185211986499\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1072.5401\t1\t\t537.28\tVEADLVENGK\t\t\t\tDIEVGSPKIEGAKVEADLVENGKNR, GAKVEADLVENGKNRTILIFKKRRR, IIEVGSPTVEGAKVEADLVENGKNR, NIEVGSPIVEGAKVEADLVENGKNR, NIEVGSPTVEGAKVEADLVENGK, NIEVGSPTVEGAKVEADLVENGKNR, SIEVGSPTVEGAKVEADLVENGK, SIEVGSPTVEGAKVEADLVENGKNR, SIEVGSPVVEGAKVEADLVENGK, SIEVGSPVVEGAKVEADLVENGKNR, TIEVGSPTVEGAKVEADLVENGKNR, TIEVGSPTVKGAKVEADLVENGKNR, TIEVGSPVVEGAKVEADLVENGK, TIEVGSPVVEGAKVEADLVENGKNR, VEADLVENGK, VEADLVENGKNR, VEADLVENGKNRTDRK, VEADLVENGKNRTILIFK, VEADLVENGKNRTILIFKK, VEADLVENGKNRTILIFKKR, VEADLVENGKNRTILIFKKRR, VEADLVENGKNRTILIFKKRRKIGR, VEADLVENGKNRTILIFKKRRR, VEADLVENGKNRTILIFKKRRRQNSKIGR, VEADLVENGKNRTILIFKKRRRQNSR, VEADLVENGKNRTILIFKKRRRQNSRDRK, VEADLVENGKNRTILIFKKRRRQNSRR, VEADLVENGKNRTILIFKKRRRQNSRRK\t3019.6588886802583\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1073.5175\t1\t\t537.77\tVIDNMPETR\t\t\t\tIAHVDYQRVIDNMPETR, IAHVDYQRVIDNMPETRALTVTLEK, IGHIDYQRVIDNMPETRALGTTLEKLGK, IGHVDYQRVIDNMPETR, IGHVDYQRVIDNMPETRALTVTLEK, IGHVDYQRVIDNMPETRALTVTLEKLGK, VIDNMPETRALGTTLEKLGK, VIDNMPETRALTVTLEKLGK, VIDNMPETRALTVTLEKLGKSYQSEIEGLK\t3137.589632720652\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1124.4887\t1\t\t563.25225413568\tWADETGGSFR\t\t\t\tFDKSFNEAAFAGAQRWADETGGSFR, FDKSFNEAAFKGAERWADETGGSFR, GAERWADETGGSFREVELQSEAQR, SFNEAAFAGAQRWADETGGSFR, SFNESAFTGAQRWADETGGSFR, WADETGGSFR, WADETGGSFREIELQSEAQR, WADETGGSFREIELQSEAQREQALR, WADETGGSFREIELQSEAQREQALRR\t3912.125039395705\t\t\t\t\t\n' |
| b |
| diff -r b4098353ee73 -r 8f0e76ad46ef test-data/input/mbr_output/mbr_test2_match.txt --- a/test-data/input/mbr_output/mbr_test2_match.txt Fri Jan 05 12:47:36 2018 -0500 +++ b/test-data/input/mbr_output/mbr_test2_match.txt Thu Jan 18 00:51:56 2018 -0500 |
| [ |
| b'@@ -1,260 +1,260 @@\n aas after\taas before\tcharge\tcode_unique\tconfidence [%]\td-score\tfixed modifications\tidentification charge\tisotope number\tlocalization confidence\tmass\tmatched\tmod_peptide\tmz\tpeptide\tposition\tprecursor m/z error [ppm]\tprobabilistic ptm score\tprot\trt\tspectrum file\tspectrum scan number\tspectrum title\tvalidation\tvariable modifications\n-EV; ; EV; ; EV\tNW; NW; NW; NW; NW; NW\t2+\tNH2-RDVGINNTVK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1114.6095\t0\tNH2-RDVGINNTVK-COOH\t558.312235432\tRDVGINNTVK\t10; 10; 10; 10; 10; 10\t0.400593042907\t\tLVELAGQNWRDVGINNTVK, LVELAGQNWRDVGINNTVKEVTTDEYR, LVEVAGQNWRDVGINNTVK, LVEVAGQNWRDVGINNTVKEVTTDEYR, LVEVTGQNWRDVGINNTVK, LVEVTGQNWRDVGINNTVKEVTTDEYR\t2322.17\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.13283.13283.2\tDoubtful\t\n-\t\t3+\tNH2-ADAHITSNVEANK-COOH\t99.8278829604\t\t\t3+\t0.0\t\t1368.6634\t0\tNH2-ADAHITSNVEANK-COOH\t457.23\tADAHITSNVEANK\t1\t3.50950236447\t\tADAHITSNVEANK\t2335.35\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.13493.13493.3\tDoubtful\t\n-DF; DF; DF; DF; ; DF; DF; DF; \tAK; AK; ; ; ; AK; AK; AK; S; AK\t2+\tNH2-HQIVEAPAR-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1019.5512\t0\tNH2-HQIVEAPAR-COOH\t510.783866967\tHQIVEAPAR\t8; 8; 1; 1; 1; 8; 8; 8; 2; 16\t1.91229342584\t\tDFFPNAKHQIVEAPAR, DFFPNAKHQIVEAPARDFQEVLSMR, HQIVEAPARDFQEVLSMR, HQIVEAPARDFQEVLSMRADAHITSNVEAK, HQIVEAPARDFQEVLSMRDRK, QFFPNAKHQIVEAPAR, QFFPNAKHQIVEAPARDFQEVLSMR, QFFPNAKHQIVEAPARDFQEVR, SHQIVEAPARDFQEVLSMR, STQETQVKQFFPNAKHQIVEAPAR\t2384.64\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.14185.14185.2\tDoubtful\t\n-YI; YI; ; ; YI; ; ; ; ; ; YI; YI\tLR; LR; LR; LR; ; ; LR; LR; LR; LA; LR; LR; LR\t2+\tNH2-EM<ox>TSTEGLAGSAK-COOH\t99.8278829604\tOxidation of M (2: 100.0)\t\t2+\t0.0\tOxidation of M (2: Very Confident)\t1296.5867\t0\tNH2-EM<ox>TSTEGLAGSAK-COOH\t649.301048825\tEMTSTEGLAGSAK\t7; 7; 7; 16; 1; 1; 16; 16; 16; 4; 4; 4; 4\t0.614952377062\tOxidation of M (2: 100.0)\tAMKVLREMTSTEGLAGSAK, AMKVLREMTSTEGLAGSAKYIAYAPWR, AMKVLREMTSTEGLAGSAKYIAYAPWRK, DGPGYADGSAMKVLREMTSTEGLAGSAK, EMTSTEGLAGSAK, EMTSTEGLAGSAKYIAYAPWRK, GGPNDANGEAMKVLREMTSTEGLAGSAK, GGPNDANGKAMKVLREMTSTEGLAGSAK, GGPNDANGNAMKVLREMTSTEGLAGSAK, VLAEMTSTEGLAGSAK, VLREMTSTEGLAGSAK, VLREMTSTEGLAGSAKYIAYAPWR, VLREMTSTEGLAGSAKYIAYAPWRK\t2476.83\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.15644.15644.2\tDoubtful\tOxidation of M(2)\n-\tIK\t2+\tNH2-GTTNGTETDFNGK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1340.5844\t0\tNH2-GTTNGTETDFNGK-COOH\t671.300172985\tGTTNGTETDFNGK\t1; 6\t1.00953138271\t\tGTTNGTETDFNGK, SVVIKGTTNGTETDFNGK\t2482.1\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.15728.15728.2\tDoubtful\t\n-\tIK\t2+\tNH2-GTTNGTETDFNGK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1340.5844\t0\tNH2-GTTNGTETDFNGK-COOH\t671.3\tGTTNGTETDFNGK\t1; 6\t0.751844938295\t\tGTTNGTETDFNGK, SVVIKGTTNGTETDFNGK\t2494.5\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.15922.15922.2\tDoubtful\t\n-SD\t\t2+\tNH2-EGGEDM<ox>FVHK-COOH\t99.8278829604\tOxidation of M (6: 100.0)\t\t2+\t0.0\tOxidation of M (6: Very Confident)\t1163.4917\t0\tNH2-EGGEDM<ox>FVHK-COOH\t582.752485263\tEGGEDMFVHK\t1\t-1.12051106098\tOxidation of M (6: 100.0)\tEGGEDMFVHKSDVDGFINEGDK\t2536.63\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.16595.16595.2\tDoubtful\tOxidation of M(6)\n-\t\t2+\tNH2-GSNSGTETDFDGK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1313.5372\t0\tNH2-GSNSGTETDFDGK-COOH\t657.775415728\tGSNSGTETDFDGK\t1\t-0.664794466436\t\tGSNSGTETDFDGK\t2545.26\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.16731.16731.2\tDoubtful\t\n-GN\tDK; ; \t2+\tNH2-SAQEAM<ox>DSVVER-COOH\t99.8278829604\tOxidation of M (6: 100.0)\t\t2+\t0.0\tOxidation of M (6: Very Confident)\t1336.5929\t0\tNH2-SAQEAM<ox>DSVVER-COOH\t669.3\tSAQEAMDSVVER\t16; 1; 1\t-5.56330571801\tOxidation of M (6: 100.0)\tGIIDEELEAIWAGDKSAQEAMDSVVER, SAQEAMDSVVER, SAQEAMDSVVERGNPLLRR\t2569.05\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.17104.17104.2\tDoubtful\tOxidation of M(6)\n-SD\t\t2+\tNH2-EGGEDM<ox>FVHK-COOH\t99.8278829604\tOxidation of M (6: 100.0)\t\t2+\t0.0\tOxidation of M (6: Very Confident)\t1163.4917\t0\tNH2-EGGEDM<ox>FVHK-COOH\t582.753674136\tEGGEDMFVHK\t1\t0.919585786126\tOxidation of M (6: 100.0)\tEGGEDMFVHKSDVDGFINEGDK\t2'..b'\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1451.7157\t1\t\t726.87\tQGAFYNQIVEQR\t\t\t\tDKPVCGKQGAFYNQIVEQRYGAK\t4936.293918844264\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1283.6544\t1\t\t642.83426629379\tQLPGGEIQPAMK\t\t\t\tQLPGGEIQPAMK, QLPGGEIQPAMKTGLIDAAEFNNQIGR, QLPGGEIQPAMKTGLIDRSEERFSR, QLPGGEIQPAMKTGLIR, RSSDLVRQLPGGEIQPAMK, SMGMVVRQLPGGEIQPAMK, SVRQLPGGEIQPAMK, TVGLAADVLLEMGMSVVQLPGGEIQPAMK, TVGLAADVLMEMGMSVVQLPGGEIQPAMK, TVGLATNVLTAMGMVVRQLPGGEIQPAMK\t3363.02180748614\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1246.5677\t1\t\t624.2926681929599\tQVEEAVQSDDK\t\t\t\tASDEEKVAIEAGIKQVEEAVQSDDK, QVEEAVQSDDK, QVEEAVQSDDKDAIDEAAK, VAIEAGIKQVEEAVQSDDK, VAIEAGIKQVEEAVQSDDKDAIDEAAK\t2123.811043928768\t\t\t\t\t\n+\t\t3+\t\t\t\t\t\t\t\t1339.7208\t1\t\t447.58029945895\tRNIADTGILPDR\t\t\t\tIIKQVGNYGESYKRNIADTGILPDR, IIKQVGNYGESYKRNIADTGILPDRGDRK, IIKQVGNYGESYKRNIADTGILPDRGPNR, IIKQVGNYGESYKRNIADTGILPDRK, IIKQVGNYGESYKRNLADTGILPDR, QVGNYGESYKRNIADTGILPDR, RNIADTGILPDR, RNIADTGILPDRGPNALWTK, RNIADTGILPDRGPNNIWTK, RNIADTGILPDRGPNNIWTQGGLLYK, RNIADTGILPDRGPNQIWTK, RNIADTGILPDRGPNQLWTK, RNIADTGILPDRSEERFSR\t4216.9465482257065\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1304.6725\t1\t\t653.3444035935\tSNDLQNIVQFK\t\t\t\tASEPVYRSNDLQNIVQFK, ASEPVYRSNDLQNIVQFKTTSYDFYR, SNDLQNIVQFK, SNDLQNIVQFKTTSYDFYR\t5603.175532049885\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1138.6598\t1\t\t570.33900043877\tSPLPIDIVSAK\t\t\t\tSNTKSPLPIDIVSAK, SNTKSPLPIDIVSAKDLVATGQTTFDK, SNTKSPLPIDIVSAKDLVSTGQTTFDK, TPQRSNTKSPLPIDIVSAK\t5586.981408529449\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1573.8464\t1\t\t787.9331259906099\tSVQAVQPSGNYAIIK\t\t\t\tIIAKSVQAVQPSGNYAIIK, SVQAVQPSGNYAIIK\t4580.013192665658\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1412.7511\t1\t\t707.38\tTAGGIIIPDTAQEK\t\t\t\tSSEKTAGGIIIPDTAQEKPQEGK, SSSEKTAGGIIIPDTAQEKPQEGK, TAGGIIIPDTAQEKPDRK, TAGGIIIPDTAQEKPQEGK, TAGGIIIPDTAQEKPQEGKVIAVEIGR, TAGGIIIPDTAQEKPQEGKVIAVGGGAK, TAGGIIIPDTAQEKPQEGKVIAVGR, TAGGIIIPDTAQEKPQEGKVVAVGDRK, VLIEVLDSSEKTAGGIIIPDTAQEK, VLIEVLDSSEKTAGGIIIPDTAQEKPQEGK, VLIEVLNSSEKTAGGIIIPDTAQEKPQEGK, VLIQVLDSSEKTAGGIIIPDTAQEKPQEGK\t4444.244783793764\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1564.8348\t1\t\t783.42\tTFDTITNTILDALK\t\t\t\tADAERTFDTITNTILDALK, ADAERTFDTITNTILDALKGDDSVK, ADAERTFDTITNTILDALKGDDTVK, ADAERTFDTITNTILDALKGDR, LSGSLNLSKADAERTFDTITNTILDALK, TFDTITNTILDALK, TFDTITNTILDALKGDDTVK, TFDTITNTILDALKGDDTVKIAGFGTYK, TFDTITNTILDALKGDEIGR\t8085.130140501289\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t858.4811\t1\t\t430.2484206127\tTGEAIQIK\t\t\t\tAATTGRNPRTGEAIQIK, AATTGRNPRTGEAIQIKASKQPKFK, NPRTGEAIQIKASKQPKFK, NPRTGEAIQIKASKQPKFKAGSPLK\t3005.2097457706814\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1117.5979\t1\t\t559.80640770461\tVAATLGTTQEK\t\t\t\tFKDWDDLNKPDVRVAATLGTTQEK, FKDWDDLNKPDVRVAATLGTTQEKQVK, SNADRFKDWDDLNKPDVRVAATLGTTQEK, VAATLGTTQEKQVK, VAATLGTTQEKQVKEYFPNAK, VAATLGTTQEKQVKSYFPDAK\t2519.966546439525\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1080.5088\t1\t\t541.26176990816\tVGYQVDGDTK\t\t\t\tEASLHISNVMLVEDGVAVRVGYQVDGDTK, EASLHISNVMLVEGGVAVRVGYQVDGDTK, KEASLHISNVMLVEDGVAVRVGYQVDGDTK, KEASLHISNVMLVEGGVAVRVGYQVDGDTK, VGYQVDGDTKTR, VGYQVDGDTKTRISK, VGYQVDGDTKTRISKK, VGYQVDGDTKTRVSK\t2778.5921037745584\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1352.7228\t1\t\t677.87\tVLIDYLVDEFK\t\t\t\tVLIDYLVDEFKKKEGVDLTSDSTAMTRIR\t7737.857270421813\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1405.6937\t1\t\t703.8545022772701\tVTSDEESGQTIIK\t\t\t\tEDPSFRVTSDEESGQTIIK, EDPSFRVTSDEESGQTIIKGMEIGR, LAKEDPSFRVTSDEESGQTIIK, LAKEDPSFRVTSDEESGQTIIKGDRK, LAKEDPSFRVTSDEESGQTIIKGMGR, LAKEDPSFRVTSDEESGQTIIKGMR, LAKEDPSFRVTSDEESGQTIIKGR, MGEALARLAKEDPSFRVTSDEESGQTIIK, MGEALGRLAKEDPSFRVTSDEESGQTIIK, SALARLAKEDPSFRVTSDEESGQTIIK, SVTSDEESGQTIIK, VTSDEESGQTIIK, VTSDEESGQTIIKGMGELHLDIIVDR, VTSDEESGQTIIKGMGELHLDIIVDRMK, VTSDEESGQTIIKGMGELHLDIIVDRMKR, VTSDEESGQTIIKGMRSEERFSR\t3269.4802262611706\t\t\t\t\t\n+\t\t2+\t\t\t\t\t\t\t\t1170.6105\t1\t\t586.31238065366\tVVNIGNAGSGQR\t\t\t\tAKVKDFAGLKGKVVNIGNAGSGQR, DFAGLEGKVVNIGNAGSGQR, DFAGLKGKVVNIGNAGSGQR, DFAGLKGKVVNIGNAGSGQRGTMEVLMDAK, GKVVNIGNAGSGQR, GKVVNIGNAGSGQRGTMEVLMDAK, GKVVNIGNAGSGQRGTMEVLMDAKGVK, GKVVNIGNAGSGQRGTMEVLMNAK, KAKVKDFAGLEGKVVNIGNAGSGQR, KAKVKDFAGLKGKVVNIGNAGSGQR, KAKVKDFAGLKGKVVNIGNAGSGQRGDRK, KKAKVKDFAGLEGKVVNIGNAGSGQR, KKAKVKDFAGLKGKVVNIGNAGSGQR, VKDFAGLEGKVVNIGNAGSGQR, VKDFAGLKGKVVNIGNAGSGQR, VVNIGNAGSGQR, VVNIGNAGSGQRGTMEVLMDAK, VVNIGNAGSGQRGTMEVLMDAKGVK, VVNIGNAGSGQRGTMEVLMDAKGVNNSFFK\t2759.485440115403\t\t\t\t\t\n' |
| b |
| diff -r b4098353ee73 -r 8f0e76ad46ef test-data/make_test_data.sh --- a/test-data/make_test_data.sh Fri Jan 05 12:47:36 2018 -0500 +++ b/test-data/make_test_data.sh Thu Jan 18 00:51:56 2018 -0500 |
| b |
| @@ -2,8 +2,8 @@ #must be run within tools-galaxyp/tools/moFF/test-data -conda create -n mofftestdata moff -source activate mofftestdata +conda create -y -n tempmoff moff=1.2.1 +source activate tempmoff moff_all.py --inputtsv input/mbr_test1.tabular input/mbr_test2.tabular \ --inputraw input/mbr_test1.mzml input/mbr_test2.mzml \ @@ -32,10 +32,9 @@ # clean up # mbr outputs for moff all -rm -r output1/mbr_output +rm -r output1/* -# logs -rm output1/*.log output2/*.log +rm output2/test_moff_result.txt output2/test__moff.log -# peptide summary for all -rm output1/peptide_summary_intensity_moFF_run.tab +source deactivate tempmoff +conda env remove -y -n tempmoff |
| b |
| diff -r b4098353ee73 -r 8f0e76ad46ef test-data/output1/mbr_test1_match_moff_result.txt --- a/test-data/output1/mbr_test1_match_moff_result.txt Fri Jan 05 12:47:36 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,265 +0,0 @@\n-aas after\taas before\tcharge\tcode_unique\tconfidence [%]\td-score\tfixed modifications\tidentification charge\tisotope number\tlocalization confidence\tmass\tmatched\tmod_peptide\tmz\tpeptide\tposition\tprecursor m/z error [ppm]\tprobabilistic ptm score\tprot\trt\tspectrum file\tspectrum scan number\tspectrum title\tvalidation\tvariable modifications\tintensity\trt_peak\tlwhm\trwhm\t5p_noise\t10p_noise\tSNR\tlog_L_R\tlog_int\n-DA; ; DA\tIK; ; ; IK; IK\t2+\tNH2-QVEEAVQSDDK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1246.5677\t0\tNH2-QVEEAVQSDDK-COOH\t624.292668193\tQVEEAVQSDDK\t15; 1; 1; 9; 9\t2.44958264245\t\tASDEEKVAIEAGIKQVEEAVQSDDK, QVEEAVQSDDK, QVEEAVQSDDKDAIDEAAK, VAIEAGIKQVEEAVQSDDK, VAIEAGIKQVEEAVQSDDKDAIDEAAK\t2125.86\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.10613.10613.2\tDoubtful\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-FT; FT; FT\t\t2+\tNH2-GTTNGTSTDFNGK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1298.5739\t0\tNH2-GTTNGTSTDFNGK-COOH\t650.293779699\tGTTNGTSTDFNGK\t1; 1; 1; 1\t-0.666230198055\t\tGTTNGTSTDFNGK, GTTNGTSTDFNGKFTLQAK, GTTNGTSTDFNGKFTLQAKSDSGR, GTTNGTSTDFNGKFTLQSK\t2274.86\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.12577.12577.2\tDoubtful\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\tNH2-ADAHITSNVEANK-COOH\t99.8278829604\t\t\t2+\t1.0\t\t1368.6634\t0\tNH2-ADAHITSNVEANK-COOH\t685.84\tADAHITSNVEANK\t1\t-0.922491400517\t\tADAHITSNVEANK\t2338.13\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.13537.13537.2\tDoubtful\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\tEK\t2+\tNH2-AGATANDSLDDGNAGK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1475.6488\t0\tNH2-AGATANDSLDDGNAGK-COOH\t738.832041435\tAGATANDSLDDGNAGK\t5\t0.474488705639\t\tAREKAGATANDSLDDGNAGK\t2344.0\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.13631.13631.2\tDoubtful\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\tEK\t2+\tNH2-AGATANDSLDDGNAGK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1475.6488\t0\tNH2-AGATANDSLDDGNAGK-COOH\t738.833460428\tAGATANDSLDDGNAGK\t5\t2.39507898017\t\tAREKAGATANDSLDDGNAGK\t2349.33\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.13710.13710.2\tDoubtful\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-KG; ; K; KG; KD; KG; KG; KD; KG\tVR; VR; VR; VR; VR; VR; VR; ; \t2+\tNH2-NPATGESFK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t949.4505\t0\tNH2-NPATGESFK-COOH\t475.732747603\tNPATGESFK\t9; 13; 13; 13; 4; 4; 4; 1; 1\t0.453938376043\t\tERPERMVRNPATGESFKKGADKVVK, IYCRERPERMVRNPATGESFK, IYCRERPERMVRNPATGESFKK, IYCRERPERMVRNPATGESFKKGADK, MVRNPATGESFKKDADKVVKMTIAKALK, MVRNPATGESFKKGADKVVKMTIAK, MVRNPATGESFKKGADKVVKMTIAKALK, NPATGESFKKDADRVVKMTIAKALK, NPATGESFKKGADKVVKMTIAKALK\t2475.54\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.15623.15623.2\tDoubtful\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-YI; YI; ; ; YI; ; ; ; ; ; YI; YI\tLR; LR; LR; LR; ; ; LR; LR; LR; LA; LR; LR; LR\t2+\tNH2-EM<ox>TSTEGLAGSAK-COOH\t99.8278829604\tOxidation of M (2: 100.0)\t\t2+\t0.0\tOxidation of M (2: Very Confident)\t1296.5867\t0\tNH2-EM<ox>TSTEGLAGSAK-COOH\t649.301568419\tEMTSTEGLAGSAK\t7; 7; 7; 16; 1; 1; 16; 16; 16; 4; 4; 4; 4\t1.41518840069\tOxidation of M (2: 100.0)\tAMKVLREMTSTEGLAGSAK, AMKVLREMTSTEGLAGSAKYIAYAPWR, AMKVLREMTSTEGLAGSAKYIAYAPWRK, DGPGYADGSAMKVLREMTSTEGLAGSAK, EMTSTEGLAGSAK, EMTSTEGLAGSAKYIAYAPWRK, GGPNDANGEAMKVLREMTSTEGLAGSAK, GGPNDANGKAMKVLREMTSTEGLAGSAK, GGPNDANGNAMKVLREMTSTEGLAGSAK, VLAEMTSTEGLAGSAK, VLREMTSTEGLAGSAK, VLREMTSTEGLAGSAKYIAYAPWR, VLREMTSTEGLAGSAKYIAYAPWRK\t2482.71\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.15737.15737.2\tDoubtful\tOxidation of M(2)\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-YI; YI; ; ; YI; ; ; ; ; ; YI; YI\tLR; LR; LR; LR; ; ; LR; LR; LR; LA; LR; LR; LR\t2+\tNH2-EM<ox>TSTEGLAGSAK-COOH\t99.8278829604\tOxidation of M (2: 100.0)\t\t2+\t0.0\tOxidation of M (2: Very Confident)\t1296.5867\t0\tNH2-EM<ox>TSTEGLAGSAK-COOH\t649.3\tEMTSTEGLAGSAK\t7; 7; 7; 16; 1; 1; 16; 16; 16; 4; 4; 4; 4\t-1.00036313327\tOxidation of M (2: 100.0)\tAMKVLREMTSTEGLAGSAK, AMKVLREMTSTEGLAGSAKYIAYAPWR, AMKVLREMTSTEGLAGSAKYIAYAPWRK, DGPGYADGSAMKVLREMTSTEGLAGSAK, EMTSTEGLAGSAK, EMTSTEGLAGSAKYIAYAPWRK, GGPNDANGEAMKVLREMTSTEGLAGSAK, GGPNDANGKAMKVLREMTSTEGLAGSAK, GGPNDANGNAMKVLREMTSTEGLAGSAK, VLAEMTSTEGLAGSAK, VLREMTSTEGLAGSAK, VLREMTSTEGLAGSAKYIAYAPWR, VLREMTSTEGLAGSAKYIAYAPWRK\t2494.56\ttrimmed_2016_Jan_12_QE2'..b'NSFFKSTTELTSSEQVKALCDGKR, GVSNSFFKSTTELTSSEQVK, GVSNSFFKSTTELTSSEQVKALCDGK, NSFFKSTTELTSSEQVKALCDGK, SAKGVNNSFFKSTTELTSSEQVK, SDAKGVSNSFFKSTTELTSSEQVK, SNSFFKSTTELTSSEQVKALCDGK, SSDLFKSTTELTSSEQVKALCDGK, STTELTSSEQVK, STTELTSSEQVKADRK, STTELTSSEQVKALCDGK, STTELTSSEQVKALCDGKIDAFGR, STTELTSSEQVKALCDGKIDAFGYR, STTELTSSEQVKALCDGKIDAFGYSEIGR, STTELTSSEQVKALCDGKIDAFGYSVR, STTELTSSEQVKALCDGKIDAFRSEER, SVLMDAKGVNNSFFKSTTELTSSEQVK\t2821.27314818\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1952.0215\t1\t\t977.52\tTAGGIIIPDTAQEKPQEGK\t\t\t\tSSEKTAGGIIIPDTAQEKPQEGK, SSSEKTAGGIIIPDTAQEKPQEGK, TAGGIIIPDTAQEKPQEGK, TAGGIIIPDTAQEKPQEGKVIAVEIGR, TAGGIIIPDTAQEKPQEGKVIAVGGGAK, TAGGIIIPDTAQEKPQEGKVIAVGR, TAGGIIIPDTAQEKPQEGKVVAVGDRK, VLIEVLDSSEKTAGGIIIPDTAQEKPQEGK, VLIEVLNSSEKTAGGIIIPDTAQEKPQEGK, VLIQVLDSSEKTAGGIIIPDTAQEKPQEGK\t4102.46028615\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t3+\t\t\t\t\t\t\t\t1952.0215\t1\t\t651.684056525\tTAGGIIIPDTAQEKPQEGK\t\t\t\tSSEKTAGGIIIPDTAQEKPQEGK, SSSEKTAGGIIIPDTAQEKPQEGK, TAGGIIIPDTAQEKPQEGK, TAGGIIIPDTAQEKPQEGKVIAVEIGR, TAGGIIIPDTAQEKPQEGKVIAVGGGAK, TAGGIIIPDTAQEKPQEGKVIAVGR, TAGGIIIPDTAQEKPQEGKVVAVGDRK, VLIEVLDSSEKTAGGIIIPDTAQEKPQEGK, VLIEVLNSSEKTAGGIIIPDTAQEKPQEGK, VLIQVLDSSEKTAGGIIIPDTAQEKPQEGK\t4097.89567617\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t951.5025\t1\t\t476.76\tTAGTFASVAK\t\t\t\tDLDKSFGSMPGSMNKKTAGTFASVAK, DLNKSFGSIPGSMNEKTAGTFASVAK, DLNKSFGSIPGSMNKKTAGTFASVAK, DLNKSFGSMPGSMNEKTAGTFASVAK, DLNKSFGSMPGSMNKKTAGTFASVAK, KTAGTFASVAK, SFGSIPGSMNKKTAGTFASVAK, SFGSLPGSMNEKTAGTFASVAK, SFGSMPGSMNEKTAGTFASVAK, SFGSMPGSMNKKTAGTFASVAK, SGSMNKKTAGTFASVAK, TAGTFASVAK\t3093.88124482\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t2089.0539\t1\t\t1046.03\tTNDEAGDGTTTATILAQAIVK\t\t\t\tEVASRTNDEAGDGTTTATILAQAIVK, TNDEAGDGTTTATILAQAIVK, TNDEAGDGTTTATILAQAIVKEGMK\t6407.89796011\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1074.5306\t1\t\t538.271566384\tTTGDIQVEGR\t\t\t\tTTGDIQVEGR, TTGDIQVEGRVDGDIR, TTGDIQVEGRVEGDIR\t2772.79039798\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1436.7147\t1\t\t719.37\tTTPSIVAFTESER\t\t\t\tTTPSIVAFTESER, TTPSIVAFTESERLVGQPAK, TTPSIVAFTESERLVGQPAKR, VIENAEGARTTPSIVAFTESER, VIENAEGARTTPSIVAFTESERLVGQPAK\t5425.87755759\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1479.7093\t1\t\t740.86\tTTPSVVAFTEDGEK\t\t\t\tSENAEGARTTPSVVAFTEDGEK, SGARTTPSVVAFTEDGEK, TTPSVVAFTEDGEK, TTPSVVAFTEDGEKLEIGRAVQQECRDR, TTPSVVAFTEDGEKLVGQPAK, TTPSVVAFTEDGEKLVGQPAKR, TTPSVVAFTEDGEKLVGQPAKRQDRK, TTPSVVAFTEDGEKLVGQPDRK, TTPSVVAFTEDGEKLVGQSAKR, VLENAEGARTTPSVVAFTEDGEK, VLENAEGARTTPSVVAFTEDGEKLVGQPAK, VLENAEGTRTTPSVVAFTEDGEK, VLENTEGARTTPSVVAFTEDGEK\t4801.18521199\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1072.5401\t1\t\t537.28\tVEADLVENGK\t\t\t\tDIEVGSPKIEGAKVEADLVENGKNR, GAKVEADLVENGKNRTILIFKKRRR, IIEVGSPTVEGAKVEADLVENGKNR, NIEVGSPIVEGAKVEADLVENGKNR, NIEVGSPTVEGAKVEADLVENGK, NIEVGSPTVEGAKVEADLVENGKNR, SIEVGSPTVEGAKVEADLVENGK, SIEVGSPTVEGAKVEADLVENGKNR, SIEVGSPVVEGAKVEADLVENGK, SIEVGSPVVEGAKVEADLVENGKNR, TIEVGSPTVEGAKVEADLVENGKNR, TIEVGSPTVKGAKVEADLVENGKNR, TIEVGSPVVEGAKVEADLVENGK, TIEVGSPVVEGAKVEADLVENGKNR, VEADLVENGK, VEADLVENGKNR, VEADLVENGKNRTDRK, VEADLVENGKNRTILIFK, VEADLVENGKNRTILIFKK, VEADLVENGKNRTILIFKKR, VEADLVENGKNRTILIFKKRR, VEADLVENGKNRTILIFKKRRKIGR, VEADLVENGKNRTILIFKKRRR, VEADLVENGKNRTILIFKKRRRQNSKIGR, VEADLVENGKNRTILIFKKRRRQNSR, VEADLVENGKNRTILIFKKRRRQNSRDRK, VEADLVENGKNRTILIFKKRRRQNSRR, VEADLVENGKNRTILIFKKRRRQNSRRK\t3019.65888868\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1073.5175\t1\t\t537.77\tVIDNMPETR\t\t\t\tIAHVDYQRVIDNMPETR, IAHVDYQRVIDNMPETRALTVTLEK, IGHIDYQRVIDNMPETRALGTTLEKLGK, IGHVDYQRVIDNMPETR, IGHVDYQRVIDNMPETRALTVTLEK, IGHVDYQRVIDNMPETRALTVTLEKLGK, VIDNMPETRALGTTLEKLGK, VIDNMPETRALTVTLEKLGK, VIDNMPETRALTVTLEKLGKSYQSEIEGLK\t3137.58963272\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1124.4887\t1\t\t563.252254136\tWADETGGSFR\t\t\t\tFDKSFNEAAFAGAQRWADETGGSFR, FDKSFNEAAFKGAERWADETGGSFR, GAERWADETGGSFREVELQSEAQR, SFNEAAFAGAQRWADETGGSFR, SFNESAFTGAQRWADETGGSFR, WADETGGSFR, WADETGGSFREIELQSEAQR, WADETGGSFREIELQSEAQREQALR, WADETGGSFREIELQSEAQREQALRR\t3912.1250394\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n' |
| b |
| diff -r b4098353ee73 -r 8f0e76ad46ef test-data/output1/mbr_test2_match_moff_result.txt --- a/test-data/output1/mbr_test2_match_moff_result.txt Fri Jan 05 12:47:36 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,260 +0,0 @@\n-aas after\taas before\tcharge\tcode_unique\tconfidence [%]\td-score\tfixed modifications\tidentification charge\tisotope number\tlocalization confidence\tmass\tmatched\tmod_peptide\tmz\tpeptide\tposition\tprecursor m/z error [ppm]\tprobabilistic ptm score\tprot\trt\tspectrum file\tspectrum scan number\tspectrum title\tvalidation\tvariable modifications\tintensity\trt_peak\tlwhm\trwhm\t5p_noise\t10p_noise\tSNR\tlog_L_R\tlog_int\n-EV; ; EV; ; EV\tNW; NW; NW; NW; NW; NW\t2+\tNH2-RDVGINNTVK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1114.6095\t0\tNH2-RDVGINNTVK-COOH\t558.312235432\tRDVGINNTVK\t10; 10; 10; 10; 10; 10\t0.400593042907\t\tLVELAGQNWRDVGINNTVK, LVELAGQNWRDVGINNTVKEVTTDEYR, LVEVAGQNWRDVGINNTVK, LVEVAGQNWRDVGINNTVKEVTTDEYR, LVEVTGQNWRDVGINNTVK, LVEVTGQNWRDVGINNTVKEVTTDEYR\t2322.17\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.13283.13283.2\tDoubtful\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t3+\tNH2-ADAHITSNVEANK-COOH\t99.8278829604\t\t\t3+\t0.0\t\t1368.6634\t0\tNH2-ADAHITSNVEANK-COOH\t457.23\tADAHITSNVEANK\t1\t3.50950236447\t\tADAHITSNVEANK\t2335.35\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.13493.13493.3\tDoubtful\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-DF; DF; DF; DF; ; DF; DF; DF; \tAK; AK; ; ; ; AK; AK; AK; S; AK\t2+\tNH2-HQIVEAPAR-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1019.5512\t0\tNH2-HQIVEAPAR-COOH\t510.783866967\tHQIVEAPAR\t8; 8; 1; 1; 1; 8; 8; 8; 2; 16\t1.91229342584\t\tDFFPNAKHQIVEAPAR, DFFPNAKHQIVEAPARDFQEVLSMR, HQIVEAPARDFQEVLSMR, HQIVEAPARDFQEVLSMRADAHITSNVEAK, HQIVEAPARDFQEVLSMRDRK, QFFPNAKHQIVEAPAR, QFFPNAKHQIVEAPARDFQEVLSMR, QFFPNAKHQIVEAPARDFQEVR, SHQIVEAPARDFQEVLSMR, STQETQVKQFFPNAKHQIVEAPAR\t2384.64\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.14185.14185.2\tDoubtful\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-YI; YI; ; ; YI; ; ; ; ; ; YI; YI\tLR; LR; LR; LR; ; ; LR; LR; LR; LA; LR; LR; LR\t2+\tNH2-EM<ox>TSTEGLAGSAK-COOH\t99.8278829604\tOxidation of M (2: 100.0)\t\t2+\t0.0\tOxidation of M (2: Very Confident)\t1296.5867\t0\tNH2-EM<ox>TSTEGLAGSAK-COOH\t649.301048825\tEMTSTEGLAGSAK\t7; 7; 7; 16; 1; 1; 16; 16; 16; 4; 4; 4; 4\t0.614952377062\tOxidation of M (2: 100.0)\tAMKVLREMTSTEGLAGSAK, AMKVLREMTSTEGLAGSAKYIAYAPWR, AMKVLREMTSTEGLAGSAKYIAYAPWRK, DGPGYADGSAMKVLREMTSTEGLAGSAK, EMTSTEGLAGSAK, EMTSTEGLAGSAKYIAYAPWRK, GGPNDANGEAMKVLREMTSTEGLAGSAK, GGPNDANGKAMKVLREMTSTEGLAGSAK, GGPNDANGNAMKVLREMTSTEGLAGSAK, VLAEMTSTEGLAGSAK, VLREMTSTEGLAGSAK, VLREMTSTEGLAGSAKYIAYAPWR, VLREMTSTEGLAGSAKYIAYAPWRK\t2476.83\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.15644.15644.2\tDoubtful\tOxidation of M(2)\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\tIK\t2+\tNH2-GTTNGTETDFNGK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1340.5844\t0\tNH2-GTTNGTETDFNGK-COOH\t671.300172985\tGTTNGTETDFNGK\t1; 6\t1.00953138271\t\tGTTNGTETDFNGK, SVVIKGTTNGTETDFNGK\t2482.1\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.15728.15728.2\tDoubtful\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\tIK\t2+\tNH2-GTTNGTETDFNGK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1340.5844\t0\tNH2-GTTNGTETDFNGK-COOH\t671.3\tGTTNGTETDFNGK\t1; 6\t0.751844938295\t\tGTTNGTETDFNGK, SVVIKGTTNGTETDFNGK\t2494.5\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.15922.15922.2\tDoubtful\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-SD\t\t2+\tNH2-EGGEDM<ox>FVHK-COOH\t99.8278829604\tOxidation of M (6: 100.0)\t\t2+\t0.0\tOxidation of M (6: Very Confident)\t1163.4917\t0\tNH2-EGGEDM<ox>FVHK-COOH\t582.752485263\tEGGEDMFVHK\t1\t-1.12051106098\tOxidation of M (6: 100.0)\tEGGEDMFVHKSDVDGFINEGDK\t2536.63\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.16595.16595.2\tDoubtful\tOxidation of M(6)\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\tNH2-GSNSGTETDFDGK-COOH\t99.8278829604\t\t\t2+\t0.0\t\t1313.5372\t0\tNH2-GSNSGTETDFDGK-COOH\t657.775415728\tGSNSGTETDFDGK\t1\t-0.664794466436\t\tGSNSGTETDFDGK\t2545.26\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.16731.16731.2\tDoubtful\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-GN\tDK; ; \t2+\tNH2-SAQEAM<ox>DSVVER-COOH\t99.8278829604\tOxidation of M (6: 100.0)\t\t2+\t0.0\tOxidation of M (6: Very Confident)\t1336.5929\t0\tNH2-SAQEAM<ox>DSVVER-COOH\t669.3\tSAQEAMDSVVER\t16; 1; 1\t-5.56330571801\tOxidation of M (6: 100.0)\tGIIDEELEAIWAGDKSAQEAMDSVVER, SAQEAMDSVVER, SAQEAMDSVVERGNPLLRR\t2569.05\ttrimmed_2016_Jan_12_QE2_47.mgf\t\t2016_Jan_12_QE2_47.171'..b'PGGEIQPAMK, TVGLAADVLLEMGMSVVQLPGGEIQPAMK, TVGLAADVLMEMGMSVVQLPGGEIQPAMK, TVGLATNVLTAMGMVVRQLPGGEIQPAMK\t3363.02180749\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1246.5677\t1\t\t624.292668193\tQVEEAVQSDDK\t\t\t\tASDEEKVAIEAGIKQVEEAVQSDDK, QVEEAVQSDDK, QVEEAVQSDDKDAIDEAAK, VAIEAGIKQVEEAVQSDDK, VAIEAGIKQVEEAVQSDDKDAIDEAAK\t2123.81104393\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t3+\t\t\t\t\t\t\t\t1339.7208\t1\t\t447.580299459\tRNIADTGILPDR\t\t\t\tIIKQVGNYGESYKRNIADTGILPDR, IIKQVGNYGESYKRNIADTGILPDRGDRK, IIKQVGNYGESYKRNIADTGILPDRGPNR, IIKQVGNYGESYKRNIADTGILPDRK, IIKQVGNYGESYKRNLADTGILPDR, QVGNYGESYKRNIADTGILPDR, RNIADTGILPDR, RNIADTGILPDRGPNALWTK, RNIADTGILPDRGPNNIWTK, RNIADTGILPDRGPNNIWTQGGLLYK, RNIADTGILPDRGPNQIWTK, RNIADTGILPDRGPNQLWTK, RNIADTGILPDRSEERFSR\t4216.94654823\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1304.6725\t1\t\t653.344403594\tSNDLQNIVQFK\t\t\t\tASEPVYRSNDLQNIVQFK, ASEPVYRSNDLQNIVQFKTTSYDFYR, SNDLQNIVQFK, SNDLQNIVQFKTTSYDFYR\t5603.17553205\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1138.6598\t1\t\t570.339000439\tSPLPIDIVSAK\t\t\t\tSNTKSPLPIDIVSAK, SNTKSPLPIDIVSAKDLVATGQTTFDK, SNTKSPLPIDIVSAKDLVSTGQTTFDK, TPQRSNTKSPLPIDIVSAK\t5586.98140853\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1573.8464\t1\t\t787.933125991\tSVQAVQPSGNYAIIK\t\t\t\tIIAKSVQAVQPSGNYAIIK, SVQAVQPSGNYAIIK\t4580.01319267\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1412.7511\t1\t\t707.38\tTAGGIIIPDTAQEK\t\t\t\tSSEKTAGGIIIPDTAQEKPQEGK, SSSEKTAGGIIIPDTAQEKPQEGK, TAGGIIIPDTAQEKPDRK, TAGGIIIPDTAQEKPQEGK, TAGGIIIPDTAQEKPQEGKVIAVEIGR, TAGGIIIPDTAQEKPQEGKVIAVGGGAK, TAGGIIIPDTAQEKPQEGKVIAVGR, TAGGIIIPDTAQEKPQEGKVVAVGDRK, VLIEVLDSSEKTAGGIIIPDTAQEK, VLIEVLDSSEKTAGGIIIPDTAQEKPQEGK, VLIEVLNSSEKTAGGIIIPDTAQEKPQEGK, VLIQVLDSSEKTAGGIIIPDTAQEKPQEGK\t4444.24478379\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1564.8348\t1\t\t783.42\tTFDTITNTILDALK\t\t\t\tADAERTFDTITNTILDALK, ADAERTFDTITNTILDALKGDDSVK, ADAERTFDTITNTILDALKGDDTVK, ADAERTFDTITNTILDALKGDR, LSGSLNLSKADAERTFDTITNTILDALK, TFDTITNTILDALK, TFDTITNTILDALKGDDTVK, TFDTITNTILDALKGDDTVKIAGFGTYK, TFDTITNTILDALKGDEIGR\t8085.1301405\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t858.4811\t1\t\t430.248420613\tTGEAIQIK\t\t\t\tAATTGRNPRTGEAIQIK, AATTGRNPRTGEAIQIKASKQPKFK, NPRTGEAIQIKASKQPKFK, NPRTGEAIQIKASKQPKFKAGSPLK\t3005.20974577\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1117.5979\t1\t\t559.806407705\tVAATLGTTQEK\t\t\t\tFKDWDDLNKPDVRVAATLGTTQEK, FKDWDDLNKPDVRVAATLGTTQEKQVK, SNADRFKDWDDLNKPDVRVAATLGTTQEK, VAATLGTTQEKQVK, VAATLGTTQEKQVKEYFPNAK, VAATLGTTQEKQVKSYFPDAK\t2519.96654644\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1080.5088\t1\t\t541.261769908\tVGYQVDGDTK\t\t\t\tEASLHISNVMLVEDGVAVRVGYQVDGDTK, EASLHISNVMLVEGGVAVRVGYQVDGDTK, KEASLHISNVMLVEDGVAVRVGYQVDGDTK, KEASLHISNVMLVEGGVAVRVGYQVDGDTK, VGYQVDGDTKTR, VGYQVDGDTKTRISK, VGYQVDGDTKTRISKK, VGYQVDGDTKTRVSK\t2778.59210377\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1352.7228\t1\t\t677.87\tVLIDYLVDEFK\t\t\t\tVLIDYLVDEFKKKEGVDLTSDSTAMTRIR\t7737.85727042\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1405.6937\t1\t\t703.854502277\tVTSDEESGQTIIK\t\t\t\tEDPSFRVTSDEESGQTIIK, EDPSFRVTSDEESGQTIIKGMEIGR, LAKEDPSFRVTSDEESGQTIIK, LAKEDPSFRVTSDEESGQTIIKGDRK, LAKEDPSFRVTSDEESGQTIIKGMGR, LAKEDPSFRVTSDEESGQTIIKGMR, LAKEDPSFRVTSDEESGQTIIKGR, MGEALARLAKEDPSFRVTSDEESGQTIIK, MGEALGRLAKEDPSFRVTSDEESGQTIIK, SALARLAKEDPSFRVTSDEESGQTIIK, SVTSDEESGQTIIK, VTSDEESGQTIIK, VTSDEESGQTIIKGMGELHLDIIVDR, VTSDEESGQTIIKGMGELHLDIIVDRMK, VTSDEESGQTIIKGMGELHLDIIVDRMKR, VTSDEESGQTIIKGMRSEERFSR\t3269.48022626\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-\t\t2+\t\t\t\t\t\t\t\t1170.6105\t1\t\t586.312380654\tVVNIGNAGSGQR\t\t\t\tAKVKDFAGLKGKVVNIGNAGSGQR, DFAGLEGKVVNIGNAGSGQR, DFAGLKGKVVNIGNAGSGQR, DFAGLKGKVVNIGNAGSGQRGTMEVLMDAK, GKVVNIGNAGSGQR, GKVVNIGNAGSGQRGTMEVLMDAK, GKVVNIGNAGSGQRGTMEVLMDAKGVK, GKVVNIGNAGSGQRGTMEVLMNAK, KAKVKDFAGLEGKVVNIGNAGSGQR, KAKVKDFAGLKGKVVNIGNAGSGQR, KAKVKDFAGLKGKVVNIGNAGSGQRGDRK, KKAKVKDFAGLEGKVVNIGNAGSGQR, KKAKVKDFAGLKGKVVNIGNAGSGQR, VKDFAGLEGKVVNIGNAGSGQR, VKDFAGLKGKVVNIGNAGSGQR, VVNIGNAGSGQR, VVNIGNAGSGQRGTMEVLMDAK, VVNIGNAGSGQRGTMEVLMDAKGVK, VVNIGNAGSGQRGTMEVLMDAKGVNNSFFK\t2759.48544012\t\t\t\t\t\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n' |
| b |
| diff -r b4098353ee73 -r 8f0e76ad46ef test-data/output2/test_moff_result.txt --- a/test-data/output2/test_moff_result.txt Fri Jan 05 12:47:36 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,583 +0,0 @@\n-prot\tpeptide\taas before\taas after\tposition\tmod_peptide\tvariable modifications\tfixed modifications\tspectrum file\tspectrum title\tspectrum scan number\trt\tmz\tcharge\tidentification charge\tmass\tisotope number\tprecursor m/z error [ppm]\tlocalization confidence\tprobabilistic ptm score\td-score\tconfidence [%]\tvalidation\tintensity\trt_peak\tlwhm\trwhm\t5p_noise\t10p_noise\tSNR\tlog_L_R\tlog_int\n-AARAGRNPQTGAEIQIKAANVPSFKAGK, AGRNPQTGAEIQIKAANVPSFKAGK, AGRNPQTGAEIQIKAANVPSFKAGKALK, AGRNPQTGAEIQIKAANVPSFKARSEER, HRAARAGRNPQTGAEIQIK, HRAARAGRNPQTGAEIQIKAANVPSFK, HRAARAGRNPQTGAEIQIKAANVPSFKAGK, KGRNPQTGAEIQIKAK\tGRNPQTGAEIQIK\tRA; A; A; A; RA; RA; RA; K\tAA; AA; AA; AA; ; AA; AA; AK\t5; 2; 2; 2; 7; 7; 7; 2\tNH2-GRNPQTGAEIQIK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.24409.24409.2\t\t3023.92\t706.39\t2+\t2+\t1410.75792576\t0\t5.32379286054\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-NIAELGIYPAVDPLDSTSR\tNIAELGIYPAVDPLDSTSR\t\t\t1\tNH2-NIAELGIYPAVDPLDSTSR-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.77693.77693.2\t\t6459.24\t1016.02684441\t2+\t2+\t2030.0320349\t0\t3.4945013212\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-DHFVHISGLIDEINEGDQVEFDLQEGNK, DHFVHISGLVDEIREGDQVEFDLQEGNK, EGDQVEFDLQEGNK, EGDQVEFDLQEGNKGLNAVNVK\tEGDQVEFDLQEGNK\tIN; IR; ; \tGL\t15; 15; 1; 1\tNH2-EGDQVEFDLQEGNK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.49000.49000.2\t\t4619.72\t804.36\t2+\t2+\t1606.71109471\t0\t-3.5106289584\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-FGCGYEQGAK, FGCGYEQGAKHINANIK, FGCGYEQGAKHINANIKVLQK, FGCGYEQGAKHINANIKVLQKMTR, FGCGYEQGAKHINANITVLQK, FGCGYEQGAKHINTNITVLQK, SESNTIGFIGGMDIPLIAVFGCGYEQGAK, SETGTIGFVGGMDIPLISRFGCGYEQGAK, SGFVGGMDIPLISRFGCGYEQGAK\tFGCGYEQGAK\tAV; SR; SR\tHI; HI; HI; HI; HI; ; ; \t1; 1; 1; 1; 1; 1; 20; 20; 15\tNH2-FGC<cmm>GYEQGAK-COOH\t\tCarbamidomethylation of C(3)\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.21525.21525.2\t\t2843.8\t558.742780317\t2+\t2+\t1115.47059419\t0\t0.370037388577\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-DVRVAVFTQGENVEK, DVRVAVFTQGENVEKATAAGDRK, EVRVAVFTQGENVEK, GSTVLPNGTGKDVRVAVFTQGENVEK, GSTVLPNGTGKEVRVAVFTQGENVEK, SGKDVRVAVFTQGENVEK, STGKDVRVAVFTQGENVEK, VAVFTQGENVEK\tVAVFTQGENVEK\tVR; VR; VR; VR; VR; VR; VR; \tAT; ; ; ; ; ; \t4; 4; 4; 15; 15; 7; 8; 1\tNH2-VAVFTQGENVEK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.37428.37428.2\t\t3858.93\t660.844070295\t2+\t2+\t1319.67213045\t0\t1.10253902378\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-EVASQTSDVAGDGTTTATVLAQAILNEGLK\tEVASQTSDVAGDGTTTATVLAQAILNEGLK\t\t\t1\tNH2-EVASQTSDVAGDGTTTATVLAQAILNEGLK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.96993.96993.3\t\t7882.73\t987.84\t3+\t3+\t2959.49858926\t1\t-1.27374466447\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-AYAKKVMKYLLMNQPNYKLAYENEFGPIGK, KTMKYLLMNQPNYKLAYENEFGPIGKVK, KVMKYLLMNQPNYKLAYENEFGPIGK, KVMKYLLMNQPNYKLAYENEFGPIGKVK, LAYENEFGPIGK, RTMKYLLMNQPNYKLAYENEFGPIGK, RTMKYLLMNQPNYKLAYENEFGPIGKVK, YLLMNQPNYKLAYENEFGPIGK\tLAYENEFGPIGK\tYK; YK; YK; YK; ; YK; YK; YK\tVK; ; VK; ; ; VK; \t19; 15; 15; 15; 1; 15; 15; 11\tNH2-LAYENEFGPIGK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.58393.58393.2\t\t5223.31\t669.341354352\t2+\t2+\t1336.66631679\t0\t1.37372570057\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-EASLHISNVMLVEDGVAVRVGYQVDGDTK, EASLHISNVMLVEGGVAVRVGYQVDGDTK, KEASLHISNVMLVEDGVAVRVGYQVDGDTK, KEASLHISNVMLVEGGVAVRVGYQVDGDTK, VGYQVDGDTKTR, VGYQVDGDTKTRISK, VGYQVDGDTKTRISKK, VGYQVDGDTKTRVSK\tVGYQVDGDTK\tVR; VR; VR; VR; ; ; ; \tTR; TR; TR; TR\t20; 20; 21; 21; 1; 1; 1; 1\tNH2-VGYQVDGDTK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.20503.20503.2\t\t2780.07\t541.261769908\t2+\t2+\t1080.50875352\t0\t0.215574089053\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-FKDWDDLNKPDVRVAATLGTTQEK, FKDWDDLNKPDVRVAATLGTTQEKQVK, SNADRFKDWDDLNKPDVRVAATLGTTQEK, VAATLGTTQEKQVK, VAATLGTTQEKQVKEYFPNAK, VAATLGTTQEKQVKSYFPDAK\tVAATLGTTQEK\tVR; VR; VR; ; ; \tQV; ; QV; QV; QV\t14; 14; 19; 1; 1; 1\tNH2-VAATLGTTQEK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_4'..b'_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.68946.68946.2\t\t5898.1\t1015.52\t2+\t2+\t2029.02152979\t0\t1.92870904099\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-DVASANKSLGQFNLEGIPNAPK, EIASANKSLGQFNLEGIPNAPK, EVASANKSLGQFNLEGIPNAPK, SLGQFNLEGIPNAPK\tSLGQFNLEGIPNAPK\tNK; NK; NK; \t\t8; 8; 8; 1\tNH2-SLGQFNLEGIPNAPK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.69858.69858.2\t\t5956.17\t792.920609469\t2+\t2+\t1583.83075635\t0\t-2.57928107518\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-AQIEETTSDYDKEKLQERLAK, CNQIRAQIEETTSDYDKEKLQERLAK, DDIAARCNQIRAQIEETTSDYDK\tAQIEETTSDYDK\tIR; IR\tEK; EK; \t1; 6; 12\tNH2-AQIEETTSDYDK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.25447.25447.2\t\t3088.77\t700.32\t2+\t2+\t1398.61506906\t0\t7.40952793854\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-GSNSGTETDFDGK\tGSNSGTETDFDGK\t\t\t1\tNH2-GSNSGTETDFDGK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.16731.16731.2\t\t2545.26\t657.775415728\t2+\t2+\t1313.53715309\t0\t-0.664794466436\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-DHFVHISGLIDEINEGDQVEFDLQEGNK, DHFVHISGLVDEIREGDQVEFDLQEGNK, EGDQVEFDLQEGNK, EGDQVEFDLQEGNKGLNAVNVK\tEGDQVEFDLQEGNK\tIN; IR; ; \tGL\t15; 15; 1; 1\tNH2-EGDQVEFDLQEGNK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.42848.42848.2\t\t4230.29\t804.363314906\t2+\t2+\t1606.71109471\t0\t0.610528847251\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-ETLDVDGVEYPLVK, ETLDVDGVEYPLVKLEISR, ETLDVDGVEYPLVKLEISRTSHPFYTGK, ETLDVDGVEYPLVKLEISRTSHPFYTGKSK, STADTKETLDVDGVEYPLVK, STADTKETLDVDGVEYPLVKLEISR, STAETKETLDVDGVEYPLVK, STAETKETLDVDGVEYPLVKLEISR, STVDTKETLDVDGVEYPLVKLEISR\tETLDVDGVEYPLVK\tTK; TK; TK; TK; TK\tLE; LE; LE; ; LE; ; LE; LE\t1; 1; 1; 1; 7; 7; 7; 7; 7\tNH2-ETLDVDGVEYPLVK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.71416.71416.2\t\t6056.55\t789.41\t2+\t2+\t1575.80320418\t1\t-0.704743199656\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-GTTNGTETDFNGK, SVVIKGTTNGTETDFNGK\tGTTNGTETDFNGK\tIK\t\t1; 6\tNH2-GTTNGTETDFNGK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.15728.15728.2\t\t2482.1\t671.300172985\t2+\t2+\t1340.58443764\t0\t1.00953138271\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-ILTVGDAVNFIAGK\tILTVGDAVNFIAGK\t\t\t1\tNH2-ILTVGDAVNFIAGK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.92389.92389.2\t\t7528.49\t709.407175505\t2+\t2+\t1416.79766531\t0\t1.50320427751\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-AQIESSTSDYDKEK, AQIESSTSDYDKEKLQERLAK, ARINQIKAQIESSTSDYDK, ARINQIKAQIESSTSDYDKEK, ARINQIKAQIESSTSDYDKEKLQER, ARINQIKAQIESSTSDYDKEKLQERLAK, INQIKAQIESSTSDYDKEKLQERLAK\tAQIESSTSDYDK\tIK; IK; IK; IK; IK\tEK; EK; ; EK; EK; EK; EK\t1; 1; 8; 8; 8; 8; 6\tNH2-AQIESSTSDYDK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.20057.20057.2\t\t2752.89\t672.300992424\t2+\t2+\t1342.58885431\t0\t-1.05785835196\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-EGQAVTMEVTQGQK, RSLQEGQKVTMEVTQGQK, SLKEGQAVTMEVTQGQK, SLKEGQAVTMEVTQGQKGAQAENRSEER\tVTMEVTQGQK\tQA; QK; QA; QA\tGA\t5; 9; 8; 8\tNH2-VTMEVTQGQK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.33393.33393.2\t\t3592.24\t560.785120573\t2+\t2+\t1119.55940919\t0\t-3.31764053028\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-DLDKSFGSMPGSMNKKTAGTFASVAK, DLNKSFGSIPGSMNEKTAGTFASVAK, DLNKSFGSIPGSMNKKTAGTFASVAK, DLNKSFGSMPGSMNEKTAGTFASVAK, DLNKSFGSMPGSMNKKTAGTFASVAK, KTAGTFASVAK, SFGSIPGSMNKKTAGTFASVAK, SFGSLPGSMNEKTAGTFASVAK, SFGSMPGSMNEKTAGTFASVAK, SFGSMPGSMNKKTAGTFASVAK, SGSMNKKTAGTFASVAK, TAGTFASVAK\tTAGTFASVAK\tKK; EK; KK; EK; KK; K; KK; EK; EK; KK; KK; \t\t17; 17; 17; 17; 17; 2; 13; 13; 13; 13; 8; 1\tNH2-TAGTFASVAK-COOH\t\t\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.25503.25503.2\t\t3092.13\t476.76\t2+\t2+\t951.502545939\t0\t3.04255362505\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n-CGGEPKPSSQWQGENINR\tCGGEPKPSSQWQGENINR\t\t\t1\tNH2-C<cmm>GGEPKPSSQWQGENINR-COOH\t\tCarbamidomethylation of C(1)\ttrimmed_2016_Jan_12_QE2_47.mgf\t2016_Jan_12_QE2_47.31423.31423.3\t\t3464.93\t681.98\t3+\t3+\t2042.92283589\t0\t-2.28026242106\t\t\t\t99.8278829604\tDoubtful\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\t-1\n' |