| Previous changeset 15:da885fff7cf6 (2019-05-06) Next changeset 17:2952bae8a1ea (2020-01-24) |
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Commit message:
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty |
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modified:
add_protein_features.R add_protein_features.xml proteore_nextprot_ref.loc.sample test-data/Add_information_from_neXtProt.tsv tool_data_table_conf.xml.sample |
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added:
test-data/Lacombe_et_al_2017.tsv tool-data/nextprot_ref_07-05-2019.tsv tool-data/nextprot_ref_08-10-2018.tsv |
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removed:
test-data/FKW_ID_Converter_Lacombe_et_al_2017_OK.tsv tool-data/nextprot_ref_09-03-2019.tsv |
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| diff -r da885fff7cf6 -r 7caa90759aba add_protein_features.R --- a/add_protein_features.R Mon May 06 06:08:26 2019 -0400 +++ b/add_protein_features.R Fri Jun 28 05:05:25 2019 -0400 |
| [ |
| @@ -20,6 +20,7 @@ } get_list_from_cp <-function(list){ + list = gsub(";","\t",list) list = strsplit(list, "[ \t\n]+")[[1]] list = gsub("NA","",list) list = list[list != ""] #remove empty entry |
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| diff -r da885fff7cf6 -r 7caa90759aba add_protein_features.xml --- a/add_protein_features.xml Mon May 06 06:08:26 2019 -0400 +++ b/add_protein_features.xml Fri Jun 28 05:05:25 2019 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="prot_features" name="Add protein features" version="2019.05.06"> +<tool id="prot_features" name="Add protein features" version="2019.06.27.2"> <description>[neXtProt] </description> <requirements> @@ -34,7 +34,7 @@ <inputs> <conditional name="inputtype"> - <param name="filetype" type="select" label="Enter your IDs (neXtProt or UniProt)" help="Copy/paste or from a file" > + <param name="filetype" type="select" label="Enter your IDs (neXtProt or UniProt; e.g. P05090 or NX_P05090)" help="Copy/paste or from a file" > <option value="file" selected="true">Input file containing your IDs </option> <option value="copy_paste">Copy/paste your list of IDs</option> </param> @@ -64,28 +64,30 @@ </conditional> <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false"> - <option value="Uniprot_AC" selected="true">Uniprot accession number</option> - <option value="NextprotID" selected="false">neXtProt IDs</option> + <option value="NextprotID" selected="true">neXtProt IDs</option> + <option value="Uniprot_AC" selected="false">UniProt accession number</option> </param> - <section name="Nextprot_params" title="Select features" expanded="True"> - <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="" display="checkboxes" optional="false"> + <section name="Nextprot_params" title="Select features (Physico-chemical, localization, disease infiormation)" expanded="True"> + <param name="pc_features" type="select" label="Select information to add to your list" multiple="true" help="" display="checkboxes" optional="false"> <option value="SeqLength" selected="false">Sequence Length</option> <option value="MW" selected="false">Molecular Weight</option> <option value="IsoPoint" selected="false">Isoelectric point</option> <option value="TMDomains" selected="false">Number of transmembrane domains</option> <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option> + </param> + + <param name="localization" type="select" label="Localization" multiple="true" help="" display="checkboxes" optional="true"> + <option value="Chr" selected="false">Chromosome</option> + <option value="SubcellLocations" selected="false">Subcellular Location</option> </param> - <param name="localization" type="select" label="Localization" multiple="true" help="" display="checkboxes" optional="true"> - <option value="Chr" selected="false">Chromosome</option> - <option value="SubcellLocations" selected="false">Subcellular Location</option> - </param> - - <param name="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Disease information" /> + <param name="diseases_info" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Disease information" /> </section> <param name="ref_file" type="select" label="Release of neXtProt reference file to use"> - <options from_data_table="proteore_nextprot_ref"/> + <options from_data_table="proteore_nextprot_ref"> + <filter type="sort_by" column="0"/> + </options> </param> </inputs> @@ -101,13 +103,13 @@ <tests> <test> <conditional name="inputtype"> - <param name="filetype " value="file"/> - <param name="genelist" value="FKW_ID_Converter_Lacombe_et_al_2017_OK.tsv"/> + <param name="filetype" value="file"/> + <param name="genelist" value="Lacombe_et_al_2017.tsv"/> <param name="column" value="c1"/> <param name="header" value="true"/> </conditional> - <param name="idtype" value="uniprot"/> + <param name="idtype" value="Uniprot_AC"/> <section name="Nextprot_params"> <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/> @@ -115,6 +117,7 @@ <param name="diseases_info" value="true"/> </section> + <param name="ref_file" value="test-data/cached_locally/nextprot_ref_07-05-2019.tsv"/> <output name="output" file="Add_information_from_neXtProt.tsv"/> </test> </tests> @@ -131,11 +134,15 @@ A list of of Uniprot Accession Number (e.g. P05090) or neXtProt IDs (e.g. NX_P05090) entered in a copy/paste mode or a file containing one or multiple columns with **at least one column of Uniprot accession number or neXtProt IDs**. If your input file contains other type of IDs, please use the ID_Converter tool. +.. class:: warningmark + +In copy/paste mode, the number of IDs considered in input is limited to 5000. + ----- **Parameters** -"Select features": three categories of annotation can be retrieved: physico-chemical features, localisation (chromosome, subcellular) and disease information (set to "Yes" by default). Select each feature according to your interest by clicking the corresponding checkbox. +"Select features": select each feature of your interest by clicking the corresponding checkbox. Disease information is set to "Yes" by default. ----- @@ -147,10 +154,13 @@ **Data source (release date)** -Annotations have been retrieved from the neXtProt released on 21/02/2018 using the latest data from peptideAtlas (release January 2018) +Annotations have been retrieved using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et al., 2017) -using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et al., 2017) - + neXtProt releases : + +- nextProt release 07-05-2019 (release Feb 13, 2019) +- neXtProt release 08-10-2018 (release Feb 21, 2018) + ----- .. class:: infomark @@ -163,7 +173,7 @@ This work has been partially funded through the French National Agency for Research (ANR) IFB project. -Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. +Help: contact@proteore.org for any questions or concerns about this tool. ]]></help> <citations> |
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| diff -r da885fff7cf6 -r 7caa90759aba proteore_nextprot_ref.loc.sample --- a/proteore_nextprot_ref.loc.sample Mon May 06 06:08:26 2019 -0400 +++ b/proteore_nextprot_ref.loc.sample Fri Jun 28 05:05:25 2019 -0400 |
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| @@ -1,3 +1,3 @@ -#<id> <name> <value> -nextprot_ref_08-10-2018 neXtProt release 08-10-2018 tool-data/nextprot_ref_08-10-2018.tsv -nextprot_ref_09-03-2019 neXtProt release 09-03-2019 tool-data/nextprot_ref_09-03-2019.tsv +#<id> <release> <name> <value> +9979818992 nextprot_ref_08-10-2018 neXtProt release 08-10-2018 tool-data/nextprot_ref_08-10-2018.tsv +9979809493 nextprot_ref_07-05-2019 neXtProt release 07-05-2019 tool-data/nextprot_ref_07-05-2019.tsv |
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| diff -r da885fff7cf6 -r 7caa90759aba test-data/Add_information_from_neXtProt.tsv --- a/test-data/Add_information_from_neXtProt.tsv Mon May 06 06:08:26 2019 -0400 +++ b/test-data/Add_information_from_neXtProt.tsv Fri Jun 28 05:05:25 2019 -0400 |
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| b'@@ -1,148 +1,162 @@\n-V1\tneXtProt_ID\tUniProt.AC\tUniProt.ID\tGeneID\tRefSeq\tGI\tPDB\tGO\tPIR\tMIM\tUniGene\tEnsembl\tEnsembl_TRS\tEnsembl_PRO\tSeqLength\tMW\tIsoPoint\tTMDomains\tProteinExistence\tChr\tSubcellLocations\tDiseases\n-P61626\tNX_P61626\tP61626\tLYSC_HUMAN\t4069\tNP_000230.1\t3659963; 7546189; 11513929; 159046751; 157832582; 13399629; 12084272; 550545696; 157833671; 667484857; 9955039; 157833900; 157834290; 3402140; 9955034; 157834712; 1065034; 157834217; 22218809; 157831824; 157834219; 34811083; 157836837; 157835341; 157835054; 4930021; 30750167; 6729883; 157835322; 1065033; 157834715; 14278475; 11513935; 17942573; 157833905; 734458781; 159046750; 159046754; 157833673; 6730357; 550545697; 14278470; 7767015; 9955033; 157831913; 4557894; 12084274; 14278467; 157831912; 17942569; 17942570; 157831552; 14278476; 12084398; 5107557; 157831823; 38492671; 6729884; 157832584; 3659959; 22218808; 270346492; 13399627; 157831359; 157835056; 15825835; 159046753; 14278473; 9955036; 157834714; 219689184; 323462871; 50514025; 6980458; 159046752; 3402139; 9955035; 157834288; 5821956; 12084400; 4930015; 157835338; 6730358; 157834708; 4388847; 157832586; 157835344; 157835340; 157831910; 847820; 12084275; 667484859; 17942567; 157834216; 6729881; 12084397; 157834220; 157831908; 157834707; 353529987; 323462872; 9955030; 13399630; 157834716; 219689182; 6729882; 5821955; 17942572; 7767021; 48428995; 215794704; 13399625; 157834702; 14278474; 157833914; 12084396; 4930017; 157831825; 6729876; 14278471; 7767016; 157834706; 157835339; 159046755; 157831857; 9955031; 157831754; 157831571; 1827553; 6730356; 157833672; 4930014; 157831914; 307141; 17942566; 12084273; 253723297; 15825837; 157831554; 157832581; 9955029; 9256911; 157831553; 9955038; 157834705; 11513931; 5821957; 11514208; 6729879; 4930023; 6980888; 157834291; 12084403; 1827555; 9955327; 219689183; 157835057; 17942574; 157832585; 157834218; 15825836; 157829563; 13399626; 157834711; 24987350; 6729705; 157835053; 157832578; 157835342; 4930020; 157831820; 3659960; 11513937; 9955037; 157834289; 4930022; 157831822; 157833668; 12084409; 157835052; 9955028; 9955032; 157834709; 12084402; 15988350; 4930016; 17942571; 3402142; 17942568; 1335210; 157830185; 157835343; 157832587; 157834292; 157832579; 5107681; 11513927; 13399628; 157834704; 157831853; 157831921; 3659961; 12084399; 6729878; 157834215; 6729880; 157831551; 3402143; 12084401; 6980459; 5107556; 3659962; 157833921; 157834703; 157834710; 6729885; 157832583; 3659958; 157832580; 4388848; 157835055; 6729877; 159046756; 157831821; 9955027; 157829561; 15825838; 11513933; 14278472; 157834713\t133L:A; 134L:A; 1B5U:A; 1B5V:A; 1B5W:A; 1B5X:A; 1B5Y:A; 1B5Z:A; 1B5Z:B; 1B7L:A; 1B7M:A; 1B7N:A; 1B7O:A; 1B7P:A; 1B7Q:A; 1B7R:A; 1B7S:A; 1BB3:A; 1BB3:B; 1BB4:A; 1BB4:B; 1BB5:A; 1BB5:B; 1C43:A; 1C45:A; 1C46:A; 1C7P:A; 1CJ6:A; 1CJ7:A; 1CJ8:A; 1CJ9:A; 1CKC:A; 1CKD:A; 1CKF:A; 1CKG:A; 1CKG:B; 1CKH:A; 1D6P:A; 1D6Q:A; 1DI3:A; 1DI4:A; 1DI5:A; 1EQ4:A; 1EQ5:A; 1EQE:A; 1GAY:A; 1GAZ:A; 1GB0:A; 1GB2:A; 1GB3:A; 1GB5:A; 1GB6:A; 1GB7:A; 1GB8:A; 1GB9:A; 1GBO:A; 1GBW:A; 1GBX:A; 1GBY:A; 1GBZ:A; 1GDW:A; 1GDX:A; 1GE0:A; 1GE1:A; 1GE2:A; 1GE3:A; 1GE4:A; 1GEV:A; 1GEZ:A; 1GF0:A; 1GF3:A; 1GF4:A; 1GF5:A; 1GF6:A; 1GF7:A; 1GF8:A; 1GF9:A; 1GFA:A; 1GFE:A; 1GFG:A; 1GFH:A; 1GFJ:A; 1GFK:A; 1GFR:A; 1GFT:A; 1GFU:A; 1GFV:A; 1HNL:A; 1I1Z:A; 1I20:A; 1I22:A; 1I22:B; 1I22:C; 1I22:D; 1INU:A; 1IOC:A; 1IP1:A; 1IP2:A; 1IP3:A; 1IP3:B; 1IP4:A; 1IP5:A; 1IP6:A; 1IP7:A; 1IP7:B; 1IWT:A; 1IWU:A; 1IWV:A; 1IWW:A; 1IWX:A; 1IWY:A; 1IWZ:A; 1IX0:A; 1IY3:A; 1IY4:A; 1JKA:A; 1JKB:A; 1JKC:A; 1JKD:A; 1JSF:A; 1JWR:A; 1LAA:A; 1LHH:A; 1LHI:A; 1LHJ:A; 1LHK:A; 1LHL:A; 1LHM:A; 1LMT:A; 1LOZ:A; 1LYY:A; 1LZ1:A; 1LZ4:A; 1LZ5:A; 1LZ6:A; 1LZR:A; 1LZS:A; 1LZS:B; 1OP9:B; 1OUA:A; 1OUB:A; 1OUC:A; 1OUD:A; 1OUE:A; 1OUF:A; 1OUG:A; 1OUH:A; 1OUI:A; 1OUJ:A; 1QSW:A; 1QSW:B; 1QSW:C; 1QSW:D; 1RE2:A; 1REM:A; 1REX:A; 1REY:A; 1REZ:A; 1TAY:A; 1TBY:A; 1TCY:A; 1TDY:A; 1UBZ:A; 1W08:A; 1WQM:A; 1WQN:A; 1WQO:A; 1WQP:A; 1WQQ:A; 1WQR:A; 1YAM:A; 1YAN:A; 1YAO:A; 1YAP:A; 1YAQ:A; 207L:A'..b'mia, dominant, inclusion body type;Heinz body anemias;Beta-thalassemia;Sickle cell anemia\n+P78386\tKeratin, type II cuticular Hb5\t 2\t 507\t 55802\t 6.27\t 0\tPE1\t12\tNA\tEctodermal dysplasia 4, hair/nail type\n+P80188\tNeutrophil gelatinase-associated lipocalin\t 3\t 198\t 22588\t 9.02\t 0\tPE1\t9\tCytoplasmic granule lumen;Cytoplasmic vesicle lumen;Endoplasmic reticulum;Secreted\tNA\n+P81605\tDermcidin\t 3\t 110\t 11284\t 6.09\t 0\tPE1\t12\tSecreted\tNA\n+Q01469\tFatty acid-binding protein 5, epidermal\t15\t 135\t 15164\t 6.60\t 0\tPE1\t8\tSynapse;Secreted;Cytosol;Cytoplasm;Cell membrane;Nucleus;Postsynaptic density\tNA\n+Q02413\tDesmoglein-1\t24\t1049\t113748\t 4.90\t 1\tPE1\t18\tDesmosome;Cell membrane\tErythroderma, congenital, with palmoplantar keratoderma, hypotrichosis, and hyper IgE;Palmoplantar keratoderma 1, striate, focal, or diffuse\n+Q04695\tKeratin, type I cytoskeletal 17\t18\t 432\t 48106\t 4.97\t 0\tPE1\t17\tCytoplasm\tSteatocystoma multiplex;Pachyonychia congenita 2\n+Q06830\tPeroxiredoxin-1\t 9\t 199\t 22110\t 8.27\t 0\tPE1\t1\tMitochondrion;Cytoplasm;Melanosome\tNA\n+Q08188\tProtein-glutamine gamma-glutamyltransferase E\t12\t 693\t 76632\t 5.62\t 0\tPE1\t20\tCytoplasm\tUncombable hair syndrome 2\n+Q13867\tBleomycin hydrolase\t 5\t 455\t 52562\t 5.87\t 0\tPE1\t17\tNucleoplasm;Cytoplasm;Nucleus;Cytosol\tNA\n+Q14574\tDesmocollin-3\t 4\t 896\t 99969\t 5.77\t 1\tPE1\t18\tDesmosome;Cell junction;Cell membrane\tHypotrichosis and recurrent skin vesicles\n+Q15149\tPlectin\t15\t4684\t531791\t 5.74\t 0\tPE1\t8\tCytosol;Cytoplasm;Focal adhesion;Hemidesmosome;Cytoskeleton\tLimb-girdle muscular dystrophy 2Q;Epidermolysis bullosa simplex, Ogna type;Epidermolysis bullosa simplex, with muscular dystrophy;Epidermolysis bullosa simplex with nail dystrophy;Epidermolysis bullosa simplex with pyloric atresia\n+Q15828\tCystatin-M\t 3\t 149\t 16511\t 8.32\t 0\tPE1\t11\tCytosol;Cell membrane;Secreted\tNA\n+Q5D862\tFilaggrin-2\t14\t2391\t248073\t 8.45\t 0\tPE1\t1\tCytoplasm;Cytoplasmic granule\tNA\n+Q5T749\tKeratinocyte proline-rich protein\t13\t 579\t 64136\t 8.72\t 0\tPE1\t1\tCytoplasm\tNA\n+Q5T750\tSkin-specific protein 32\t 4\t 250\t 26238\t 8.41\t 0\tPE1\t1\tNA\tNA\n+Q6KB66\tKeratin, type II cytoskeletal 80\t13\t 452\t 50525\t 5.58\t 0\tPE1\t12\tCytoskeleton\tNA\n+Q6P4A8\tPhospholipase B-like 1\t 5\t 553\t 63255\t 9.11\t 0\tPE1\t12\tLysosome\tNA\n+Q6UWP8\tSuprabasin\t 4\t 590\t 60541\t 6.50\t 0\tPE1\t19\tCytoplasmic vesicle;Secreted\tNA\n+Q86YZ3\tHornerin\t11\t2850\t282390\t10.05\t 0\tPE1\t1\tMitochondrion;Cytoplasmic granule\tNA\n+Q8IW75\tSerpin A12\t 3\t 414\t 47175\t 9.31\t 0\tPE1\t14\tSecreted\tNA\n+Q8N1N4\tKeratin, type II cytoskeletal 78\t18\t 520\t 56866\t 5.79\t 0\tPE1\t12\tNA\tNA\n+Q8TAX7\tMucin-7\t 2\t 377\t 39159\t 8.99\t 0\tPE1\t4\tSecreted\tAsthma\n+Q8WVV4\tProtein POF1B\t 8\t 589\t 68065\t 5.89\t 0\tPE1\tX\tNucleoplasm;Tight junction;Golgi apparatus\tPremature ovarian failure 2B\n+Q92820\tGamma-glutamyl hydrolase\t 5\t 318\t 35964\t 6.66\t 0\tPE1\t8\tExtracellular space;Melanosome;Lysosome\tNA\n+Q96DA0\tZymogen granule protein 16 homolog B\t 5\t 208\t 22739\t 6.74\t 0\tPE1\t16\tCytoplasmic vesicle;Nucleoplasm;Secreted\tNA\n+Q96FX8\tp53 apoptosis effector related to PMP-22\t 2\t 193\t 21386\t 6.68\t 4\tPE1\t6\tDesmosome;Cell membrane\tNA\n+Q96P63\tSerpin B12\t 9\t 405\t 46276\t 5.36\t 0\tPE1\t18\tCytoplasm\tNA\n+Q9C075\tKeratin, type I cytoskeletal 23\t 4\t 422\t 48131\t 6.09\t 0\tPE1\t17\tCytosol;Cytoskeleton\tNA\n+Q9HC84\tMucin-5B\t21\t5762\t596340\t 6.20\t 0\tPE1\t11\tCytoplasmic vesicle;Secreted\tPulmonary fibrosis, idiopathic\n+Q9HCY8\tProtein S100-A14\t 3\t 104\t 11662\t 5.16\t 0\tPE1\t1\tCytosol;Cytoplasm;Nucleus;Cell junction;Cell membrane\tNA\n+Q9NZH8\tInterleukin-36 gamma\t 6\t 169\t 18721\t 5.06\t 0\tPE1\t2\tSecreted\tNA\n+Q9NZT1\tCalmodulin-like protein 5\t 8\t 146\t 15893\t 4.34\t 0\tPE1\t10\tCytosol;Cell membrane\tNA\n+Q9UGM3\tDeleted in malignant brain tumors 1 protein\t 6\t2413\t260735\t 5.18\t 0\tPE1\t10\tSecreted;Microtubule organizing center\tGlioma\n+Q9UI42\tCarboxypeptidase A4\t 6\t 421\t 47351\t 6.23\t 0\tPE1\t7\tCytosol;Nucleoplasm;Centrosome;Secreted\tNA\n+Q9UIV8\tSerpin B13\t 2\t 391\t 44276\t 5.48\t 0\tPE1\t18\tCytosol;Cytoplasm;Nucleus speckle\tNA\n+Q9Y6R7\tIgGFc-binding protein\t 3\t5405\t572017\t 5.14\t 0\tPE1\t19\tCytoskeleton;Golgi apparatus;Cell membrane;Secreted\tNA\n' |
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| diff -r da885fff7cf6 -r 7caa90759aba test-data/FKW_ID_Converter_Lacombe_et_al_2017_OK.tsv --- a/test-data/FKW_ID_Converter_Lacombe_et_al_2017_OK.tsv Mon May 06 06:08:26 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,149 +0,0 @@\n-V1\tneXtProt_ID\tUniProt.AC\tUniProt.ID\tGeneID\tRefSeq\tGI\tPDB\tGO\tPIR\tMIM\tUniGene\tEnsembl\tEnsembl_TRS\tEnsembl_PRO\n-\n-P61626\tNX_P61626\tP61626\tLYSC_HUMAN\t4069\tNP_000230.1\t3659963; 7546189; 11513929; 159046751; 157832582; 13399629; 12084272; 550545696; 157833671; 667484857; 9955039; 157833900; 157834290; 3402140; 9955034; 157834712; 1065034; 157834217; 22218809; 157831824; 157834219; 34811083; 157836837; 157835341; 157835054; 4930021; 30750167; 6729883; 157835322; 1065033; 157834715; 14278475; 11513935; 17942573; 157833905; 734458781; 159046750; 159046754; 157833673; 6730357; 550545697; 14278470; 7767015; 9955033; 157831913; 4557894; 12084274; 14278467; 157831912; 17942569; 17942570; 157831552; 14278476; 12084398; 5107557; 157831823; 38492671; 6729884; 157832584; 3659959; 22218808; 270346492; 13399627; 157831359; 157835056; 15825835; 159046753; 14278473; 9955036; 157834714; 219689184; 323462871; 50514025; 6980458; 159046752; 3402139; 9955035; 157834288; 5821956; 12084400; 4930015; 157835338; 6730358; 157834708; 4388847; 157832586; 157835344; 157835340; 157831910; 847820; 12084275; 667484859; 17942567; 157834216; 6729881; 12084397; 157834220; 157831908; 157834707; 353529987; 323462872; 9955030; 13399630; 157834716; 219689182; 6729882; 5821955; 17942572; 7767021; 48428995; 215794704; 13399625; 157834702; 14278474; 157833914; 12084396; 4930017; 157831825; 6729876; 14278471; 7767016; 157834706; 157835339; 159046755; 157831857; 9955031; 157831754; 157831571; 1827553; 6730356; 157833672; 4930014; 157831914; 307141; 17942566; 12084273; 253723297; 15825837; 157831554; 157832581; 9955029; 9256911; 157831553; 9955038; 157834705; 11513931; 5821957; 11514208; 6729879; 4930023; 6980888; 157834291; 12084403; 1827555; 9955327; 219689183; 157835057; 17942574; 157832585; 157834218; 15825836; 157829563; 13399626; 157834711; 24987350; 6729705; 157835053; 157832578; 157835342; 4930020; 157831820; 3659960; 11513937; 9955037; 157834289; 4930022; 157831822; 157833668; 12084409; 157835052; 9955028; 9955032; 157834709; 12084402; 15988350; 4930016; 17942571; 3402142; 17942568; 1335210; 157830185; 157835343; 157832587; 157834292; 157832579; 5107681; 11513927; 13399628; 157834704; 157831853; 157831921; 3659961; 12084399; 6729878; 157834215; 6729880; 157831551; 3402143; 12084401; 6980459; 5107556; 3659962; 157833921; 157834703; 157834710; 6729885; 157832583; 3659958; 157832580; 4388848; 157835055; 6729877; 159046756; 157831821; 9955027; 157829561; 15825838; 11513933; 14278472; 157834713\t133L:A; 134L:A; 1B5U:A; 1B5V:A; 1B5W:A; 1B5X:A; 1B5Y:A; 1B5Z:A; 1B5Z:B; 1B7L:A; 1B7M:A; 1B7N:A; 1B7O:A; 1B7P:A; 1B7Q:A; 1B7R:A; 1B7S:A; 1BB3:A; 1BB3:B; 1BB4:A; 1BB4:B; 1BB5:A; 1BB5:B; 1C43:A; 1C45:A; 1C46:A; 1C7P:A; 1CJ6:A; 1CJ7:A; 1CJ8:A; 1CJ9:A; 1CKC:A; 1CKD:A; 1CKF:A; 1CKG:A; 1CKG:B; 1CKH:A; 1D6P:A; 1D6Q:A; 1DI3:A; 1DI4:A; 1DI5:A; 1EQ4:A; 1EQ5:A; 1EQE:A; 1GAY:A; 1GAZ:A; 1GB0:A; 1GB2:A; 1GB3:A; 1GB5:A; 1GB6:A; 1GB7:A; 1GB8:A; 1GB9:A; 1GBO:A; 1GBW:A; 1GBX:A; 1GBY:A; 1GBZ:A; 1GDW:A; 1GDX:A; 1GE0:A; 1GE1:A; 1GE2:A; 1GE3:A; 1GE4:A; 1GEV:A; 1GEZ:A; 1GF0:A; 1GF3:A; 1GF4:A; 1GF5:A; 1GF6:A; 1GF7:A; 1GF8:A; 1GF9:A; 1GFA:A; 1GFE:A; 1GFG:A; 1GFH:A; 1GFJ:A; 1GFK:A; 1GFR:A; 1GFT:A; 1GFU:A; 1GFV:A; 1HNL:A; 1I1Z:A; 1I20:A; 1I22:A; 1I22:B; 1I22:C; 1I22:D; 1INU:A; 1IOC:A; 1IP1:A; 1IP2:A; 1IP3:A; 1IP3:B; 1IP4:A; 1IP5:A; 1IP6:A; 1IP7:A; 1IP7:B; 1IWT:A; 1IWU:A; 1IWV:A; 1IWW:A; 1IWX:A; 1IWY:A; 1IWZ:A; 1IX0:A; 1IY3:A; 1IY4:A; 1JKA:A; 1JKB:A; 1JKC:A; 1JKD:A; 1JSF:A; 1JWR:A; 1LAA:A; 1LHH:A; 1LHI:A; 1LHJ:A; 1LHK:A; 1LHL:A; 1LHM:A; 1LMT:A; 1LOZ:A; 1LYY:A; 1LZ1:A; 1LZ4:A; 1LZ5:A; 1LZ6:A; 1LZR:A; 1LZS:A; 1LZS:B; 1OP9:B; 1OUA:A; 1OUB:A; 1OUC:A; 1OUD:A; 1OUE:A; 1OUF:A; 1OUG:A; 1OUH:A; 1OUI:A; 1OUJ:A; 1QSW:A; 1QSW:B; 1QSW:C; 1QSW:D; 1RE2:A; 1REM:A; 1REX:A; 1REY:A; 1REZ:A; 1TAY:A; 1TBY:A; 1TCY:A; 1TDY:A; 1UBZ:A; 1W08:A; 1WQM:A; 1WQN:A; 1WQO:A; 1WQP:A; 1WQQ:A; 1WQR:A; 1YAM:A; 1YAN:A; 1YAO:A; 1YAP:A; 1YAQ:A; 207L:A; 208L:A; 2BQA:A; 2BQB:A; 2BQC:A; 2BQD:A; 2BQE:A; 2BQF:A; 2BQG:A; 2BQH:A; 2BQI:'..b'X_P13646\tP13646\tK1C13_HUMAN\t3860\tNP_002265.2; NP_705694.2\t131412228; 6016411; 269849755; 62897663; 3603253; 34033; 21750830; 30377; 131412225; 62897715\tNA\tGO:0005829; GO:0070062; GO:0045111; GO:0045095; GO:0005634; GO:0005198; GO:0071300; GO:0070268; GO:0007010; GO:0031424; GO:0009314; GO:0043587\tA37343; S06088\t148065; 615785\tHs.654550\tENSG00000171401\tENST00000246635; ENST00000336861\tENSP00000246635; ENSP00000336604\n-Q6KB66\tNX_Q6KB66\tQ6KB66\tK2C80_HUMAN\t144501\tNP_001074961.1; NP_872313.2\t119578641; 47846296; 125628632; 40807176; 166218808; 31873640; 125628636; 119578639\tNA\tGO:0005737; GO:0005829; GO:0005882; GO:0045111; GO:0045095; GO:0005198; GO:0070268; GO:0031424\tNA\t611161\tHs.140978\tENSG00000167767\tENST00000313234; ENST00000394815\tENSP00000369361; ENSP00000378292\n-Q8N1N4\tNX_Q8N1N4\tQ8N1N4\tK2C78_HUMAN\t196374\tNP_001287743.1; NP_775487.2\t664806051; 21755908; 89357932; 158255238; 119617056; 57997474; 166218809\tNA\tGO:0005829; GO:0070062; GO:0005615; GO:0045095; GO:0005198; GO:0070268; GO:0031424\tNA\t611159\tHs.665267\tENSG00000170423\tENST00000304620; ENST00000359499\tENSP00000306261; ENSP00000352479\n-P19013\tNX_P19013\tP19013\tK2C4_HUMAN\tNA\tNA\t34073; 82654947; 34077; 38014092; 16209201; 313159; 27769210\tNA\tGO:0009986; GO:0005829; GO:0005882; GO:0045111; GO:0045095; GO:0005634; GO:0005198; GO:0070268; GO:0007010; GO:0030855; GO:0031424; GO:0050680\tI37942\t123940; 193900\tHs.654610; Hs.731814\tENSG00000170477\tENST00000293774; ENST00000551956\tENSP00000293774; ENSP00000448220\n-P19012\tNX_P19012\tP19012\tK1C15_HUMAN\t3866\tNP_002266.2\t12803613; 125081; 24430190; 311033438; 193786870; 193787108; 30583361; 34071; 6729679\tNA\tGO:0005829; GO:0070062; GO:0005882; GO:0005634; GO:0097110; GO:0005200; GO:0070268; GO:0008544; GO:0031424\tS01069\t148030\tHs.654570\tENSG00000171346\tENST00000254043; ENST00000393976\tENSP00000254043; ENSP00000377546\n-Q9C075\tNX_Q9C075\tQ9C075\tK1C23_HUMAN\t25984\tNP_001269362.1; NP_056330.3; XP_005257257.1; XP_011522897.1\t27894339; 539847623; 158259921; 143811410; 530411877; 221043902; 12641919; 7023692; 18202746; 767994237\tNA\tGO:0005829; GO:0005882; GO:0005198; GO:0070268; GO:0031424\tNA\t606194\tHs.9029\tENSG00000108244; ENSG00000263309\tENST00000209718; ENST00000436344; ENST00000571258; ENST00000574480\tENSP00000209718; ENSP00000414056; ENSP00000460637; ENSP00000459021\n-Q04695\tNX_Q04695\tQ04695\tK1C17_HUMAN\t3872\tNP_000413.1\t34075; 148615520; 30379; 21754583; 14198021; 33991652; 119581157; 148615514; 148615518; 4557701; 48735384; 15080273; 148615516; 47939651; 547751; 1000379\tNA\tGO:0071944; GO:0005829; GO:0070062; GO:0005882; GO:0045111; GO:0042289; GO:0032395; GO:0005200; GO:0070268; GO:0008544; GO:0031069; GO:0045109; GO:0031424; GO:0030307; GO:0051798; GO:0045727; GO:0007165\tS30433\t148069; 167210; 184500\tHs.2785\tENSG00000128422\tENST00000311208\tENSP00000308452\n-P08779\tNX_P08779\tP08779\tK1C16_HUMAN\t3868\tNP_005548.2\t23503075; 186685; 4321795; 24659602; 1000377; 1195531; 119581153; 4091879; 24430192; 158255142\tNA\tGO:0005856; GO:0005829; GO:0070062; GO:0005882; GO:0005634; GO:0005200; GO:0007568; GO:0008283; GO:0070268; GO:0007010; GO:0008544; GO:0061436; GO:0042633; GO:0006954; GO:0045087; GO:0045104; GO:0031424; GO:0030216; GO:0051546; GO:0002009; GO:0030336\tA33652; JC4313\t148067; 167200; 613000\tHs.655160\tENSG00000186832\tENST00000301653\tENSP00000301653\n-P02538\tNX_P02538\tP02538\tK2C6A_HUMAN\t3853\tNP_005545.1\t34069; 46812692; 1346344; 5031839; 914833; 15559584\t5KI0:A\tGO:0005829; GO:0070062; GO:0045095; GO:0016020; GO:0005634; GO:0005200; GO:0061844; GO:0030154; GO:0070268; GO:0051801; GO:0050830; GO:0031424; GO:0002009; GO:0001899; GO:2000536; GO:0008284; GO:0042060\tA57398; I61769\t148041; 615726\tHs.700779\tENSG00000205420\tENST00000330722\tENSP00000369317\n-P04259\tNX_P04259\tP04259\tK2C6B_HUMAN\t3854\tNP_005546.2\t1346345; 311396606; 386849; 908790; 908805; 238054404; 119703753; 21961227\tNA\tGO:0005829; GO:0070062; GO:0045095; GO:0005200; GO:0070268; GO:0007398; GO:0031424\tI61767; I61771\t148042; 615728\tHs.708950\tENSG00000185479\tENST00000252252\tENSP00000252252\n' |
| b |
| diff -r da885fff7cf6 -r 7caa90759aba test-data/Lacombe_et_al_2017.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Lacombe_et_al_2017.tsv Fri Jun 28 05:05:25 2019 -0400 |
| [ |
| @@ -0,0 +1,162 @@ +Protein accession number (UniProt) Protein name Number of peptides (razor + unique) +P15924 Desmoplakin 69 +P02538 Keratin, type II cytoskeletal 6A 53 +P02768 Serum albumin 44 +P08779 Keratin, type I cytoskeletal 16 29 +Q02413 Desmoglein-1 24 +P07355 "Annexin A2;Putative annexin A2-like protein" 22 +P14923 Junction plakoglobin 22 +P02788 Lactotransferrin 21 +Q9HC84 Mucin-5B 21 +P29508 Serpin B3 20 +P63261 Actin, cytoplasmic 2 19 +Q8N1N4 Keratin, type II cytoskeletal 78 18 +Q04695 Keratin, type I cytoskeletal 17 18 +P01876 Ig alpha-1 chain C region 16 +Q01469 Fatty acid-binding protein 5, epidermal 15 +P31944 Caspase-14 15 +P01833 Polymeric immunoglobulin receptor 15 +P06733 Alpha-enolase 15 +P25311 Zinc-alpha-2-glycoprotein 15 +Q15149 Plectin 15 +P19013 Keratin, type II cytoskeletal 4 13 +Q6KB66 Keratin, type II cytoskeletal 80 13 +Q08188 Protein-glutamine gamma-glutamyltransferase E 12 +P13646 Keratin, type I cytoskeletal 13 11 +Q86YZ3 Hornerin 11 +P04259 Keratin, type II cytoskeletal 6B 10 +P02545 "Prelamin-A/C;Lamin-A/C" 10 +P04083 Annexin A1 10 +P11021 78 kDa glucose-regulated protein 10 +P02787 Serotransferrin 9 +P04040 Catalase 9 +P31151 Protein S100-A7 9 +P31947 14-3-3 protein sigma 9 +Q96P63 Serpin B12 9 +P14618 Pyruvate kinase PKM 9 +P60174 Triosephosphate isomerase 9 +Q06830 Peroxiredoxin-1 9 +P01040 Cystatin-A 8 +P05089 Arginase-1 8 +P01834 Ig kappa chain C region 8 +P04406 Glyceraldehyde-3-phosphate dehydrogenase 8 +P0DMV9 Heat shock 70 kDa protein 1B 8 +P13639 Elongation factor 2 8 +P35579 Myosin-9 8 +P68371 Tubulin beta-4B chain 8 +Q8WVV4 Protein POF1B 8 +O75635 Serpin B7 7 +P01857 Ig gamma-1 chain C region 7 +P61626 Lysozyme C 7 +P68363 Tubulin alpha-1B chain 7 +P01009 "Alpha-1-antitrypsin;Short peptide from AAT" 6 +P07900 Heat shock protein HSP 90-alpha 6 +Q9NZH8 Interleukin-36 gamma 6 +O43707 "Alpha-actinin-4;Alpha-actinin-1" 6 +O75223 Gamma-glutamylcyclotransferase 6 +P00338 L-lactate dehydrogenase A chain 6 +P07339 Cathepsin D 6 +P62987 Ubiquitin-60S ribosomal protein L40 6 +P10599 Thioredoxin 6 +Q9UGM3 Deleted in malignant brain tumors 1 protein 6 +Q9UI42 Carboxypeptidase A4 6 +P47929 Galectin-7 5 +Q13867 Bleomycin hydrolase 5 +Q6P4A8 Phospholipase B-like 1 5 +O75369 Filamin-B 5 +P00441 Superoxide dismutase [Cu-Zn] 5 +P04792 Heat shock protein beta-1 5 +P11142 Heat shock cognate 71 kDa protein 5 +P58107 Epiplakin 5 +P60842 Eukaryotic initiation factor 4A-I 5 +P62937 Peptidyl-prolyl cis-trans isomerase A 5 +P63104 14-3-3 protein zeta/delta 5 +Q92820 Gamma-glutamyl hydrolase 5 +O75342 Arachidonate 12-lipoxygenase, 12R-type 4 +P09211 Glutathione S-transferase P 4 +P31025 Lipocalin-1 4 +P48594 Serpin B4 4 +Q14574 Desmocollin-3 4 +Q5T750 Skin-specific protein 32 4 +Q6UWP8 Suprabasin 4 +O60911 Cathepsin L2 4 +P00558 Phosphoglycerate kinase 1 4 +P04075 Fructose-bisphosphate aldolase A 4 +P07384 Calpain-1 catalytic subunit 4 +P0CG05 Ig lambda-2 chain C regions 4 +P18206 Vinculin 4 +P62258 14-3-3 protein epsilon 4 +P68871 Hemoglobin subunit beta 4 +Q9C075 Keratin, type I cytoskeletal 23 4 +A8K2U0 Alpha-2-macroglobulin-like protein 1 3 +P00738 Haptoglobin 3 +P01011 Alpha-1-antichymotrypsin 3 +P02763 Alpha-1-acid glycoprotein 1 3 +P18510 Interleukin-1 receptor antagonist protein 3 +P22528 Cornifin-B 3 +P30740 Leukocyte elastase inhibitor 3 +P80188 Neutrophil gelatinase-associated lipocalin 3 +Q15828 Cystatin-M 3 +Q9HCY8 Protein S100-A14 3 +P01623 Ig kappa chain V-III region 3 +P01877 Ig alpha-2 chain C region 3 +P06396 Gelsolin 3 +P14735 Insulin-degrading enzyme 3 +P20933 N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase 3 +P25788 Proteasome subunit alpha type-3 3 +P26641 Elongation factor 1-gamma 3 +P36952 Serpin B5 3 +P40926 Malate dehydrogenase, mitochondrial 3 +Q9Y6R7 IgGFc-binding protein 3 +O95274 Ly6/PLAUR domain-containing protein 3 2 +P00491 Purine nucleoside phosphorylase 2 +P04080 Cystatin-B 2 +P09972 Fructose-bisphosphate aldolase C 2 +P19012 Keratin, type I cytoskeletal 15 2 +P20930 Filaggrin 2 +Q96FX8 p53 apoptosis effector related to PMP-22 2 +Q9UIV8 Serpin B13 2 +P01625 Ig kappa chain V-IV region Len 2 +P01765 Ig heavy chain V-III region TIL 2 +P01766 Ig heavy chain V-III region BRO 2 +P01860 Ig gamma-3 chain C region 2 +P01871 Ig mu chain C region 2 +P05090 Apolipoprotein D 2 +P06870 Kallikrein-1 2 +P07858 Cathepsin B 2 +P08865 40S ribosomal protein SA 2 +P11279 Lysosome-associated membrane glycoprotein 1 2 +P13473 Lysosome-associated membrane glycoprotein 2 2 +P19971 Thymidine phosphorylase 2 +P23284 Peptidyl-prolyl cis-trans isomerase B 2 +P23396 40S ribosomal protein S3 2 +P25705 ATP synthase subunit alpha, mitochondrial 2 +P27482 Calmodulin-like protein 3 2 +P31949 Protein S100-A11 2 +P40121 Macrophage-capping protein 2 +P42357 Histidine ammonia-lyase 2 +P47756 F-actin-capping protein subunit beta 2 +P48637 Glutathione synthetase 2 +P49720 Proteasome subunit beta type-3 2 +P50395 Rab GDP dissociation inhibitor beta 2 +P59998 Actin-related protein 2/3 complex subunit 4 2 +P61160 Actin-related protein 2 2 +P61916 Epididymal secretory protein E1 2 +P04745 Alpha-amylase 1 23 +Q9NZT1 Calmodulin-like protein 5 8 +P12273 Prolactin-inducible protein 6 +Q96DA0 Zymogen granule protein 16 homolog B 5 +P01036 Cystatin-S 5 +Q8TAX7 Mucin-7 2 +P01037 Cystatin-SN 2 +P09228 Cystatin-SA 2 +P04264 Keratin, type II cytoskeletal 1 61 +P35908 Keratin, type II cytoskeletal 2 epidermal 40 +P13645 Keratin, type I cytoskeletal 10 40 +Q5D862 Filaggrin-2 14 +Q5T749 Keratinocyte proline-rich protein 13 +Q8IW75 Serpin A12 3 +P81605 Dermcidin 3 +P22531 Small proline-rich protein 2E 3 +P59666 Neutrophil defensin 3 2 +P78386 Keratin, type II cuticular Hb5 2 |
| b |
| diff -r da885fff7cf6 -r 7caa90759aba tool-data/nextprot_ref_07-05-2019.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/nextprot_ref_07-05-2019.tsv Fri Jun 28 05:05:25 2019 -0400 |
| b |
| b'@@ -0,0 +1,20400 @@\n+NextprotID\tMW\tSeqLength\tIsoPoint\tChr\tSubcellLocations\tDiseases\tTMDomains\tProteinExistence\r\n+NX_A0A024RBG1\t20434\t181\t5.99\t1\tCytoplasm\tNA\t0\tPE1\r\n+NX_A0A075B6H9\t12773\t119\t6.01\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6I0\t12814\t122\t4.33\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6I1\t12987\t120\t5.8\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6I4\t12395\t117\t7.85\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6I9\t12468\t117\t6.69\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6J1\t13277\t123\t4.75\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6J6\t12549\t115\t3.95\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6J9\t12412\t118\t4.66\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6K0\t12466\t115\t4.58\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6K2\t12387\t115\t5.34\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6K4\t12441\t115\t4.72\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6K5\t12332\t115\t6.81\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6K6\t13330\t122\t5.39\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6N1\t12769\t114\t6.53\t7\tCell membrane\tNA\t0\tPE1\r\n+NX_A0A075B6N2\t12175\t111\t8.52\t7\tCell membrane\tNA\t0\tPE1\r\n+NX_A0A075B6N3\t12929\t115\t7.68\t7\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6N4\t12983\t114\t5.91\t7\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6P5\t12957\t120\t5.61\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6Q5\t12891\t118\t7.69\t14\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6R2\t12848\t117\t9.64\t14\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6S2\t13143\t120\t6.53\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6S4\t12835\t117\t9.22\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6S5\t12712\t117\t8.5\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A075B6S6\t13215\t120\t7.79\t2\tCell membrane;Secreted\tNA\t0\tPE3\r\n+NX_A0A075B6T6\t12838\t113\t6.17\t14\tCell membrane\tNA\t0\tPE1\r\n+NX_A0A075B6T7\t15362\t132\t9.2\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6T8\t12354\t112\t4.83\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6U4\t12598\t112\t8.39\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6V5\t12697\t113\t6.57\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6W5\t13545\t121\t8.45\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6X5\t12414\t111\t5.26\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A075B6Y3\t2097\t20\t11\t14\tCell membrane\tNA\t0\tPE4\r\n+NX_A0A075B706\t1761\t16\t8.26\t14\tCell membrane\tNA\t0\tPE1\r\n+NX_A0A075B759\t18197\t164\t9.43\t1\tCytoplasm\tNA\t0\tPE3\r\n+NX_A0A075B767\t18208\t164\t9.19\t1\tCytoplasm\tNA\t0\tPE3\r\n+NX_A0A087WSX0\t13162\t123\t6.69\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A087WSY4\t13025\t118\t9.7\t3\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A087WSY6\t12534\t115\t5.14\t2\tCell membrane;Secreted\tNA\t0\tPE3\r\n+NX_A0A087WSZ0\t12837\t117\t7.62\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A087WSZ9\t12582\t112\t8.58\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A087WT01\t12043\t109\t5.7\t14\tCell membrane\tNA\t0\tPE1\r\n+NX_A0A087WT02\t12289\t112\t5.26\t14\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A087WT03\t12306\t109\t7.76\t14\tCell membrane\tNA\t0\tPE1\r\n+NX_A0A087WTH1\t11832\t108\t7.61\t16\tMembrane\tNA\t2\tPE2\r\n+NX_A0A087WTH5\t15028\t132\t8.73\t21\tMembrane\tNA\t1\tPE3\r\n+NX_A0A087WUL8\t440408\t3843\t4.53\t1\tCytoplasm\tNA\t0\tPE5\r\n+NX_A0A087WV62\t12845\t115\t6.7\t7\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A087WVF3\t62187\t549\t9.2\t17\tCell membrane\tNA\t0\tPE2\r\n+NX_A0A087WW87\t13310\t121\t4.43\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n+NX_A0A087WX78\t41674\t387\t8.87\t18\tNucleus\tNA\t0\tPE5\r\n+NX_A0A087WXM9\t40829\t373\t8.65\t5\tKinetochore;Centromere\tNA\t0\tPE1\r\n+NX_A0A087WXS9\t62205\t549\t9.2\t17\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A087X0M5\t13028\t115\t9.14\t7\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A087X179\t62131\t549\t9.18\t17\tCell membrane\tNA\t0\tPE2\r\n+NX_A0A087X1C5\t57489\t515\t8.7\t22\tMitochondrion;Cytoplasm;Membrane\tNA\t2\tPE5\r\n+NX_A0A087X1G2\t62171\t549\t9.23\t17\tCell membrane\tNA\t0\tPE3\r\n+NX_A0A096LNP1\t8156\t70\t8.26\t11\tSecreted\tNA\t0\tPE2\r\n+NX_A0A096LP01\t10908\t95\t6.24\t20\tNucleoplasm;Cytosol;Membrane\tNA\t1\tPE1\r\n+NX_A0A096LP49\t114856\t1063\t9.76\t9\tNA\tNA\t0\tPE1\r\n+NX_A0A096LP55\t10752\t91\t4.39\t1\tMitochondrion inner membrane\tNA\t0\tPE3\r\n+NX_A0A096LPI5\t11989\t108\t8.8\t6\tNA\tNA\t0\tPE4\r\n+NX_A0A0A0MRZ7\t13297\t120\t4.9\t2\tCell membrane;Secreted\tNA\t0\tPE3\r\n+NX_A0A0A0MRZ8\t12625\t115\t5.15\t2\tCell membrane;Secreted\tNA\t0\tPE3\r\n+NX_A0A0A0MRZ9\t13446\t124\t7.76\t22\tCell m'..b'227\t1575\t6.14\t9\tBasement membrane\tCortical malformations occipital\t0\tPE1\r\n+NX_Q9Y6N7\t180930\t1651\t5.7\t3\tAxon;Endoplasmic reticulum-Golgi intermediate compartment membrane;Cell membrane\tNA\t1\tPE1\r\n+NX_Q9Y6N8\t88451\t788\t4.83\t5\tCell membrane\tNA\t1\tPE1\r\n+NX_Q9Y6N9\t62211\t552\t5.36\t11\tCytosol;Microvillus;Cytoskeleton\tDeafness, autosomal recessive, 18A;Usher syndrome 1C\t0\tPE1\r\n+NX_Q9Y6P5\t56557\t492\t5.68\t6\tCytoplasm;Nucleolus;Nucleus\tNA\t0\tPE1\r\n+NX_Q9Y6Q1\t74576\t641\t6.62\tX\tCytosol;Perinuclear region;Spindle\tNA\t0\tPE1\r\n+NX_Q9Y6Q2\t83141\t735\t5.82\t2\tCytoplasm;Membrane\tNA\t0\tPE1\r\n+NX_Q9Y6Q3\t71209\t630\t9.26\t9\tCytoplasmic vesicle;Nucleus\tNA\t0\tPE1\r\n+NX_Q9Y6Q5\t48108\t423\t8.23\t19\tCytoplasmic vesicle;Clathrin-coated vesicle membrane;Golgi apparatus\tNA\t0\tPE1\r\n+NX_Q9Y6Q6\t66034\t616\t5.21\t18\tCytosol;Cell membrane\tPaget disease of bone 2, early-onset;Osteopetrosis, autosomal recessive 7;Familial expansile osteolysis\t1\tPE1\r\n+NX_Q9Y6Q9\t155293\t1424\t7.16\t20\tCytosol;Nucleoplasm;Nucleus;Cytoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6R0\t64891\t609\t9.1\t19\tCytoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6R1\t121461\t1079\t6.35\t4\tBasolateral cell membrane\tRenal tubular acidosis, proximal, with ocular abnormalities and mental retardation\t12\tPE1\r\n+NX_Q9Y6R4\t181685\t1608\t5.94\t6\tCytosol;Perinuclear region\tNA\t0\tPE1\r\n+NX_Q9Y6R6\t96807\t833\t9.17\t19\tNucleus\tNA\t0\tPE1\r\n+NX_Q9Y6R7\t572017\t5405\t5.14\t19\tCytoskeleton;Golgi apparatus;Cell membrane;Secreted\tNA\t0\tPE1\r\n+NX_Q9Y6R9\t57368\t512\t10.27\t19\tNucleus\tNA\t0\tPE1\r\n+NX_Q9Y6S9\t60036\t549\t7.06\t14\tNucleoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6T7\t90595\t804\t8.11\t7\tCytoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6U3\t80489\t715\t5.5\t7\tCytoskeleton;Podosome;Cell membrane\tNA\t0\tPE1\r\n+NX_Q9Y6U7\t41101\t377\t8.98\t22\tCytoskeleton;Nucleolus;Membrane\tNA\t2\tPE2\r\n+NX_Q9Y6V0\t560699\t5142\t6.07\t7\tNucleus speckle;Synapse;Cell membrane\tPontocerebellar hypoplasia 3\t0\tPE1\r\n+NX_Q9Y6V7\t54226\t483\t9.21\t19\tMitochondrion;Nucleolus\tNA\t0\tPE1\r\n+NX_Q9Y6W3\t92652\t813\t7.55\t3\tNucleus\tNA\t0\tPE1\r\n+NX_Q9Y6W5\t54284\t498\t5.38\t1\tCytosol;Cytoplasm;Cytoskeleton;Cell membrane;Lamellipodium\tNA\t0\tPE1\r\n+NX_Q9Y6W6\t52642\t482\t7.87\t1\tCytosol;Nucleoplasm;Nucleus;Golgi apparatus;Cytoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6W8\t22625\t199\t9.01\t2\tCell membrane;Secreted\tImmunodeficiency, common variable, 1\t1\tPE1\r\n+NX_Q9Y6X0\t175008\t1596\t9.76\t18\tCytosol;Nucleus\tSchinzel-Giedion midface retraction syndrome;Leukemia, acute myelogenous;Leukemia, juvenile myelomonocytic;Myelodysplastic syndrome;Mental retardation, autosomal dominant 29;Leukemia, chronic myeloid, atypical\t0\tPE1\r\n+NX_Q9Y6X1\t7374\t66\t11.01\t3\tEndoplasmic reticulum membrane;Endoplasmic reticulum;Cell membrane;Membrane\tNA\t1\tPE1\r\n+NX_Q9Y6X2\t68017\t628\t7.81\t1\tNucleoplasm;Nucleus speckle;Nucleus;Cytoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6X3\t69082\t613\t6.84\t19\tNucleoplasm;Nucleus;Chromosome\tNA\t0\tPE1\r\n+NX_Q9Y6X4\t74955\t670\t4.52\t5\tCytosol;Nucleus inner membrane;Nucleus envelope;Nucleus membrane\tNA\t0\tPE1\r\n+NX_Q9Y6X5\t51641\t453\t5.71\t6\tCell membrane\tNA\t1\tPE1\r\n+NX_Q9Y6X6\t206129\t1858\t6.37\t13\tCytoplasmic vesicle;Cytoplasm\tNA\t0\tPE1\r\n+NX_Q9Y6X8\t92307\t837\t6.42\t8\tNucleoplasm;Nucleus\tNA\t0\tPE1\r\n+NX_Q9Y6X9\t117823\t1032\t8.6\t22\tCytosol;Nucleus\tCharcot-Marie-Tooth disease 2Z\t0\tPE1\r\n+NX_Q9Y6Y0\t71729\t642\t5.33\t1\tNucleoplasm;Cytoplasm;Cytoskeleton;Cytosol\tNA\t0\tPE1\r\n+NX_Q9Y6Y1\t183672\t1673\t7.29\t1\tCytosol;Cytoplasm;Nucleolus;Nucleus\tCerebellar ataxia, non-progressive, with mental retardation\t0\tPE1\r\n+NX_Q9Y6Y8\t111076\t1000\t5.35\t10\tCytoplasmic vesicle;COPII-coated vesicle membrane;Endoplasmic reticulum\tNA\t0\tPE1\r\n+NX_Q9Y6Y9\t18546\t160\t8.8\t8\tCytoplasmic vesicle;Extracellular space;Secreted\tNA\t0\tPE1\r\n+NX_Q9Y6Z2\t6189\t57\t5.98\t6\tNA\tNA\t0\tPE4\r\n+NX_Q9Y6Z4\t19411\t181\t9.48\t6\tNA\tNA\t0\tPE5\r\n+NX_Q9Y6Z5\t26128\t254\t11.81\t6\tNA\tNA\t0\tPE5\r\n+NX_Q9Y6Z7\t30705\t277\t6.96\t8\tCytoplasm;Golgi apparatus;Secreted\t3MC syndrome 3\t0\tPE1\r\n+NX_Q9YNA8\t74183\t666\t9.05\t19\tCell membrane\tNA\t0\tPE1\r\n+NX_S4R3P1\t2751\t24\t5.87\t4\tCytoplasm;Secreted\tNA\t0\tPE3\r\n+NX_S4R3Y5\t2737\t24\t7.98\t1\tCytoplasm;Secreted\tNA\t0\tPE2\r\n+NX_U3KPV4\t38754\t340\t9.39\t1\tGolgi stack membrane\tNA\t1\tPE2\r\n+NX_W5XKT8\t36333\t324\t6.15\t19\tMembrane\tNA\t1\tPE1\r\n+NX_W6CW81\t12732\t113\t5.57\t1\tNA\tNA\t0\tPE1\r\n' |
| b |
| diff -r da885fff7cf6 -r 7caa90759aba tool-data/nextprot_ref_08-10-2018.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/nextprot_ref_08-10-2018.tsv Fri Jun 28 05:05:25 2019 -0400 |
| b |
| b'@@ -0,0 +1,20231 @@\n+NextprotID\tMW\tSeqLength\tIsoPoint\tChr\tSubcellLocations\tDiseases\tTMDomains\tProteinExistence\n+NX_Q7RTS7\t57865\t529\t7.59\t12\tNA\tEctodermal dysplasia 7, hair/nail type;Woolly hair autosomal dominant;Hypotrichosis 3\t0\tPE1\n+NX_Q7RTS9\t75935\t669\t5.56\t18\tGolgi apparatus;Cytoplasm;Golgi apparatus;Membrane\tSmith-McCort dysplasia 1;Dyggve-Melchior-Clausen syndrome\t0\tPE1\n+NX_Q7RTT3\t21553\t188\t9.19\tX\tNA\tNA\t0\tPE2\n+NX_Q7RTT4\t21859\t187\t9.46\tX\tNA\tNA\t0\tPE2\n+NX_Q7RTT5\t21591\t188\t9.19\tX\tNA\tNA\t0\tPE2\n+NX_Q7RTT6\t21688\t188\t9.32\tX\tNA\tNA\t0\tPE5\n+NX_Q7RTT9\t58059\t530\t7.64\t7\tCytoskeleton;Cytoskeleton;Apical cell membrane;Cell membrane\tNA\t10\tPE1\n+NX_Q7RTU0\t17516\t167\t10.24\t8\tNucleus\tNA\t0\tPE3\n+NX_Q7RTU1\t23309\t214\t11.33\t2\tNucleus\tNA\t0\tPE2\n+NX_Q7RTU3\t29358\t272\t9.54\t6\tNucleus\tNA\t0\tPE1\n+NX_Q7RTU4\t24132\t235\t11.21\t17\tNucleus;Cytoplasm\tCamptosynpolydactyly, complex;Syndactyly, mesoaxial synostotic, with phalangeal reduction;Split-hand/foot malformation with long bone deficiency 3\t0\tPE1\n+NX_Q7RTU5\t29462\t278\t8.71\t1\tNucleus\tNA\t0\tPE3\n+NX_Q7RTU7\t21596\t201\t10.17\t8\tNucleus\tNA\t0\tPE3\n+NX_Q7RTU9\t192967\t1775\t5.27\t15\tKinocilium;Stereocilium;Cell surface\tDeafness, autosomal recessive, 16;Deafness-infertility syndrome\t0\tPE2\n+NX_Q7RTV0\t12405\t110\t8.79\t22\tNucleoplasm;Nucleus;Nucleus speckle\tNA\t0\tPE1\n+NX_Q7RTV2\t25722\t222\t7.74\t6\tCytoplasm\tNA\t0\tPE1\n+NX_Q7RTV3\t38411\t350\t8.07\t9\tNucleus;Nucleoplasm\tNA\t0\tPE1\n+NX_Q7RTV5\t24857\t226\t9.07\t9\tNA\tNA\t0\tPE1\n+NX_Q7RTW8\t128533\t1153\t5.53\t16\tExtracellular matrix;Apical cell membrane\tDeafness, autosomal recessive, 22\t0\tPE1\n+NX_Q7RTX0\t93386\t852\t6.75\t1\tCell membrane\tNA\t7\tPE1\n+NX_Q7RTX1\t93074\t841\t8.32\t1\tCell membrane\tNA\t7\tPE2\n+NX_Q7RTX7\t54092\t472\t5.15\t1\tFlagellum membrane\tNA\t6\tPE1\n+NX_Q7RTX9\t56254\t510\t6.45\t2\tCytosol;Cell membrane\tNA\t12\tPE2\n+NX_Q7RTY0\t44992\t426\t6.44\t17\tGolgi apparatus;Golgi apparatus membrane;Cell membrane\tDiabetes mellitus, non-insulin-dependent\t12\tPE1\n+NX_Q7RTY1\t55794\t509\t8.25\t10\tCell membrane;Cell junction;Nucleus\tNA\t12\tPE1\n+NX_Q7RTY3\t29329\t260\t8.42\t3\tNA\tNA\t0\tPE2\n+NX_Q7RTY5\t35970\t328\t7.49\t4\tSecreted\tNA\t0\tPE2\n+NX_Q7RTY7\t125066\t1134\t8.67\t12\tSecreted\tNA\t0\tPE1\n+NX_Q7RTY8\t94415\t843\t8.84\t3\tCell membrane\tNA\t1\tPE2\n+NX_Q7RTY9\t35078\t318\t9.36\t16\tCell membrane\tNA\t0\tPE1\n+NX_Q7RTZ1\t62642\t564\t7.22\t11\tSecreted\tNA\t0\tPE1\n+NX_Q7RTZ2\t59590\t530\t7.81\t8\tEndoplasmic reticulum;Nucleus\tNA\t0\tPE3\n+NX_Q7Z2D5\t82983\t763\t9\t1\tMembrane\tNA\t6\tPE1\n+NX_Q7Z2E3\t40740\t356\t9.27\t9\tCytoplasm;Nucleolus;Nucleus;Nucleoplasm;Nucleolus\tAtaxia-oculomotor apraxia syndrome\t0\tPE1\n+NX_Q7Z2F6\t14454\t126\t4.9\t16\tNucleoplasm;Cytosol\tNA\t0\tPE2\n+NX_Q7Z2G1\t19618\t175\t10.69\tX\tNucleus membrane;Chromosome\tNA\t0\tPE1\n+NX_Q7Z2H8\t53076\t476\t6.54\t5\tEndoplasmic reticulum;Cell membrane;Lysosome membrane\tNA\t11\tPE1\n+NX_Q7Z2K6\t100231\t904\t7.2\t9\tNucleus;Nucleolus;Endoplasmic reticulum membrane\tNA\t9\tPE1\n+NX_Q7Z2K8\t102399\t1008\t8.33\t5\tCell membrane;Cytoplasmic vesicle;Cell membrane;Growth cone\tNA\t0\tPE1\n+NX_Q7Z2Q7\t70301\t622\t9.02\t5\tMembrane\tNA\t1\tPE2\n+NX_Q7Z2R9\t10995\t100\t12.15\t1\tSecreted\tNA\t0\tPE5\n+NX_Q7Z2T5\t81747\t733\t8.11\t1\tNucleolus;Nucleus\tNA\t0\tPE1\n+NX_Q7Z2V1\t23111\t217\t6.41\t16\tNA\tNA\t0\tPE1\n+NX_Q7Z2W4\t101431\t902\t8.72\t7\tCytosol;Nucleus;Golgi apparatus;Cytoplasm\tNA\t0\tPE1\n+NX_Q7Z2W7\t127685\t1104\t6.91\t2\tCell membrane;Membrane raft;Endoplasmic reticulum membrane\tNA\t6\tPE1\n+NX_Q7Z2W9\t22815\t205\t9.91\t11\tNucleoplasm;Mitochondrion;Mitochondrion\tNA\t0\tPE1\n+NX_Q7Z2X4\t28272\t250\t6.53\t2\tEndoplasmic reticulum;Cytoplasm\tNA\t0\tPE1\n+NX_Q7Z2X7\t12090\t111\t4\tX\tNA\tNA\t0\tPE1\n+NX_Q7Z2Y5\t178479\t1582\t5.93\tX\tCytoplasm;Cytosol;Nucleoplasm\tNA\t0\tPE1\n+NX_Q7Z2Y8\t279048\t2422\t6.12\t11\tCytosol;Nucleus\tNA\t0\tPE2\n+NX_Q7Z2Z1\t210857\t1910\t9\t15\tNucleus;Nucleoplasm\tNA\t0\tPE1\n+NX_Q7Z2Z2\t125430\t1120\t5.66\t15\tCytosol\tNA\t0\tPE1\n+NX_Q7Z304\t77556\t686\t5.05\t9\tEndoplasmic reticulum;Extracellular matrix\tNA\t0\tPE1\n+NX_Q7Z309\t26928\t247\t5.98\tX\tNucleus;Nucleoplasm\tNA\t0\tPE1\n+NX_Q7Z333\t302880\t2677\t6.83\t9\tCytoskeleton;Nucleus;Nucleolus;Nucleus;Nucleoplasm;Cytoplasm;Chromosome;Telomere;Axon;Growth cone\tSpinocerebellar ataxia, autosomal recessive, 1;Amyotrophic lateral sclerosis 4'..b'3\t36596\t318\t8.13\t16\tCytoskeleton;Membrane;Cytosol;Nucleoplasm;Perinuclear region;Endoplasmic reticulum\tNA\t2\tPE1\n+NX_Q7L5N1\t36163\t327\t5.47\t7\tNucleus;Nucleoplasm;Nucleus;Cytoplasm\tNA\t0\tPE1\n+NX_Q7L5N7\t60208\t544\t6.14\t16\tLipid droplet;Golgi apparatus membrane;Endoplasmic reticulum membrane;Lipid droplet;Endoplasmic reticulum\tNA\t1\tPE1\n+NX_Q7L5Y1\t49786\t443\t6.03\t18\tMitochondrion\tNA\t0\tPE1\n+NX_Q7L5Y6\t63848\t550\t7.32\t15\tNucleoplasm;Cytoskeleton;Nucleus\tNA\t0\tPE1\n+NX_Q7L5Y9\t45287\t396\t8.95\t4\tNucleoplasm;Nucleus matrix;Cell membrane;Cytoskeleton\tNA\t0\tPE1\n+NX_Q7L622\t80504\t706\t7.9\t14\tCytoplasm;Nucleolus\tNA\t0\tPE1\n+NX_Q7L775\t70370\t607\t5.77\t3\tEndoplasmic reticulum\tNA\t0\tPE1\n+NX_Q7L7L0\t14121\t130\t11.05\t1\tNucleus;Chromosome\tNA\t0\tPE1\n+NX_Q7L7V1\t84419\t743\t4.88\t10\tNucleus;Mitochondrion\tNA\t0\tPE1\n+NX_Q7L7X3\t116070\t1001\t7.3\t17\tCytoplasm\tNA\t0\tPE1\n+NX_Q7L804\t58279\t512\t9.33\t10\tCytoplasmic vesicle;Nucleoplasm;Cell membrane;Recycling endosome membrane\tNA\t0\tPE1\n+NX_Q7L8A9\t40957\t365\t9.5\t14\tSecreted\tNA\t0\tPE1\n+NX_Q7L8C5\t46885\t426\t7.6\t11\tGolgi apparatus;Cytoplasmic vesicle;Membrane\tNA\t1\tPE1\n+NX_Q7L8J4\t43499\t393\t5.57\t1\tGolgi apparatus;Cytoplasmic vesicle;Nucleoplasm\tNA\t0\tPE1\n+NX_Q7L8L6\t86574\t764\t8.41\t20\tMitochondrion nucleoid\tNA\t0\tPE1\n+NX_Q7L8S5\t33300\t288\t6.29\tX\tNA\tNA\t0\tPE1\n+NX_Q7L8W6\t30307\t267\t5.24\t15\tNucleus;Nucleolus\tNA\t0\tPE1\n+NX_Q7L945\t52853\t461\t9.18\t19\tNucleolus;Nucleus;Nucleus\tNA\t0\tPE1\n+NX_Q7L985\t68066\t606\t8.44\t9\tMembrane\tNA\t1\tPE1\n+NX_Q7L9B9\t62403\t569\t8.64\t7\tNucleus speckle;Cytoplasmic vesicle;Cell membrane\tNA\t0\tPE1\n+NX_Q7L9L4\t25091\t216\t6.24\t4\tCytoplasm;Nucleus\tNA\t0\tPE1\n+NX_Q7LBC6\t191581\t1761\t6.78\t5\tNucleus;Nucleoplasm\tNA\t0\tPE1\n+NX_Q7LBE3\t86988\t791\t8.47\t1\tMembrane;Nucleus;Cell junction\tNA\t13\tPE1\n+NX_Q7LBR1\t22109\t199\t7.81\t18\tNucleus;Late endosome membrane;Midbody;Cytosol;Endosome\tNA\t0\tPE1\n+NX_Q7LC44\t45316\t396\t5.45\t8\tCytoskeleton;Synapse;Cytoplasmic vesicle;Cytoskeleton;Endosome;Acrosome;Postsynaptic density;Dendrite;Dendritic spine\tNA\t0\tPE1\n+NX_Q7LDG7\t69248\t609\t7.89\t11\tSynaptosome;Ruffle membrane;Cell membrane;Cytosol\tBleeding disorder, platelet-type 18\t0\tPE1\n+NX_Q7LDI9\t74079\t666\t9.11\t7\tCell membrane\tNA\t0\tPE1\n+NX_Q7LFL8\t32977\t322\t9.27\t5\tCytosol;Nucleoplasm;Nucleus;Cytoplasm\tNA\t0\tPE1\n+NX_Q7LFX5\t64926\t561\t8.56\t10\tCentrosome;Cytosol;Golgi apparatus membrane\tNA\t1\tPE1\n+NX_Q7LG56\t40737\t351\t4.89\t8\tNucleus;Nucleoplasm;Cytoplasm;Cytosol\tProgressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant, 5;Mitochondrial DNA depletion syndrome 8A;Mitochondrial DNA depletion syndrome 8B\t0\tPE1\n+NX_Q7LGA3\t41881\t356\t8.83\t1\tMitochondrion;Golgi apparatus membrane\tNA\t1\tPE1\n+NX_Q7LGC8\t54706\t479\t8.84\t10\tCytosol;Golgi apparatus;Golgi apparatus membrane\tSpondyloepiphyseal dysplasia with congenital joint dislocations\t1\tPE1\n+NX_Q7M4L6\t46768\t423\t6.01\t15\tNucleus\tNA\t0\tPE1\n+NX_Q7RTM1\t67353\t612\t8.71\t4\tExtracellular space;Membrane\tNA\t10\tPE2\n+NX_Q7RTN6\t48369\t431\t6.02\t17\tCytosol;Nucleoplasm;Cytoplasm;Nucleus\tNA\t0\tPE1\n+NX_Q7RTP0\t34562\t329\t8.7\t15\tCell membrane;Early endosome\tSpastic paraplegia 6, autosomal dominant\t9\tPE1\n+NX_Q7RTP6\t224295\t2002\t5.43\t22\tCytosol;Cytoplasm;Cell membrane;Nucleoplasm;Cell cortex;Cilium basal body;Spindle;Midbody;Nucleus;Cytoskeleton\tNA\t0\tPE1\n+NX_Q7RTR0\t113312\t991\t6.08\t19\tCytoplasm;Inflammasome\tNA\t0\tPE1\n+NX_Q7RTR2\t114658\t1065\t8.64\t16\tCytosol;Microtubule organizing center;Cytoplasm\tNA\t0\tPE1\n+NX_Q7RTR8\t36195\t314\t9.64\t12\tMembrane;Focal adhesion;Nucleoplasm;Cytoskeleton\tNA\t7\tPE2\n+NX_Q7RTS1\t20818\t189\t11.26\t7\tNucleoplasm;Nucleus;Golgi apparatus\tNA\t0\tPE1\n+NX_Q7RTS3\t34970\t328\t5.1\t10\tNucleus;Nucleoplasm;Cytoplasm\tPancreatic agenesis 2;Pancreatic and cerebellar agenesis\t0\tPE1\n+NX_Q7RTS5\t66296\t596\t8.96\t17\tMembrane\tNA\t12\tPE1\n+NX_Q7RTS6\t62236\t562\t7.04\t17\tMembrane\tNA\t10\tPE1\n+NX_Q8WZ42\t3816030\t34350\t6.02\t2\tCytoplasm;Nucleus Early-onset myopathy with fatal cardiomyopathy;Cardiomyopathy, familial hypertrophic 9;Cardiomyopathy, dilated 1G;Tardive tibial muscular dystrophy;Hereditary myopathy with early respiratory failure;Limb-girdle muscular dystrophy\t2J\t0\tPE1\n' |
| b |
| diff -r da885fff7cf6 -r 7caa90759aba tool-data/nextprot_ref_09-03-2019.tsv --- a/tool-data/nextprot_ref_09-03-2019.tsv Mon May 06 06:08:26 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,20400 +0,0 @@\n-NextprotID\tMW\tSeqLength\tIsoPoint\tChr\tSubcellLocations\tDiseases\tTMDomains\tProteinExistence\r\n-NX_A0A024RBG1\t20434\t181\t5.99\t1\tCytoplasm\tNA\t0\tPE1\r\n-NX_A0A075B6H9\t12773\t119\t6.01\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6I0\t12814\t122\t4.33\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6I1\t12987\t120\t5.8\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6I4\t12395\t117\t7.85\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6I9\t12468\t117\t6.69\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6J1\t13277\t123\t4.75\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6J6\t12549\t115\t3.95\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6J9\t12412\t118\t4.66\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6K0\t12466\t115\t4.58\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6K2\t12387\t115\t5.34\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6K4\t12441\t115\t4.72\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6K5\t12332\t115\t6.81\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6K6\t13330\t122\t5.39\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6N1\t12769\t114\t6.53\t7\tCell membrane\tNA\t0\tPE1\r\n-NX_A0A075B6N2\t12175\t111\t8.52\t7\tCell membrane\tNA\t0\tPE1\r\n-NX_A0A075B6N3\t12929\t115\t7.68\t7\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A075B6N4\t12983\t114\t5.91\t7\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A075B6P5\t12957\t120\t5.61\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6Q5\t12891\t118\t7.69\t14\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6R2\t12848\t117\t9.64\t14\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6S2\t13143\t120\t6.53\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6S4\t12835\t117\t9.22\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6S5\t12712\t117\t8.5\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A075B6S6\t13215\t120\t7.79\t2\tCell membrane;Secreted\tNA\t0\tPE3\r\n-NX_A0A075B6T6\t12838\t113\t6.17\t14\tCell membrane\tNA\t0\tPE1\r\n-NX_A0A075B6T7\t15362\t132\t9.2\t14\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A075B6T8\t12354\t112\t4.83\t14\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A075B6U4\t12598\t112\t8.39\t14\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A075B6V5\t12697\t113\t6.57\t14\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A075B6W5\t13545\t121\t8.45\t14\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A075B6X5\t12414\t111\t5.26\t14\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A075B6Y3\t2097\t20\t11\t14\tCell membrane\tNA\t0\tPE4\r\n-NX_A0A075B706\t1761\t16\t8.26\t14\tCell membrane\tNA\t0\tPE1\r\n-NX_A0A075B759\t18197\t164\t9.43\t1\tCytoplasm\tNA\t0\tPE3\r\n-NX_A0A075B767\t18208\t164\t9.19\t1\tCytoplasm\tNA\t0\tPE3\r\n-NX_A0A087WSX0\t13162\t123\t6.69\t22\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A087WSY4\t13025\t118\t9.7\t3\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A087WSY6\t12534\t115\t5.14\t2\tCell membrane;Secreted\tNA\t0\tPE3\r\n-NX_A0A087WSZ0\t12837\t117\t7.62\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A087WSZ9\t12582\t112\t8.58\t14\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A087WT01\t12043\t109\t5.7\t14\tCell membrane\tNA\t0\tPE1\r\n-NX_A0A087WT02\t12289\t112\t5.26\t14\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A087WT03\t12306\t109\t7.76\t14\tCell membrane\tNA\t0\tPE1\r\n-NX_A0A087WTH1\t11832\t108\t7.61\t16\tMembrane\tNA\t0\tPE2\r\n-NX_A0A087WTH5\t15028\t132\t8.73\t21\tMembrane\tNA\t0\tPE3\r\n-NX_A0A087WUL8\t440408\t3843\t4.53\t1\tCytoplasm\tNA\t0\tPE5\r\n-NX_A0A087WV62\t12845\t115\t6.7\t7\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A087WVF3\t62187\t549\t9.2\t17\tCell membrane\tNA\t0\tPE2\r\n-NX_A0A087WW87\t13310\t121\t4.43\t2\tCell membrane;Secreted\tNA\t0\tPE1\r\n-NX_A0A087WX78\t41674\t387\t8.87\t18\tNucleus\tNA\t0\tPE5\r\n-NX_A0A087WXM9\t40829\t373\t8.65\t5\tKinetochore;Centromere\tNA\t0\tPE1\r\n-NX_A0A087WXS9\t62205\t549\t9.2\t17\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A087X0M5\t13028\t115\t9.14\t7\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A087X179\t62131\t549\t9.18\t17\tCell membrane\tNA\t0\tPE2\r\n-NX_A0A087X1C5\t57489\t515\t8.7\t22\tMitochondrion;Cytoplasm;Membrane\tNA\t0\tPE5\r\n-NX_A0A087X1G2\t62171\t549\t9.23\t17\tCell membrane\tNA\t0\tPE3\r\n-NX_A0A096LNP1\t8156\t70\t8.26\t11\tSecreted\tNA\t0\tPE2\r\n-NX_A0A096LP01\t10908\t95\t6.24\t20\tNucleoplasm;Cytosol;Membrane\tNA\t0\tPE1\r\n-NX_A0A096LP49\t114856\t1063\t9.76\t9\tNA\tNA\t0\tPE1\r\n-NX_A0A096LP55\t10752\t91\t4.39\t1\tMitochondrion inner membrane\tNA\t0\tPE3\r\n-NX_A0A096LPI5\t11989\t108\t8.8\t6\tNA\tNA\t0\tPE4\r\n-NX_A0A0A0MRZ7\t13297\t120\t4.9\t2\tCell membrane;Secreted\tNA\t0\tPE3\r\n-NX_A0A0A0MRZ8\t12625\t115\t5.15\t2\tCell membrane;Secreted\tNA\t0\tPE3\r\n-NX_A0A0A0MRZ9\t13446\t124\t7.76\t22\tCell m'..b'1227\t1575\t6.14\t9\tBasement membrane\tCortical malformations occipital\t0\tPE1\r\n-NX_Q9Y6N7\t180930\t1651\t5.7\t3\tAxon;Endoplasmic reticulum-Golgi intermediate compartment membrane;Cell membrane\tNA\t0\tPE1\r\n-NX_Q9Y6N8\t88451\t788\t4.83\t5\tCell membrane\tNA\t0\tPE1\r\n-NX_Q9Y6N9\t62211\t552\t5.36\t11\tCytosol;Microvillus;Cytoskeleton\tDeafness, autosomal recessive, 18A;Usher syndrome 1C\t0\tPE1\r\n-NX_Q9Y6P5\t56557\t492\t5.68\t6\tCytoplasm;Nucleolus;Nucleus\tNA\t0\tPE1\r\n-NX_Q9Y6Q1\t74576\t641\t6.62\tX\tCytosol;Perinuclear region;Spindle\tNA\t0\tPE1\r\n-NX_Q9Y6Q2\t83141\t735\t5.82\t2\tCytoplasm;Membrane\tNA\t0\tPE1\r\n-NX_Q9Y6Q3\t71209\t630\t9.26\t9\tCytoplasmic vesicle;Nucleus\tNA\t0\tPE1\r\n-NX_Q9Y6Q5\t48108\t423\t8.23\t19\tCytoplasmic vesicle;Clathrin-coated vesicle membrane;Golgi apparatus\tNA\t0\tPE1\r\n-NX_Q9Y6Q6\t66034\t616\t5.21\t18\tCytosol;Cell membrane\tPaget disease of bone 2, early-onset;Osteopetrosis, autosomal recessive 7;Familial expansile osteolysis\t0\tPE1\r\n-NX_Q9Y6Q9\t155293\t1424\t7.16\t20\tCytosol;Nucleoplasm;Nucleus;Cytoplasm\tNA\t0\tPE1\r\n-NX_Q9Y6R0\t64891\t609\t9.1\t19\tCytoplasm\tNA\t0\tPE1\r\n-NX_Q9Y6R1\t121461\t1079\t6.35\t4\tBasolateral cell membrane\tRenal tubular acidosis, proximal, with ocular abnormalities and mental retardation\t0\tPE1\r\n-NX_Q9Y6R4\t181685\t1608\t5.94\t6\tCytosol;Perinuclear region\tNA\t0\tPE1\r\n-NX_Q9Y6R6\t96807\t833\t9.17\t19\tNucleus\tNA\t0\tPE1\r\n-NX_Q9Y6R7\t572017\t5405\t5.14\t19\tCytoskeleton;Golgi apparatus;Cell membrane;Secreted\tNA\t0\tPE1\r\n-NX_Q9Y6R9\t57368\t512\t10.27\t19\tNucleus\tNA\t0\tPE1\r\n-NX_Q9Y6S9\t60036\t549\t7.06\t14\tNucleoplasm\tNA\t0\tPE1\r\n-NX_Q9Y6T7\t90595\t804\t8.11\t7\tCytoplasm\tNA\t0\tPE1\r\n-NX_Q9Y6U3\t80489\t715\t5.5\t7\tCytoskeleton;Podosome;Cell membrane\tNA\t0\tPE1\r\n-NX_Q9Y6U7\t41101\t377\t8.98\t22\tCytoskeleton;Nucleolus;Membrane\tNA\t0\tPE2\r\n-NX_Q9Y6V0\t560699\t5142\t6.07\t7\tNucleus speckle;Synapse;Cell membrane\tPontocerebellar hypoplasia 3\t0\tPE1\r\n-NX_Q9Y6V7\t54226\t483\t9.21\t19\tMitochondrion;Nucleolus\tNA\t0\tPE1\r\n-NX_Q9Y6W3\t92652\t813\t7.55\t3\tNucleus\tNA\t0\tPE1\r\n-NX_Q9Y6W5\t54284\t498\t5.38\t1\tCytosol;Cytoplasm;Cytoskeleton;Cell membrane;Lamellipodium\tNA\t0\tPE1\r\n-NX_Q9Y6W6\t52642\t482\t7.87\t1\tCytosol;Nucleoplasm;Nucleus;Golgi apparatus;Cytoplasm\tNA\t0\tPE1\r\n-NX_Q9Y6W8\t22625\t199\t9.01\t2\tCell membrane;Secreted\tImmunodeficiency, common variable, 1\t0\tPE1\r\n-NX_Q9Y6X0\t175008\t1596\t9.76\t18\tCytosol;Nucleus\tSchinzel-Giedion midface retraction syndrome;Leukemia, acute myelogenous;Leukemia, juvenile myelomonocytic;Myelodysplastic syndrome;Mental retardation, autosomal dominant 29;Leukemia, chronic myeloid, atypical\t0\tPE1\r\n-NX_Q9Y6X1\t7374\t66\t11.01\t3\tEndoplasmic reticulum membrane;Endoplasmic reticulum;Cell membrane;Membrane\tNA\t0\tPE1\r\n-NX_Q9Y6X2\t68017\t628\t7.81\t1\tNucleoplasm;Nucleus speckle;Nucleus;Cytoplasm\tNA\t0\tPE1\r\n-NX_Q9Y6X3\t69082\t613\t6.84\t19\tNucleoplasm;Nucleus;Chromosome\tNA\t0\tPE1\r\n-NX_Q9Y6X4\t74955\t670\t4.52\t5\tCytosol;Nucleus inner membrane;Nucleus envelope;Nucleus membrane\tNA\t0\tPE1\r\n-NX_Q9Y6X5\t51641\t453\t5.71\t6\tCell membrane\tNA\t0\tPE1\r\n-NX_Q9Y6X6\t206129\t1858\t6.37\t13\tCytoplasmic vesicle;Cytoplasm\tNA\t0\tPE1\r\n-NX_Q9Y6X8\t92307\t837\t6.42\t8\tNucleoplasm;Nucleus\tNA\t0\tPE1\r\n-NX_Q9Y6X9\t117823\t1032\t8.6\t22\tCytosol;Nucleus\tCharcot-Marie-Tooth disease 2Z\t0\tPE1\r\n-NX_Q9Y6Y0\t71729\t642\t5.33\t1\tNucleoplasm;Cytoplasm;Cytoskeleton;Cytosol\tNA\t0\tPE1\r\n-NX_Q9Y6Y1\t183672\t1673\t7.29\t1\tCytosol;Cytoplasm;Nucleolus;Nucleus\tCerebellar ataxia, non-progressive, with mental retardation\t0\tPE1\r\n-NX_Q9Y6Y8\t111076\t1000\t5.35\t10\tCytoplasmic vesicle;COPII-coated vesicle membrane;Endoplasmic reticulum\tNA\t0\tPE1\r\n-NX_Q9Y6Y9\t18546\t160\t8.8\t8\tCytoplasmic vesicle;Extracellular space;Secreted\tNA\t0\tPE1\r\n-NX_Q9Y6Z2\t6189\t57\t5.98\t6\tNA\tNA\t0\tPE4\r\n-NX_Q9Y6Z4\t19411\t181\t9.48\t6\tNA\tNA\t0\tPE5\r\n-NX_Q9Y6Z5\t26128\t254\t11.81\t6\tNA\tNA\t0\tPE5\r\n-NX_Q9Y6Z7\t30705\t277\t6.96\t8\tCytoplasm;Golgi apparatus;Secreted\t3MC syndrome 3\t0\tPE1\r\n-NX_Q9YNA8\t74183\t666\t9.05\t19\tCell membrane\tNA\t0\tPE1\r\n-NX_S4R3P1\t2751\t24\t5.87\t4\tCytoplasm;Secreted\tNA\t0\tPE3\r\n-NX_S4R3Y5\t2737\t24\t7.98\t1\tCytoplasm;Secreted\tNA\t0\tPE2\r\n-NX_U3KPV4\t38754\t340\t9.39\t1\tGolgi stack membrane\tNA\t0\tPE2\r\n-NX_W5XKT8\t36333\t324\t6.15\t19\tMembrane\tNA\t0\tPE1\r\n-NX_W6CW81\t12732\t113\t5.57\t1\tNA\tNA\t0\tPE1\r\n' |
| b |
| diff -r da885fff7cf6 -r 7caa90759aba tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Mon May 06 06:08:26 2019 -0400 +++ b/tool_data_table_conf.xml.sample Fri Jun 28 05:05:25 2019 -0400 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tables> <table name='proteore_nextprot_ref' comment_char="#"> - <columns>id, name, value</columns> + <columns>id, release, name, value</columns> <file path="tool-data/proteore_nextprot_ref.loc"/> </table> </tables> |