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Read in the mascot.dat file.
/* ############################################################################## # file: config_mascotdat.cs # # 'msparser' toolkit example code # ############################################################################## # COPYRIGHT NOTICE # # Copyright 1998-2015 Matrix Science Limited All Rights Reserved. # # # ############################################################################## # $Source: parser/examples/test_csharp/config_mascotdat.cs $ # # $Author: villek@matrixscience.com $ # # $Date: 2018-07-30 16:23:53 +0100 $ # # $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ # # $NoKeywords:: $ # ############################################################################## */ using System; using matrix_science.msparser; namespace MsParserExamples { public class config_mascotdat { public static void Main(string[] argv) { // ----- Object creation ----- if (argv.Length < 1) { Console.Error.WriteLine(@"The location of the mascot.dat has to be specified as a parameter The location should either be the full path to the mascot.dat file or a URL to a Mascot server - e.g. http://mascot-searver/mascot/cgi A Mascot security sessionID can optionally be passed as a second parameter"); return; } // A sessionID can optionally be passed as the second parameter // This will only be required if the 'file' is a URL ms_datfile file; if (argv.Length > 1) { ms_connection_settings cs = new ms_connection_settings(); cs.setProxyServerType(ms_connection_settings.PROXY_TYPE.PROXY_TYPE_AUTO); cs.setSessionID(argv[1]); file = new ms_datfile(argv[0], 0, cs); } else file = new ms_datfile(argv[0]); if (!file.isValid()) { Console.Error.WriteLine("There are errors. Cannot continue. The last error description:"); Console.Error.WriteLine(file.getLastErrorString()); return; } // retrieving Databases-section content ms_databases dbs = file.getDatabases(); // check if there is actually a 'Databases' section in the file if (dbs.isSectionAvailable()) { int n = dbs.getNumberOfDatabases(); Console.WriteLine("There are {0} databases configured:", n); for (int i = 0; i < n; i++) { Console.WriteLine("{0} : {1}", dbs.getDatabase(i).getName(), dbs.getDatabase(i).isActive() ? "active" : "inactive"); } } else { Console.WriteLine("Databases-section is missing"); } Console.WriteLine(); // retrieving Parse-section content ms_parseoptions parseOptions = file.getParseOptions(); // check if there is actually a 'Parse' section in the file if (parseOptions.isSectionAvailable()) { int n = parseOptions.getNumberOfParseRules(); Console.WriteLine("Parse rules configured:"); for (int i = 0; i < n; i++) { // not all of them can be specified if (parseOptions.getParseRule(i).isAvailable()) { Console.WriteLine("Rule_{0} : {1}", i, parseOptions.getParseRule(i).getRuleStr()); } } } else { Console.WriteLine("Parse-section is missing"); } Console.WriteLine(); // retrieving WWW-section content ms_wwwoptions wwwOptions = file.getWWWOptions(); // check if there is actually a 'WWWW' section in the file if (wwwOptions.isSectionAvailable()) { int n = wwwOptions.getNumberOfEntries(); Console.WriteLine("There are {0} sequence report sources configured:", n); for (int i = 0; i < n; i++) { Console.WriteLine("{0}_{1}", wwwOptions.getEntry(i).getName(), wwwOptions.getEntry(i).getType() == WWW_TYPE.WWW_SEQ ? "SEQ" : "REP"); } } else { Console.WriteLine("WWW-section is missing"); } Console.WriteLine(); // retrieving Taxonomy-sections Console.WriteLine("Available taxonomy sources:"); int maxTax = file.getMaxTaxonomyRules(); for (int taxInd = 1; taxInd <= maxTax; taxInd++) { // check whether a certain taxonomy section exists if (file.getTaxonomyRules(taxInd) != null) { Console.WriteLine("TAXONOMY_{0} {1}", taxInd, file.getTaxonomyRules(taxInd).getIdentifier()); } } Console.WriteLine(); // retrieving Cluster-section content ms_clusterparams clusterParams = file.getClusterParams(); // Check if there is a 'Cluster' section available if (clusterParams.isSectionAvailable()) { Console.WriteLine("Cluster mode : {0}", clusterParams.isEnabled() ? "enabled" : "disabled"); } else { Console.WriteLine("Cluster-section is missing"); } Console.WriteLine(); // retrieving Processor-section content ms_processoroptions procOptions = file.getProcessors(); // check if the 'Processor' section is available if (procOptions.isSectionAvailable()) { Console.WriteLine("{0} CPU(s) configured", procOptions.getNumberOfProcessors()); } else { Console.WriteLine("Processor-section is missing"); } Console.WriteLine(); // retrieving Options-section content ms_mascotoptions mascotOptions = file.getMascotOptions(); // check if there is actually an 'Options' section in the file if (mascotOptions.isSectionAvailable()) { Console.WriteLine("MascotCmdLine : {0}", mascotOptions.getMascotCmdLine()); } else { Console.WriteLine("Options-section is missing"); } Console.WriteLine(); // retrieving Cron-section content ms_cronoptions cronOptions = file.getCronOptions(); if (cronOptions.isCronEnabled()) { int n = cronOptions.getNumberOfCronJobs(); Console.WriteLine("There are {0} cron-jobs configured:", n); for (int i = 0; i < n; i++) { Console.WriteLine(cronOptions.getCronJob(i).getCommandStr()); } } else { Console.WriteLine("Cron functionality is disabled"); } Console.WriteLine(); } } } /* Running the program as config_mascotdat.exe c:\inetpub\mascot\config\mascot.dat Will give the output: There are 18 databases configured: B_subtilis : inactive Bug_11795 : inactive contaminants : active cRAP : active Human_NoIsoforms : active IPI-human : active IPI_human : active IPI_human_decoy : active Mixed_M_2013-02-07_TruncWithReverse4 : active PRIDE_PXD0000001 : active Proteome_EBV_B95.8_GenBank : inactive SwissProt : active UniProt_Arabidopsis : active UniProt_Chlamydomonas_reinhardtii : active UniProt_Human : active UniProt_Papillomaviridae : active UniProt_Pig : active UniProt_Rat : active Parse rules configured: Rule_1 : >[^|]*|[ABCDEFGHIJKLMNOPQRSTUVWXYZ]\([^ |]*\) Rule_2 : >[^ ]* [^ ]* \(.*\) Rule_3 : \*\(.*\)> Rule_4 : >\(gi|[0-9]*\) Rule_5 : >[^ ]* \(.*\) Rule_6 : >\([^ ]*\) Rule_7 : >[^ ]* \(.*\) Rule_8 : \*\(.*\)> Rule_9 : >..|\([^|]*\) Rule_10 : \(.*\) Rule_11 : >..|[ABCDEFGHIJKLMNOPQRSTUVWXYZ]\([^|]*\) Rule_12 : >IPI:\([^| ]*\) Rule_13 : ^ID \([^ .]*\) Rule_14 : \*\(.*\)> Rule_15 : \*.*\(ID IPI[0-9.]* .*\) Rule_16 : >IPI:\([^| .]*\) Rule_17 : ^ID \([^ .]*\) Rule_18 : >[^ ]* \(.*\) Rule_19 : \*\(.*\)> Rule_20 : \*.*\(ID IPI[0-9.]* .*\) Rule_21 : >\([^|]*\) Rule_22 : >\([^ ]*\) Rule_23 : >\(.*\) Rule_24 : >..|[^|]*|\([^ ]*\) Rule_25 : ^ID \([^ ]*\) Rule_26 : >[^ ]* \(.*\) Rule_27 : \*\(.*\)> Rule_28 : \*.*\(ID [-A-Z0-9_].*\) Rule_29 : human *release *\([0-9.][0-9.]*\) Rule_30 : Swiss-Prot *.*Release *\([0-9._][0-9._]*\) Rule_31 : >IPI:\([^| .]*\) Rule_32 : >[^|]*|\\w\([^ |]*\) Rule_33 : >..|\\w\([^|]*\) Rule_34 : human *release *\([0-9.][0-9.]*\) There are 27 sequence report sources configured: B_subtilis_SEQ Bug_11795_SEQ contaminants_SEQ cRAP_SEQ Human_NoIsoforms_SEQ IPI-human_SEQ IPI_human_SEQ IPI_human_decoy_SEQ Mixed_M_2013-02-07_TruncWithReverse4_SEQ PRIDE_PXD0000001_SEQ Proteome_EBV_B95.8_GenBank_SEQ SwissProt_SEQ UniProt_Arabidopsis_SEQ UniProt_Chlamydomonas_reinhardtii_SEQ UniProt_Human_SEQ UniProt_Papillomaviridae_SEQ UniProt_Pig_SEQ UniProt_Rat_SEQ IPI-human_REP IPI_human_REP SwissProt_REP UniProt_Arabidopsis_REP UniProt_Chlamydomonas_reinhardtii_REP UniProt_Human_REP UniProt_Papillomaviridae_REP UniProt_Pig_REP UniProt_Rat_REP Available taxonomy sources: TAXONOMY_1 All human with TaxID 9606 TAXONOMY_2 SwissProt FASTA TAXONOMY_3 All human with TaxID 9606 TAXONOMY_4 All mouse with TaxID 10090 TAXONOMY_5 EMBL EST Fasta TAXONOMY_6 HUPO PSI PEFF Format TAXONOMY_7 MSDB REF TAXONOMY_8 NCBI nucleotide FASTA using GI2TAXID TAXONOMY_9 NCBI protein FASTA using GI2TAXID TAXONOMY_10 OWL REF TAXONOMY_11 Obsolete_1 TAXONOMY_12 Obsolete_2 TAXONOMY_13 Obsolete_3 TAXONOMY_14 Swiss-prot DAT TAXONOMY_15 SwissProt FASTA TAXONOMY_16 UniRef Fasta Cluster mode : disabled Processor-section is missing MascotCmdLine : ../cgi/nph-mascot.exe There are 5 cron-jobs configured: C:\Perl64\bin\perl.exe C:/inetpub/mascot/bin/dbman_add_task.pl SwissProt C:\Perl64\bin\perl.exe C:/inetpub/mascot/bin/dbman_add_task.pl UniProt_Chlamydomonas_reinhardtii C:\Perl64\bin\perl.exe C:/inetpub/mascot/bin/dbman_add_task.pl UniProt_Rat C:\Perl64\bin\perl.exe C:/inetpub/mascot/bin/dbman_add_task.pl UniProt_Pig C:\Perl64\bin\perl.exe C:/inetpub/mascot/bin/dbman_process_tasks.pl */
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