Package au.org.intersect.samifier.parser

Examples of au.org.intersect.samifier.parser.PeptideSearchResultsParser

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        genome = genomeParser.parseGenomeFile(genomeFile);

        ProteinToOLNParser proteinToOLNParser = new ProteinToOLNParserImpl();
        proteinToOLNMap = proteinToOLNParser.parseMappingFile(mapFile);

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser.parseResults(searchResultsPaths);

        FileWriter bedWriter = null;
        if (bedfilePath != null) {
            bedWriter = new FileWriter(bedfilePath);
        }
        FileWriter sam = new FileWriter(outfile);
        // sort search result by proteins
        peptideSearchResults = peptideSearchResultsParser.sortResultsByChromosome(peptideSearchResults, proteinToOLNMap, genome);
        createSAM(peptideSearchResults, sam, bedWriter);
    }
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        GenomeParserImpl genomeParser = new GenomeParserImpl();
        genome = genomeParser.parseGenomeFile(genomeFile);

        proteinToOLNMap = new EqualProteinOLNMap();

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
                .parseResults(searchResultsPaths);
        translationTable = CodonTranslationTable
                .parseTableFile(translationTableFile);

        for (PeptideSearchResult peptideSearchResult : peptideSearchResults) {
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        ProteinToOLNParser proteinToOLNParser = new ProteinToOLNParserImpl();
        ProteinToOLNMap proteinToOLNMap = proteinToOLNParser
                .parseMappingFile(proteinToOLNMapFile);

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
                .parseResults(searchResultsPaths);
        peptideSearchResults = peptideSearchResultsParser
                .sortResultsByChromosome(peptideSearchResults, proteinToOLNMap,
                        genome);
        PeptideSequenceGenerator sequenceGenerator = new PeptideSequenceGeneratorImpl(
                genome, proteinToOLNMap, chromosomeDir);
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        ProteinToOLNParser proteinToOLNParser = new ProteinToOLNParserImpl();
        ProteinToOLNMap proteinToOLNMap = proteinToOLNParser
                .parseMappingFile(proteinToOLNMapFile);

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
                .parseResults(searchResultsPaths);
        PeptideSequenceGenerator sequenceGenerator = new PeptideSequenceGeneratorImpl(
                genome, proteinToOLNMap, chromosomeDir);
        peptideSearchResults = peptideSearchResultsParser
                .sortResultsByChromosome(peptideSearchResults, proteinToOLNMap,
                        genome);
        FileWriter output = new FileWriter(outputFile);

        for (PeptideSearchResult peptideSearchResult : peptideSearchResults) {
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Related Classes of au.org.intersect.samifier.parser.PeptideSearchResultsParser

  • au.org.intersect.samifier.generator.VirtualProteinMascotLocationGenerator
  • au.org.intersect.samifier.runner.ResultAnalyserRunner
  • au.org.intersect.samifier.runner.SamifierRunner
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