Package au.org.intersect.samifier.runner

Examples of au.org.intersect.samifier.runner.ProteinGeneratorRunner

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                if (intInterval < 2) {
                    outputWriter.close();
                    throw new ParseException("Interval must be greater than  1");
                }
            }
            ProteinGeneratorRunner runner = new ProteinGeneratorRunner(
                    glimmerFilePath, genomeFile, interval, databaseName,
                    outputWriter, translationTableFile, gffWriter,
                    accessionWriter);
            runner.run();
        } catch (ParseException pe) {
            System.err.println("Version = " + VERSION);
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("protein_generator", options, true);
        } catch (Exception e) {
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            String glimmerFile = "test/resources/protein_generator/glimmer_contig.txt";
            StringWriter out = new StringWriter();
            StringWriter gff = new StringWriter();
            StringWriter accession = new StringWriter();

            ProteinGeneratorRunner runner = new ProteinGeneratorRunner(glimmerFile, genomeFile, null, "testdb", out, tableFile, gff, accession);
            runner.run();
            verifyExpectedOutput(out,  "test/resources/protein_generator/expected_contig_file.fa");
            verifyExpectedOutput(gff,  "test/resources/protein_generator/expected_gff_contig_glimmer.gff");
            verifyExpectedOutput(accession, "test/resources/protein_generator/expected_accession_file_contig_glimmer.txt");
        }
       
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            File tableFile = new File("test/resources/protein_generator/bacterial_translation_table.txt");
            StringWriter out = new StringWriter();
            StringWriter gff = new StringWriter();
            StringWriter accession = new StringWriter();
           
            ProteinGeneratorRunner runner = new ProteinGeneratorRunner(null, genomeFile, "100", "testdb", out, tableFile, gff, accession);
            runner.run();
            verifyExpectedOutput(out,  "test/resources/protein_generator/expected_contig_interval.fa");
            verifyExpectedOutput(gff,  "test/resources/protein_generator/expected_gff_contig_interval.gff");
            verifyExpectedOutput(accession, "test/resources/protein_generator/expected_accession_file_contig_interval.txt");
           
        }
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Related Classes of au.org.intersect.samifier.runner.ProteinGeneratorRunner

  • au.org.intersect.samifier.domain.AccessionOutputterGenerator
  • au.org.intersect.samifier.domain.GffOutputterGenerator
  • au.org.intersect.samifier.domain.ProteinOutputterGenerator
  • au.org.intersect.samifier.generator.CodonsPerIntervalLocationGenerator
  • au.org.intersect.samifier.generator.GlimmerFileLocationGenerator
  • au.org.intersect.samifier.generator.LocationGenerator
  • au.org.intersect.samifier.generator.ProteinGeneratorWithContigTest
  • au.org.intersect.samifier.parser.FastaParserImpl
  • au.org.intersect.samifier.ProteinGenerator
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