internal void FetchGeneDisplay(GeneCollection geneCollection, string[] geneArray, string originSequence) { GbkFeatureFetcher fetcher = new GbkFeatureFetcher(); GeneCollection updatedGeneCollection = fetcher.FetchGeneData(geneCollection, geneArray, originSequence); foreach (Gene gene in updatedGeneCollection.collection) { String geneMessage = ""; if (gene.ID != "") { geneMessage += ">" + gene.ID + newLine; } else { geneMessage += ">" + gene.LocusTag + newLine; } //Print sequence in substrings of 80. String sequence = gene.Sequence; int length = sequence.Length; for (int start = 0; start < length;) { int end = start + 80; if (end < length) { geneMessage += sequence.Substring(start, 80) + newLine; } else { geneMessage += sequence.Substring(start, (length - start)); } start += 80; } Console.WriteLine(geneMessage); } Console.WriteLine(newLine); }
public void FetchCDSs(CodingSequenceCollection cdsCollection, string[] cdsArray) { GbkFeatureFetcher fetcher = new GbkFeatureFetcher(); CodingSequenceCollection updatedCodingSequenceCollection = fetcher.FetchCodingSequenceData(cdsCollection, cdsArray); foreach (CodingSequence codingSequence in updatedCodingSequenceCollection.collection) { string cdsMesasge = ""; if (codingSequence.GeneID != "") { cdsMesasge += ">CDS " + codingSequence.GeneID + " sequence" + newLine; } else { cdsMesasge += ">CDS " + codingSequence.LocusTag + " sequence" + newLine; } string sequence = codingSequence.TranslatedSequence; int length = sequence.Length; for (int start = 0; start < length;) { int end = start + 80; if (end < length) { cdsMesasge += sequence.Substring(start, 80) + newLine; } else { cdsMesasge += sequence.Substring(start, (length - start)); } start += 80; } Console.WriteLine(cdsMesasge); } Console.WriteLine(newLine); }
public void FetchFeatures(GeneCollection geneCollection, CodingSequenceCollection cdsCollection, string[] featureArray) { Console.Write("FEATURE;TYPE;START;STOP;ORIENTATION"); GbkFeatureFetcher fetcher = new GbkFeatureFetcher(); SiteFeatureCollection siteFeatureCollection = fetcher.FetchSiteFeatures(geneCollection, cdsCollection, featureArray); foreach (SiteFeature siteFeature in siteFeatureCollection.collection) { Console.WriteLine(siteFeature.GeneID + ";" + siteFeature.Type + ";" + siteFeature.StartCoordinate + ";" + siteFeature.EndCoordinate + ";" + siteFeature.Orientation); } Console.WriteLine(newLine); }
public void FetchSites(GeneCollection geneCollection, string originSequence, string[] siteArray) { Console.Write("POSITION;SEQUENCE;GENE"); GbkFeatureFetcher fetcher = new GbkFeatureFetcher(); List <SearchSiteCollection> list = fetcher.FetchSearchSiteData(geneCollection, originSequence, siteArray); foreach (SearchSiteCollection searchSiteCollection in list) { foreach (SearchSite searchSite in searchSiteCollection.collection) { Console.WriteLine(searchSite.StartPosition + ";" + searchSite.Site + ";" + searchSite.GeneName); } } Console.WriteLine(newLine); }