public void GetProteinAccessions()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string uniprotAccession = "[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}";
var uniProtPattern = new Regex(uniprotAccession);
const string databaseFilePath = @"H:\Research\IPRG2015\Henry_results\iPRG2015.TargDecoy.fasta";
if (!File.Exists(databaseFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, databaseFilePath);
}
var database = new FastaDatabase(databaseFilePath);
database.Read();
var nameToAccession = new Dictionary<string, string>();
foreach (var proteinName in database.GetProteinNames())
{
var start = proteinName.IndexOf('|');
var end = proteinName.LastIndexOf('|');
//var accession = proteinName.Substring(start + 1, end - start - 1);
var name = proteinName.Substring(end + 1);
if (proteinName.StartsWith("DECOY")) name = name + "-DECOY";
// Console.WriteLine(name + " -> " +accession);
Assert.IsTrue(uniProtPattern.IsMatch(proteinName));
nameToAccession.Add(name, proteinName);
// Console.WriteLine(name);
}
const string resultPath = @"H:\Research\IPRG2015\Henry_results\ProteinNames.txt";
if (!File.Exists(resultPath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultPath);
}
foreach (var line in File.ReadLines(resultPath))
{
if (line.Length == 0) continue;
var name = line;
// if (name.Contains(";"))
// {
// }
name = name.Split()[0];
if (name.Contains('|')) name = name.Substring(name.LastIndexOf('|') + 1);
string proteinName;
if (nameToAccession.TryGetValue(name, out proteinName))
{
Console.WriteLine(proteinName);
}
else
{
Console.WriteLine(name);
Assert.IsTrue(false);
}
}
}
