/// <summary>
/// Verify that the file contains the given protein names and descriptions (anywhere in the file)
/// </summary>
/// <param name="reader"></param>
/// <param name="proteinNames">Delimited list of protein names</param>
/// <param name="proteinDescriptions">Delimited list of protein descriptions</param>
/// <param name="delimiter">Delimiter to use</param>
public static void CheckProteinDescription(ProteinFileReaderBaseClass reader, string proteinNames, string proteinDescriptions, char delimiter)
{
var proteinsToFind = new Dictionary <string, string>();
var proteinNameList = proteinNames.Split(delimiter).ToList();
var proteinDescriptionList = proteinDescriptions.Split(delimiter).ToList();
if (string.IsNullOrWhiteSpace(proteinNames) && string.IsNullOrWhiteSpace(proteinDescriptions))
{
proteinNameList.Clear();
proteinDescriptionList.Clear();
}
Assert.AreEqual(proteinNameList.Count, proteinDescriptionList.Count);
for (var i = 0; i < proteinNameList.Count; i++)
{
proteinsToFind.Add(proteinNameList[i], proteinDescriptionList[i]);
}
var matchedProteinsInFile = new Dictionary <string, string>();
var proteinsRead = 0;
while (reader.ReadNextProteinEntry())
{
proteinsRead++;
if (!proteinsToFind.ContainsKey(reader.ProteinName))
{
continue;
}
matchedProteinsInFile.Add(reader.ProteinName, reader.ProteinDescription);
}
Console.WriteLine("Read {0} proteins", proteinsRead);
Console.WriteLine();
if (proteinsToFind.Count == 0)
{
Console.WriteLine("Name verification has been skipped since proteinsToFind is empty");
return;
}
foreach (var expectedProtein in proteinsToFind)
{
var proteinName = expectedProtein.Key;
var proteinDescription = expectedProtein.Value;
if (!matchedProteinsInFile.TryGetValue(proteinName, out var description))
{
Assert.Fail("Expected protein not found: " + expectedProtein);
}
Console.WriteLine(proteinName + ": " + description);
Assert.AreEqual(proteinDescription, description);
}
}
public static void CheckProteinStats(ProteinFileReaderBaseClass reader, int proteinCountExpected, int totalResidueCountExpected)
{
var proteins = new List <string>();
var totalResidueCount = 0;
while (reader.ReadNextProteinEntry())
{
proteins.Add(reader.ProteinName);
totalResidueCount += reader.ProteinSequence.Length;
}
Console.WriteLine("Proteins loaded: " + proteins.Count);
Console.WriteLine("Total residue count: " + totalResidueCount);
if (proteinCountExpected == 0 && totalResidueCountExpected == 0)
{
return;
}
Assert.AreEqual(proteinCountExpected, proteins.Count);
Assert.AreEqual(totalResidueCountExpected, totalResidueCount);
}
/// <summary>
/// Verify that the file starts with and ends with the expected proteins
/// </summary>
/// <param name="reader"></param>
/// <param name="expectedFirstProteinNamesOrSequences">Comma separated list of protein names or sequences that should be at the start of the file</param>
/// <param name="expectedLastProteinNamesOrSequences">Comma separated list of protein names or sequences that should be at the end of the file</param>
/// <param name="checkName">When true, checking protein names; when false, checking protein sequences</param>
public static void CheckProteinNamesOrSequences(
ProteinFileReaderBaseClass reader,
string expectedFirstProteinNamesOrSequences,
string expectedLastProteinNamesOrSequences,
bool checkName = true)
{
var expectedFirstNamesOrSequences = expectedFirstProteinNamesOrSequences.Split(',').ToList();
var expectedLastNamesOrSequences = expectedLastProteinNamesOrSequences.Split(',').ToList();
if (string.IsNullOrWhiteSpace(expectedFirstProteinNamesOrSequences) && string.IsNullOrWhiteSpace(expectedLastProteinNamesOrSequences))
{
expectedFirstNamesOrSequences.Clear();
expectedLastNamesOrSequences.Clear();
}
var firstItems = new List <string>();
var lastItems = new Queue <string>();
var firstItemsToStore = expectedFirstNamesOrSequences.Count == 0 ? 5 : expectedFirstNamesOrSequences.Count;
var lastItemsToStore = expectedLastNamesOrSequences.Count == 0 ? 5 : expectedLastNamesOrSequences.Count;
while (reader.ReadNextProteinEntry())
{
string nameOrSequence;
if (checkName)
{
nameOrSequence = reader.ProteinName;
}
else
{
nameOrSequence = reader.ProteinSequence;
}
lastItems.Enqueue(nameOrSequence);
if (lastItems.Count > lastItemsToStore)
{
lastItems.Dequeue();
}
if (firstItems.Count >= firstItemsToStore)
{
continue;
}
firstItems.Add(nameOrSequence);
}
if (expectedLastNamesOrSequences.Count == 0 && expectedLastNamesOrSequences.Count == 0)
{
Console.WriteLine();
Console.WriteLine("First {0} proteins", 5);
foreach (var nameOrSequence in firstItems)
{
Console.WriteLine(nameOrSequence);
}
Console.WriteLine();
Console.WriteLine("Last {0} proteins", 5);
foreach (var nameOrSequence in lastItems)
{
Console.WriteLine(nameOrSequence);
}
return;
}
string itemDescription;
if (checkName)
{
itemDescription = expectedFirstNamesOrSequences.Count > 1 ? "proteins" : "protein";
}
else
{
itemDescription = expectedFirstNamesOrSequences.Count > 1 ? "sequences" : "sequence";
}
Console.WriteLine("First {0} {1}", expectedFirstNamesOrSequences.Count, itemDescription);
for (var i = 0; i < expectedFirstNamesOrSequences.Count; i++)
{
var nameOrSequence = firstItems[i];
Console.WriteLine(nameOrSequence);
Assert.AreEqual(expectedFirstNamesOrSequences[i], nameOrSequence);
}
Console.WriteLine();
Console.WriteLine("Last {0} {1}", expectedLastNamesOrSequences.Count, itemDescription);
foreach (var expectedProtein in expectedLastNamesOrSequences)
{
if (string.IsNullOrWhiteSpace(expectedProtein))
{
continue;
}
var nameOrSequence = lastItems.Dequeue();
Console.WriteLine(nameOrSequence);
Assert.AreEqual(expectedProtein, nameOrSequence);
}
}
