public static FastQCBasicStatisticItem ParseFromFile(string filename)
{
FastQCBasicStatisticItem result = new FastQCBasicStatisticItem();
using (StreamReader sr = new StreamReader(filename))
{
string line = sr.ReadLine();
if (line.StartsWith("##FastQC"))
{
result.FastQCVersion = line.StringAfter("\t").Trim();
}
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith(">>Basic Statistics"))
{
result.Passed = line.StringAfter("\t").Trim().Equals("pass") ? true : false;
break;
}
}
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith(">>"))
{
break;
}
var parts = line.Split('\t');
if (parts[0].Equals("Filename"))
{
result.FileName = parts[1];
}
else if (parts[0].Equals("File type"))
{
result.FileType = parts[1];
}
else if (parts[0].Equals("Encoding"))
{
result.Encoding = parts[1];
}
else if (parts[0].Equals("Total Sequences"))
{
result.TotalSequences = long.Parse(parts[1]);
}
else if (parts[0].Equals("Filtered Sequences"))
{
result.FilteredSequences = long.Parse(parts[1]);
}
else if (parts[0].Equals("Sequence length"))
{
result.SequenceLength = int.Parse(parts[1]);
}
else if (parts[0].Equals("%GC"))
{
result.GC = double.Parse(parts[1]);
}
}
}
return result;
}
public static FastQCItem ParseFromDirectory(string directory)
{
FastQCItem result = new FastQCItem();
result.Name = Path.GetFileName(directory);
foreach (var dir in Directory.GetDirectories(directory))
{
var file = dir + "/fastqc_data.txt";
if (File.Exists(file))
{
result.Items.Add(FastQCBasicStatisticItem.ParseFromFile(file));
}
}
if (result.Items.Count == 0)
{
return(null);
}
return(result);
}
public static FastQCBasicStatisticItem ParseFromFile(string filename)
{
FastQCBasicStatisticItem result = new FastQCBasicStatisticItem();
using (StreamReader sr = new StreamReader(filename))
{
string line = sr.ReadLine();
if (line.StartsWith("##FastQC"))
{
result.FastQCVersion = line.StringAfter("\t").Trim();
}
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith(">>Basic Statistics"))
{
result.Passed = line.StringAfter("\t").Trim().Equals("pass") ? true : false;
break;
}
}
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith(">>"))
{
break;
}
var parts = line.Split('\t');
if (parts[0].Equals("Filename"))
{
result.FileName = parts[1];
}
else if (parts[0].Equals("File type"))
{
result.FileType = parts[1];
}
else if (parts[0].Equals("Encoding"))
{
result.Encoding = parts[1];
}
else if (parts[0].Equals("Total Sequences"))
{
result.TotalSequences = long.Parse(parts[1]);
}
else if (parts[0].Equals("Filtered Sequences"))
{
result.FilteredSequences = long.Parse(parts[1]);
}
else if (parts[0].Equals("Sequence length"))
{
result.SequenceLength = int.Parse(parts[1]);
}
else if (parts[0].Equals("%GC"))
{
result.GC = double.Parse(parts[1]);
}
}
}
return(result);
}
