/// <summary>
/// Make sure no data duplicated
/// </summary>
public void FilterDatasetByMD5(string[] datasetByPriority)
{
var dsMap = (from dir in GetDatasetDirectories()
let dataset = Path.GetFileName(dir)
from file in CelFile.GetCelFiles(dir)
select new { Dataset = dataset, File = file, MD5 = HashUtils.GetDecompressedMD5Hash(file) }).ToGroupDictionary(m => m.Dataset);
foreach (var dataset in datasetByPriority)
{
var fileMap = dsMap[dataset].ToDictionary(m => m.MD5);
foreach (var ds in dsMap)
{
if (ds.Key.Equals(dataset))
{
continue;
}
var dsfiles = ds.Value;
foreach (var cel in dsfiles)
{
if (!File.Exists(cel.File))
{
continue;
}
if (fileMap.ContainsKey(cel.MD5))
{
Console.WriteLine("Excluding " + cel.File);
ExcludeFile(cel.File);
}
}
}
}
}
public static Dictionary <string, string> GetGsmNameFileMap(string directory)
{
Console.WriteLine(directory);
var files = CelFile.GetCelFiles(directory);
var groups = files.GroupBy(m => GetGsmName(m));
foreach (var group in groups)
{
if (group.Count() > 1)
{
Console.WriteLine("{0} : {1}", group.Key, group.ToList().ConvertAll(m => Path.GetFileName(m)).Merge(", "));
}
}
return(groups.ToDictionary(m => m.Key, m => m.First()));
}
/// <summary>
/// Filter GSM files based on accept function. The rejected files will be removed to exclusion directory.
/// </summary>
/// <param name="gseName"></param>
/// <param name="accept"></param>
public void FilterGseSource(string gseName, Func <SampleItem, bool> accept)
{
var gseDirectory = Path.Combine(DataDir, gseName);
if (!Directory.Exists(gseDirectory))
{
return;
}
var gseExcluded = Path.Combine(ExclusionDir, gseName);
var samples = ReadSampleItem(gseDirectory);
var sg = samples.ToDictionary(m => m.Sample.ToLower());
var celFiles = CelFile.GetCelFiles(gseDirectory);
foreach (var cel in celFiles)
{
var gsm = GeoUtils.GetGsmName(cel);
if (!sg.ContainsKey(gsm))
{
throw new Exception("Cannot find sample information of " + gsm + " in " + gseDirectory);
}
var sample = sg[gsm];
if (!accept(sample))
{
if (!Directory.Exists(gseExcluded))
{
Directory.CreateDirectory(gseExcluded);
}
var target = Path.Combine(gseExcluded, Path.GetFileName(cel));
Console.WriteLine("\t{0}\t{1}\t{2}\t{3}", Path.GetFileName(cel), sample.Sample, sample.SourceName, sample.SampleTitle);
if (File.Exists(target))
{
File.Delete(target);
}
File.Move(cel, target);
}
}
}
public List <BreastCancerSampleItem> ParseDataset(string datasetDirectory)
{
var files = new HashSet <string>(from f in CelFile.GetCelFiles(datasetDirectory, false)
select Path.GetFileNameWithoutExtension(f));
var sdrfFile = Directory.GetFiles(datasetDirectory, "*.sdrf.txt");
if (sdrfFile.Length == 0)
{
throw new ArgumentException("Cannot find sdrf file in directory " + datasetDirectory);
}
var ann = new AnnotationFormat("^#").ReadFromFile(sdrfFile[0]);
return((from a in ann
let filename = Path.GetFileNameWithoutExtension(FindValue(a, ColumnName.Sample))
where files.Contains(filename)
select new BreastCancerSampleItem()
{
Dataset = Path.GetFileName(datasetDirectory),
Sample = filename,
Age = FindValue(a, ColumnName.Age),
ER = new StatusValue(FindValue(a, ColumnName.ER)).Value,
PR = new StatusValue(FindValue(a, ColumnName.PR)).Value,
HER2 = new StatusValue(FindValue(a, ColumnName.HER2)).Value,
Stage = FindValue(a, ColumnName.Stage),
TumorStatus = FindValue(a, ColumnName.TumorStage),
Grade = FindValue(a, ColumnName.Grade),
NodalStatus = FindValue(a, ColumnName.NodalStatus),
PCR = FindValue(a, ColumnName.PCR),
DFS = FindValue(a, ColumnName.DFS),
DFSTime = FindValue(a, ColumnName.DFSTime),
RFS = FindValue(a, ColumnName.RFS),
RFSTime = FindValue(a, ColumnName.RFSTime),
DMFS = FindValue(a, ColumnName.DMFS),
DMFSTime = FindValue(a, ColumnName.DMFSTime),
OverallSurvival = FindValue(a, ColumnName.OverallServive),
DeadOfDisease = FindValue(a, ColumnName.DeadOfDisease)
}).ToList());
}
public void Step_07_CelListFile(string root)
{
using (var sw = new StreamWriter(root + @"\Step_07_CelFileList.tsv"))
{
sw.WriteLine("File\tType\tName\tDataset");
foreach (var dir in Directory.GetDirectories(root))
{
Console.WriteLine(dir);
var cels = CelFile.GetCelFiles(dir);
//var cels = GetCelFiles(dir).Take(3);
foreach (var cel in cels)
{
var name = Path.GetFileNameWithoutExtension(cel).Replace("-", ".");
if (char.IsNumber(name[0]))
{
name = "X" + name;
}
sw.WriteLine("{0}\t{1}\t{2}\t{3}", cel.Substring(root.Length + 1).Replace("\\", "/"), CelFile.GetChipType(cel), name, Path.GetFileName(dir));
}
}
}
}
/// <summary>
/// Build cel count and chip type summary file
/// </summary>
public void BuildChipTypeTable(string tableFileName, string summaryFileName)
{
if (!FileUtils.IsAbsolutePath(tableFileName))
{
tableFileName = Path.Combine(DataDir, tableFileName);
}
if (!FileUtils.IsAbsolutePath(summaryFileName))
{
summaryFileName = Path.Combine(DataDir, summaryFileName);
}
var dic = CelFile.GetChipTypes(this.rExecute, DataDir, true, tableFileName);
using (StreamWriter sw = new StreamWriter(summaryFileName))
{
sw.WriteLine("Dataset\tChiptype\tSample");
var dsMap = dic.ToGroupDictionary(m => Path.GetFileName(Path.GetDirectoryName(m.Key)));
var subdirs = GetDatasetDirectories();
foreach (var subdir in subdirs)
{
var dsName = Path.GetFileName(subdir);
if (dsMap.ContainsKey(dsName))
{
var grp = dsMap[dsName].GroupBy(m => m.Value);
var bFirst = true;
foreach (var g in grp)
{
var name = bFirst ? new DirectoryInfo(subdir).Name : string.Empty;
bFirst = false;
sw.WriteLine("{0}\t{1}\t{2}", name, g.Key, g.Count());
}
}
}
}
}
/// <summary>
/// Normalization cel files and return the file contains all cel file names
/// </summary>
/// <param name="root"></param>
/// <param name="outputFile"></param>
/// <returns></returns>
public string Normalization(string root, string outputFile)
{
var cels = CelFile.GetCelFiles(root);
if (cels.Count == 0)
{
Progress.SetMessage("No cel file found in directory " + DataDir);
return(string.Empty);
}
var inputFile = Path.Combine(root, "celfiles.tsv");
using (var sw = new StreamWriter(inputFile))
{
foreach (var cel in cels)
{
sw.WriteLine(FileUtils.ToLinuxFormat(cel));
}
}
var roptions = new RTemplateProcessorOptions();
roptions.RExecute = rExecute;
roptions.InputFile = inputFile;
roptions.OutputFile = inputFile;
roptions.NoResultFile = true;
roptions.RTemplate = FileUtils.GetTemplateDir() + "\\frma.r";
roptions.CreateNoWindow = true;
new RTemplateProcessor(roptions)
{
Progress = this.Progress
}.Process();
CelFile.GetChipTypes(this.rExecute, root, true, outputFile);
return(outputFile);
}
/// <summary>
/// Make sure no data duplicated
/// </summary>
public void CheckDuplication(string outputFile)
{
outputFile = CheckFileName(outputFile);
var cels = new Dictionary <string, HashSet <string> >();
var dirs = GetDatasetDirectories();
foreach (var subdir in dirs)
{
Console.Out.WriteLine(subdir);
var files = CelFile.GetCelFiles(subdir);
foreach (var file in files)
{
try
{
string md5 = HashUtils.GetDecompressedMD5Hash(file);
var name = Path.GetFileName(subdir) + ":" + Path.GetFileName(file);
if (cels.ContainsKey(md5))
{
cels[md5].Add(name);
}
else
{
cels[md5] = new HashSet <string>(new string[] { name });
}
}
catch (Exception)
{
Console.Error.WriteLine(file);
if (Path.GetFileName(file).ToLower().StartsWith("gsm"))
{
var gsm = GeoUtils.GetGsmName(file).ToUpper();
var filename = Path.GetFileNameWithoutExtension(file);
WebClient webClient = new WebClient();
var uri = string.Format(@"http://www.ncbi.nlm.nih.gov/geosuppl/?acc={0}&file={1}%2ECEL%2Egz", gsm, filename);
Console.WriteLine(uri);
webClient.DownloadFile(uri, file + ".gz");
}
throw;
}
}
}
var dupfile = Path.Combine(DataDir, outputFile);
using (StreamWriter sw = new StreamWriter(dupfile))
{
sw.WriteLine("Duplicated entries = " + cels.Count(m => m.Value.Count > 1).ToString());
sw.WriteLine("Duplicated cels = " + (from cel in cels
where cel.Value.Count > 1
select cel.Value.Count).Sum().ToString());
var dscount = (from c in cels.Values
from v in c
select v).GroupBy(m => m.StringBefore(":")).ToDictionary(m => m.Key, m => m.Count());
var keys = cels.Keys.OrderBy(m => m).ToList();
var sets = (from c in cels
where c.Value.Count > 1
from v in c.Value
select new { MD5 = c.Key, Dataset = v.StringBefore(":"), FileName = v.StringAfter(":") });
var grp = sets.GroupBy(m => m.Dataset).OrderByDescending(m => m.Count()).ToList();
sw.WriteLine();
sw.Write("md5");
foreach (var g in grp)
{
sw.Write(string.Format("\t{0}({1}/{2})", g.Key, g.Count(), dscount[g.Key]));
}
sw.WriteLine();
foreach (var md5 in keys)
{
if (cels[md5].Count > 1)
{
sw.Write(md5);
foreach (var g in grp)
{
var m = g.FirstOrDefault(n => n.MD5.Equals(md5));
if (m != null)
{
sw.Write("\t" + m.FileName);
}
else
{
sw.Write("\t");
}
}
sw.WriteLine();
}
}
}
}
public void ParseDataset(string datasetDirectory, Dictionary <string, BreastCancerSampleItem> sampleMap)
{
var files = new HashSet <string>(from f in CelFile.GetCelFiles(datasetDirectory, false)
select Path.GetFileNameWithoutExtension(f));
var sdrfFile = Directory.GetFiles(datasetDirectory, "*.sdrf.txt");
if (sdrfFile.Length == 0)
{
throw new ArgumentException("Cannot find sdrf file in directory " + datasetDirectory);
}
var ann = new AnnotationFormat("^#").ReadFromFile(sdrfFile[0]);
var dataset = Path.GetFileName(datasetDirectory);
foreach (var a in ann)
{
var filename = Path.GetFileNameWithoutExtension(FindValue(a, ColumnName.Sample));
if (files.Contains(filename))
{
if (!sampleMap.ContainsKey(filename))
{
sampleMap[filename] = new BreastCancerSampleItem();
sampleMap[filename].Dataset = dataset;
sampleMap[filename].Sample = filename;
}
var item = sampleMap[filename];
string value;
if (FindValue(a, ColumnName.Age, out value))
{
item.Age = value;
}
if (FindValue(a, ColumnName.ER, out value))
{
item.ER = StatusValue.TransferStatus(value);
}
if (FindValue(a, ColumnName.PR, out value))
{
item.PR = StatusValue.TransferStatus(value);
}
if (FindValue(a, ColumnName.HER2, out value))
{
item.HER2 = StatusValue.TransferStatus(value);
}
if (FindValue(a, ColumnName.Stage, out value))
{
item.Stage = value;
}
if (FindValue(a, ColumnName.TumorStage, out value))
{
item.TumorStatus = value;
}
if (FindValue(a, ColumnName.Grade, out value))
{
item.Grade = value;
}
if (FindValue(a, ColumnName.NodalStatus, out value))
{
item.NodalStatus = value;
}
if (FindValue(a, ColumnName.PCR, out value))
{
item.PCR = value;
}
if (FindValue(a, ColumnName.DFS, out value))
{
item.DFS = value;
}
if (FindValue(a, ColumnName.DFSTime, out value))
{
item.DFSTime = value;
}
if (FindValue(a, ColumnName.RFS, out value))
{
item.RFS = value;
}
if (FindValue(a, ColumnName.RFSTime, out value))
{
item.RFSTime = value;
}
if (FindValue(a, ColumnName.DMFS, out value))
{
item.DMFS = value;
}
if (FindValue(a, ColumnName.DMFSTime, out value))
{
item.DMFSTime = value;
}
if (FindValue(a, ColumnName.OverallServive, out value))
{
item.OverallSurvival = value;
}
if (FindValue(a, ColumnName.DeadOfDisease, out value))
{
item.DeadOfDisease = value;
}
}
}
}
public void NewFromData(string subdir)
{
var siformat = Directory.GetFiles(subdir, "*.siformat");
TextFileDefinition prefile = new TextFileDefinition();
if (siformat.Length > 0)
{
prefile.ReadFromFile(siformat[0]);
bool bFound = false;
prefile.ForEach(m =>
{
if (m.PropertyName.Equals("TumorStage"))
{
m.PropertyName = "TumorStatus";
bFound = true;
}
if (m.PropertyName.Equals("Metastasis"))
{
m.PropertyName = "MetastasisStatus";
bFound = true;
}
});
if (bFound)
{
prefile.WriteToFile(siformat[0]);
}
}
var map = new RawSampleInfoReader().ReadDescriptionFromDirectory(subdir);
lastDirectory = subdir;
lastFile = String.Empty;
var files = new HashSet <string>(from f in CelFile.GetCelFiles(subdir, false)
select GeoUtils.GetGsmName(f));
Dictionary <string, HashSet <string> > headers = new Dictionary <string, HashSet <string> >();
foreach (var m in map)
{
var gsm = m.Key.ToLower();
if (!files.Contains(gsm))
{
continue;
}
var curmap = m.Value;
foreach (var entry in curmap)
{
if (!headers.ContainsKey(entry.Key))
{
headers[entry.Key] = new HashSet <string>();
}
headers[entry.Key].UnionWith(entry.Value);
}
}
ClearDataSource();
items.Clear();
foreach (var part in headers)
{
items.Add(new FileDefinitionItem()
{
AnnotationName = part.Key,
Example = (from v in part.Value
orderby v
select v).Merge(";")
});
}
foreach (var olditem in prefile)
{
if (!string.IsNullOrEmpty(olditem.PropertyName))
{
var newitem = items.Find(m => m.AnnotationName.Equals(olditem.AnnotationName));
if (newitem != null)
{
newitem.PropertyName = olditem.PropertyName;
}
}
}
items.DefaultValues.Clear();
foreach (var olddv in prefile.DefaultValues)
{
if (propertyNames.Contains(olddv.PropertyName))
{
items.DefaultValues.Add(new DefaultValue()
{
PropertyName = olddv.PropertyName,
Value = olddv.Value
});
}
}
items.Sort((m1, m2) => m1.AnnotationName.CompareTo(m2.AnnotationName));
UpdateDataSource();
this.Text = title + " - " + Path.GetFileName(subdir);
}
public void NewFromData(string subdir)
{
try
{
var siformat = Directory.GetFiles(subdir, "*.siformat");
TextFileDefinition prefile = new TextFileDefinition();
if (siformat.Length > 0)
{
prefile.ReadFromFile(siformat[0]);
}
var map = new RawSampleInfoReader().ReadDescriptionFromDirectory(subdir);
LastDirectory = subdir;
lastFile = String.Empty;
var files = new HashSet <string>(from f in CelFile.GetCelFiles(subdir, false)
select GeoUtils.GetGsmName(f));
Dictionary <string, HashSet <string> > headers = new Dictionary <string, HashSet <string> >();
foreach (var m in map)
{
var gsm = m.Key.ToUpper();
if (!files.Contains(gsm))
{
continue;
}
var curmap = m.Value;
foreach (var entry in curmap)
{
if (!headers.ContainsKey(entry.Key))
{
headers[entry.Key] = new HashSet <string>();
}
headers[entry.Key].UnionWith(entry.Value);
}
}
ClearDataSource();
items.Clear();
foreach (var part in headers)
{
items.Add(new FileDefinitionItem()
{
AnnotationName = part.Key,
Example = (from v in part.Value
orderby v
select v).Merge(";")
});
}
foreach (var olditem in prefile)
{
if (!string.IsNullOrEmpty(olditem.PropertyName))
{
var newitem = items.Find(m => m.AnnotationName.Equals(olditem.AnnotationName));
if (newitem != null)
{
newitem.PropertyName = olditem.PropertyName;
}
}
}
items.DefaultValues.Clear();
items.Sort((m1, m2) => m1.AnnotationName.CompareTo(m2.AnnotationName));
UpdateDataSource();
label1.Text = "Annotation/property mapping - " + Path.GetFileName(subdir);
dlgOpenDirectory.SelectedPath = subdir;
dlgSaveFormatFile.FileName = Path.Combine(subdir, Path.GetFileName(subdir) + ".siformat");
}
catch (Exception ex)
{
MessageBox.Show(this, ex.Message, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
