private List <ITCGATechnology> GetSelectedTechnologies()
{
var result = new List <ITCGATechnology>();
foreach (string obj in lbDataTypes.SelectedItems)
{
result.Add(TCGATechnology.Parse(obj));
}
return(result);
}
public TCGADatatableBuilderUI()
{
InitializeComponent();
rootDir.SetDirectoryArgument("TCGARoot", "TCGA Data Root");
targetFile.FileArgument = new SaveFileArgument("Target Data", "tsv");
lbDataTypes.Items.AddRange(TCGATechnology.GetTechnologyNames().ToArray());
lbSampleTypes.Items.AddRange(TCGASampleCode.GetSampleCodes().OrderBy(m => m.Code).ToList().ConvertAll(m => string.Format("{0}, {1}", m.ShortLetterCode, m.Definition)).ToArray());
this.Text = Constants.GetSQHTitle(title, version);
}
private void FillPlatform()
{
lbPlatforms.BeginUpdate();
try
{
var oldplatforms = GetSelectedPlatforms();
lbPlatforms.Items.Clear();
if (lbDataTypes.SelectedItem == null || !Directory.Exists(rootDir.FullName) || lbTumors.SelectedItem == null)
{
return;
}
var technology = TCGATechnology.Parse(lbDataTypes.SelectedItem as string);
var tumors = GetSelectedTumors();
var platforms = (from tumor in tumors
let dir = rootDir.FullName + "/" + tumor
let plats = Directory.GetDirectories(technology.GetTechnologyDirectory(dir))
from plat in plats
select Path.GetFileName(plat)).Distinct().OrderBy(m => m).ToList();
platforms.ForEach(m => lbPlatforms.Items.Add(m));
if (platforms.Count == 1)
{
lbPlatforms.SelectedIndex = 0;
}
else
{
if (oldplatforms.Count > 0)
{
for (int i = 0; i < lbPlatforms.Items.Count; i++)
{
if (oldplatforms.Contains(lbPlatforms.Items[i]))
{
lbPlatforms.SetSelected(i, true);
}
}
}
}
}
finally
{
lbPlatforms.EndUpdate();
}
}
private void FillTumor()
{
var map = TCGAUtils.GetTumorDescriptionMap();
object[] curitems;
if (lbDataTypes.SelectedItem != null && Directory.Exists(rootDir.FullName))
{
var tecname = lbDataTypes.SelectedItem as string;
var selected = TCGATechnology.Parse(tecname);
curitems = (from tumor in this.tumors
let dir = rootDir.FullName + "/" + tumor
where Directory.Exists(selected.GetTechnologyDirectory(dir))
select tumor).ToArray();
}
else
{
curitems = this.tumors.ToArray();
}
lbTumors.BeginUpdate();
try
{
var selected = new HashSet <string>(GetSelectedTumors().ConvertAll(m => m as string));
lbTumors.Items.Clear();
foreach (string item in curitems)
{
var name = map.ContainsKey(item.ToUpper()) ? item + ", " + map[item.ToUpper()] : item;
lbTumors.Items.Add(name);
}
if (selected.Count > 0)
{
for (int i = 0; i < lbTumors.Items.Count; i++)
{
var name = curitems[i] as string;
if (selected.Contains(name))
{
lbTumors.SetSelected(i, true);
}
}
}
}
finally
{
lbTumors.EndUpdate();
}
}
public static void ExtractData(string tcgaDir, string targetDir, string prefix, string[] tumors, string datatype, string[] platforms, TCGASampleCode[] sampleCodes = null, bool outputCountDataOnly = false)
{
var tec = TCGATechnology.Parse(datatype);
var platforms_str = (from p in platforms select p.StringBefore("_")).Merge("_");
var counts = outputCountDataOnly ? new[] { true } : new[] { true, false };
foreach (var count in counts)
{
string resultFile;
if (tec.HasCountData)
{
resultFile = string.Format(@"{0}\{1}_{2}_{3}_{4}.tsv", targetDir, prefix, datatype, platforms_str, count ? "Count" : tec.ValueName);
}
else
{
resultFile = string.Format(@"{0}\{1}_{2}_{3}.tsv", targetDir, prefix, datatype, platforms_str);
}
var options = new TCGADatatableBuilderOptions();
options.DataType = datatype;
options.TCGADirectory = tcgaDir;
options.TumorTypes = tumors.ToList();
options.Platforms = platforms;
options.IsCount = count;
options.OutputFile = resultFile;
options.TCGASampleCodeStrings = sampleCodes == null ? new List <string>() : sampleCodes.ToList().ConvertAll(m => m.ShortLetterCode).ToList();
options.WithClinicalInformationOnly = true;
if (!options.PrepareOptions())
{
throw new Exception("Error:\n" + options.ParsingErrors.Merge("\n"));
}
new TCGADatatableBuilder(options).Process();
if (!tec.HasCountData)
{
break;
}
}
}
public TCGADataDownloaderUI()
{
InitializeComponent();
targetDir.SetDirectoryArgument("DataDirectory", "TCGA Data Target");
xmlFile.FileArgument = new OpenFileArgument("TCGA Tree Xml Format", "xml");
if (!SystemUtils.IsLinux)
{
zip7File.Visible = true;
zip7File.Required = true;
zip7File.FileArgument = new OpenFileArgument("7zip execute", "exe");
}
else
{
zip7File.Visible = false;
zip7File.Required = false;
}
lbDataTypes.Items.AddRange(TCGATechnology.GetTechnologyNames().ToArray());
this.Text = Constants.GetSQHTitle(Title, Version);
}
public ITCGATechnology GetTechnology()
{
return(TCGATechnology.Parse(this.DataType));
}
public override bool PrepareOptions()
{
if (!Directory.Exists(this.TCGADirectory))
{
ParsingErrors.Add(string.Format("Directory not exists {0}.", this.TCGADirectory));
return(false);
}
try
{
TCGATechnology.Parse(this.DataType);
}
catch (Exception ex)
{
ParsingErrors.Add(ex.Message);
return(false);
}
foreach (var tumor in this.TumorTypes)
{
var tumordir = this.TCGADirectory + "/" + tumor;
if (!Directory.Exists(tumordir))
{
ParsingErrors.Add(string.Format("Directory not exists {0}.", tumordir));
return(false);
}
}
if (TCGASampleCodeStrings == null || TCGASampleCodeStrings.Count == 0)
{
TCGASampleCodeStrings = (from v in TCGASampleCode.GetSampleCodes()
select v.ShortLetterCode).ToList();
}
else
{
try
{
GetTCGASampleCodes();
}
catch (Exception ex)
{
ParsingErrors.Add(ex.Message);
return(false);
}
}
try
{
GetTechnology();
}
catch (Exception ex)
{
ParsingErrors.Add(ex.Message);
return(false);
}
if (this.Platforms == null || this.Platforms.Count == 0)
{
var tec = GetTechnology();
this.Platforms = (from tumor in TumorTypes
let dir = Path.Combine(this.TCGADirectory, tumor)
let tecdir = tec.GetTechnologyDirectory(dir)
from subdir in Directory.GetDirectories(tecdir)
select Path.GetFileName(subdir)).Distinct().OrderBy(m => m).ToList();
}
return(true);
}