public bool Parse(List <string> lst, BreastCancerSampleItem item, bool defaultReturnValue)
{
//First of all, using key to find value
foreach (var s in Keys)
{
var l = lst.Find(m => m.StartsWith(s));
if (l != null)
{
SetValue(item, l.Substring(s.Length + 1).Trim());
return(true);
}
}
//If there is line matching regex, using regex to assign value.
if (ValueRegex != null)
{
foreach (var reg in ValueRegex)
{
var mLine = lst.Find(m => reg.Match(m).Success);
if (mLine != null)
{
var m = reg.Match(mLine);
SetValue(item, m.Groups[1].Value);
return(true);
}
}
}
//Finally, find question and answer
for (int j = 0; j < lst.Count; j++)
{
if (lst[j].StartsWith("Pathological Question:") && GetAnswer(lst[j]).Equals(Question))
{
SetValue(item, GetAnswer(lst[j + 1]));
return(true);
}
}
SetValue(item, DefaultValue);
return(defaultReturnValue);
}
public void ParseDataset(string datasetDirectory, Dictionary <string, BreastCancerSampleItem> sampleMap)
{
var files = GeoUtils.GetGsmNameFileMap(datasetDirectory);
var dirname = Path.GetFileName(datasetDirectory);
var map = new RawSampleInfoReader().ReadDescriptionFromDirectory(datasetDirectory);
foreach (var key in map.Keys)
{
if (files.ContainsKey(key.ToLower()))
{
if (!sampleMap.ContainsKey(key))
{
sampleMap[key] = new BreastCancerSampleItem(dirname, key);
}
var sample = sampleMap[key];
var qsMap = map[key];
//parse information
foreach (var question in qsMap.Keys)
{
if (converters.ContainsKey(question))
{
var converter = converters[question];
var answer = qsMap[question].First();
converter.SetProperty(sample, answer);
}
}
//set defaultvalue
foreach (var dfConverter in defaultConverters)
{
dfConverter.Key.SetProperty(sample, dfConverter.Value);
}
}
}
}
public void ParseDataset(string datasetDirectory, Dictionary<string, BreastCancerSampleItem> sampleMap)
{
var files = GeoUtils.GetGsmNameFileMap(datasetDirectory);
var dirname = Path.GetFileName(datasetDirectory);
var map = new RawSampleInfoReader().ReadDescriptionFromDirectory(datasetDirectory);
foreach (var key in map.Keys)
{
if (files.ContainsKey(key.ToLower()))
{
if (!sampleMap.ContainsKey(key))
{
sampleMap[key] = new BreastCancerSampleItem(dirname, key);
}
var sample = sampleMap[key];
var qsMap = map[key];
//parse information
foreach (var question in qsMap.Keys)
{
if (converters.ContainsKey(question))
{
var converter = converters[question];
var answer = qsMap[question].First();
converter.SetProperty(sample, answer);
}
}
//set defaultvalue
foreach (var dfConverter in defaultConverters)
{
dfConverter.Key.SetProperty(sample, dfConverter.Value);
}
}
}
}
public void ParseDataset(string datasetDirectory, Dictionary <string, BreastCancerSampleItem> sampleMap)
{
var files = GeoUtils.GetGsmNameFileMap(datasetDirectory);
var dirname = Path.GetFileName(datasetDirectory);
//The status of ER, PR is on the sample title
var samples = new GseSeriesMatrixReader().ReadFromDirectory(datasetDirectory);
foreach (var a in samples)
{
var filename = a.Key.ToLower();
if (files.ContainsKey(filename.ToLower()))
{
var title = a.Value[GsmConsts.SampleTitle];
var m = r.Match(title.First());
var er = m.Groups[1].Value.Equals("p") ? "pos" : "neg";
var pr = m.Groups[2].Value.Equals("p") ? "pos" : "neg";
var ts = m.Groups[3].Value;
var n = m.Groups[4].Value;
var grade = m.Groups[5].Value;
var key = filename.ToUpper();
if (!sampleMap.ContainsKey(key))
{
sampleMap[key] = new BreastCancerSampleItem(dirname, filename.ToUpper());
}
BreastCancerSampleItem item = sampleMap[key];
item.ER = er;
item.PR = pr;
item.TumorStatus = ts;
item.Grade = grade;
}
}
}
public void ParseDataset(string datasetDirectory, Dictionary<string, BreastCancerSampleItem> sampleMap)
{
var files = GeoUtils.GetGsmNameFileMap(datasetDirectory);
var dirname = Path.GetFileName(datasetDirectory);
//The status of ER, PR is on the sample title
var samples = new GseSeriesMatrixReader().ReadFromDirectory(datasetDirectory);
foreach (var a in samples)
{
var filename = a.Key.ToLower();
if (files.ContainsKey(filename.ToLower()))
{
var title = a.Value[GsmConsts.SampleTitle];
var m = r.Match(title.First());
var er = m.Groups[1].Value.Equals("p") ? "pos" : "neg";
var pr = m.Groups[2].Value.Equals("p") ? "pos" : "neg";
var ts = m.Groups[3].Value;
var n = m.Groups[4].Value;
var grade = m.Groups[5].Value;
var key = filename.ToUpper();
if (!sampleMap.ContainsKey(key))
{
sampleMap[key] = new BreastCancerSampleItem(dirname, filename.ToUpper());
}
BreastCancerSampleItem item = sampleMap[key];
item.ER = er;
item.PR = pr;
item.TumorStatus = ts;
item.Grade = grade;
}
}
}
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 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;
}
}
}
}
