public List <MappedItemGroup> ReadFromFile(string fileName)
{
var result = new List <MappedItemGroup>();
XElement root = XElement.Load(fileName);
//Console.WriteLine("read locations ...");
Dictionary <string, SAMAlignedLocation> qmmap = root.ToSAMAlignedItems().ToSAMAlignedLocationMap();
//Console.WriteLine("read mapped items ...");
foreach (XElement groupEle in root.Element("subjectResult").Elements("subjectGroup"))
{
var group = new MappedItemGroup();
result.Add(group);
foreach (XElement mirnaEle in groupEle.Elements("subject"))
{
var mirna = new MappedItem();
group.Add(mirna);
mirna.Name = mirnaEle.Attribute("name").Value;
foreach (XElement regionEle in mirnaEle.Elements("region"))
{
var region = new SequenceRegionMapped();
mirna.MappedRegions.Add(region);
region.Region.Name = mirna.Name;
region.Region.ParseLocation(regionEle);
if (regionEle.Attribute("sequence") != null)
{
region.Region.Sequence = regionEle.Attribute("sequence").Value;
}
if (regionEle.Attribute("query_count_before_filter") != null)
{
region.QueryCountBeforeFilter = int.Parse(regionEle.Attribute("query_count_before_filter").Value);
}
if (regionEle.Attribute("pvalue") != null)
{
region.PValue = double.Parse(regionEle.Attribute("pvalue").Value);
}
foreach (XElement queryEle in regionEle.Elements("query"))
{
string qname = queryEle.Attribute("qname").Value;
string loc = queryEle.Attribute("loc").Value;
string key = SAMAlignedLocation.GetKey(qname, loc);
SAMAlignedLocation query = qmmap[key];
region.AlignedLocations.Add(query);
query.Features.Add(region.Region);
}
}
}
}
qmmap.Clear();
return(result);
}
public List <MappedMirnaGroup> ReadFromFile(string fileName)
{
List <MappedMirnaGroup> result = new List <MappedMirnaGroup>();
XElement root = XElement.Load(fileName);
var qmmap = root.ToSAMAlignedItems().ToSAMAlignedLocationMap();
foreach (var mirnaGroupEle in root.Element("mirnas").Elements("mirnagroup"))
{
var group = new MappedMirnaGroup();
result.Add(group);
foreach (var mirnaEle in mirnaGroupEle.Elements("mirna"))
{
var mirna = new MappedMirna();
group.Add(mirna);
mirna.Name = mirnaEle.Attribute("name").Value;
mirna.Sequence = mirnaEle.Attribute("sequence").Value;
foreach (var regionEle in mirnaEle.Elements("region"))
{
var region = new MappedMirnaRegion();
mirna.MappedRegions.Add(region);
region.Region.Name = mirna.Name;
ParseLocation(regionEle, region.Region);
foreach (var posEle in regionEle.Elements("position"))
{
var position = new SequenceRegionMapped();
position.Region = region.Region;
position.Offset = int.Parse(posEle.Attribute("offset").Value);
region.Mapped[position.Offset] = position;
foreach (var queryEle in posEle.Elements("query"))
{
var qname = queryEle.Attribute("qname").Value;
var loc = queryEle.Attribute("loc").Value;
var key = GenerateKey(qname, loc);
var query = qmmap[key];
position.AlignedLocations.Add(query);
query.Features.Add(region.Region);
}
}
}
}
}
qmmap.Clear();
return(result);
}
