private static Dictionary<string, Dictionary<string, FeatureItemGroup>> PrepareDictionary()
{
var fileDic = new Dictionary<string, Dictionary<string, FeatureItemGroup>>();
// in sample 1, three groups were mapped with three different queries
fileDic["Sample1"] = new Dictionary<string, FeatureItemGroup>();
fileDic["Sample1"]["tRNA1"] = new FeatureItemGroup(new FeatureItem() { Name = "tRNA:chr1.tRNA35-GlyGCC" });
fileDic["Sample1"]["tRNA1"][0].Locations.Add(new FeatureLocation());
fileDic["Sample1"]["tRNA1"][0].Locations[0].SamLocations.Add(new FeatureSamLocation(fileDic["Sample1"]["tRNA1"][0].Locations[0]) { SamLocation = new Sam.SAMAlignedLocation(new Sam.SAMAlignedItem() { Qname = "Query1" }) });
fileDic["Sample1"]["tRNA2"] = new FeatureItemGroup(new FeatureItem() { Name = "tRNA:chr2.tRNA36-GlyGCC" });
fileDic["Sample1"]["tRNA2"][0].Locations.Add(new FeatureLocation());
fileDic["Sample1"]["tRNA2"][0].Locations[0].SamLocations.Add(new FeatureSamLocation(fileDic["Sample1"]["tRNA2"][0].Locations[0]) { SamLocation = new Sam.SAMAlignedLocation(new Sam.SAMAlignedItem() { Qname = "Query2" }) });
fileDic["Sample1"]["tRNA3"] = new FeatureItemGroup(new FeatureItem() { Name = "tRNA:chr1.tRNA111-HisGTG" });
fileDic["Sample1"]["tRNA3"][0].Locations.Add(new FeatureLocation());
fileDic["Sample1"]["tRNA3"][0].Locations[0].SamLocations.Add(new FeatureSamLocation(fileDic["Sample1"]["tRNA3"][0].Locations[0]) { SamLocation = new Sam.SAMAlignedLocation(new Sam.SAMAlignedItem() { Qname = "Query3" }) });
// in sample 2, two groups were mapped with two different queries. The first group contains two tRNA with same code.
fileDic["Sample2"] = new Dictionary<string, FeatureItemGroup>();
fileDic["Sample2"]["tRNA1"] = new FeatureItemGroup(new FeatureItem() { Name = "tRNA:chr1.tRNA35-GlyGCC" });
fileDic["Sample2"]["tRNA1"][0].Locations.Add(new FeatureLocation());
fileDic["Sample2"]["tRNA1"][0].Locations[0].SamLocations.Add(new FeatureSamLocation(fileDic["Sample2"]["tRNA1"][0].Locations[0]) { SamLocation = new Sam.SAMAlignedLocation(new Sam.SAMAlignedItem() { Qname = "Query4" }) });
fileDic["Sample2"]["tRNA1"].Add(new FeatureItem() { Name = "tRNA:chr2.tRNA36-GlyGCC" });
fileDic["Sample2"]["tRNA1"][1].Locations.Add(new FeatureLocation());
fileDic["Sample2"]["tRNA1"][1].Locations[0].SamLocations.Add(new FeatureSamLocation(fileDic["Sample2"]["tRNA1"][1].Locations[0]) { SamLocation = new Sam.SAMAlignedLocation(new Sam.SAMAlignedItem() { Qname = "Query4" }) });
fileDic["Sample2"]["tRNA3"] = new FeatureItemGroup(new FeatureItem() { Name = "tRNA:chr1.tRNA111-HisGTG" });
fileDic["Sample2"]["tRNA3"][0].Locations.Add(new FeatureLocation());
fileDic["Sample2"]["tRNA3"][0].Locations[0].SamLocations.Add(new FeatureSamLocation(fileDic["Sample2"]["tRNA3"][0].Locations[0]) { SamLocation = new Sam.SAMAlignedLocation(new Sam.SAMAlignedItem() { Qname = "Query5" }) });
return fileDic;
}
public static Dictionary <string, Dictionary <string, FeatureItemGroup> > GroupByIdenticalQuery(Dictionary <string, Dictionary <string, FeatureItemGroup> > dic)
{
var featureNames = (from d in dic.Values
from fig in d.Values
from fi in fig
select fi.Name).Distinct().ToList();
var map = new Dictionary <string, FeatureItem>();
foreach (var featureName in featureNames)
{
var item = new FeatureItem()
{
Name = featureName
};
item.Locations.Add(new FeatureLocation());
map[featureName] = item;
}
foreach (var d in dic.Values)
{
foreach (var fig in d.Values)
{
foreach (var fi in fig)
{
var item = map[fi.Name];
item.Locations[0].SamLocations.AddRange(from l in fi.Locations from ll in l.SamLocations select ll);
}
}
}
var groups = map.Values.GroupByIdenticalQuery();
var result = new Dictionary <string, Dictionary <string, FeatureItemGroup> >();
foreach (var sample in dic.Keys)
{
var oldfeatures = (from v in dic[sample].Values
from vv in v
select vv).ToDictionary(m => m.Name);
var newdic = new Dictionary <string, FeatureItemGroup>();
result[sample] = newdic;
foreach (var g in groups)
{
var findfeatures = (from item in g
where oldfeatures.ContainsKey(item.Name)
select oldfeatures[item.Name]).ToList();
if (findfeatures.Count > 0)
{
var newgroup = new FeatureItemGroup();
newgroup.AddRange(findfeatures);
newdic[g.DisplayName] = newgroup;
}
}
}
return(result);
}
protected void OutputCount(StreamWriter sw, FeatureItemGroup feature, List<string> samples, int offset, bool hasNTA, string indexSuffix, string removeNamePrefix)
{
Func<FeatureSamLocation, bool> acceptOffset = m => MirnaConsts.NO_OFFSET == offset || m.Offset == offset;
if (!feature.Any(l => l.Locations.Any(k => k.SamLocations.Any(g => acceptOffset(g)))))
{
return;
}
var featureName = (from f in feature select f.Name.StringAfter(removeNamePrefix)).Merge(";");
var featureSequences = (from l in feature
select l.Sequence).ToArray();
var sequence = featureSequences.Distinct().Count() == 1 ? featureSequences.First() : featureSequences.Merge(";");
if (!hasNTA)
{
var counts = (from sample in samples
select feature.GetEstimatedCount(m => m.SamLocation.Parent.Sample.Equals(sample) && acceptOffset(m))).ToArray();
if (counts.Any(l => l >= 0.05))
{
sw.WriteLine("{0}{1}\t{2}\t{3}\t{4}", featureName, indexSuffix, feature.DisplayLocations, sequence,
(from count in counts select string.Format("{0:0.#}", count)).Merge("\t"));
}
}
else
{
var ntas = (from m in feature
from mr in m.Locations
from l in mr.SamLocations
where acceptOffset(l)
select l.SamLocation.Parent.ClippedNTA).Distinct().OrderBy(m => m).ToList();
foreach (var nta in ntas)
{
var counts = (from sample in samples
select feature.GetEstimatedCount(m => m.SamLocation.Parent.Sample.Equals(sample) && acceptOffset(m) && m.SamLocation.Parent.ClippedNTA.Equals(nta))).ToArray();
if (counts.Any(l => l >= 0.05))
{
sw.Write("{0}{1}_NTA_{2}\t{3}\t{4}\t{5}", featureName, indexSuffix, nta, feature.DisplayLocations, sequence,
(from count in counts select string.Format("{0:0.#}", count)).Merge("\t"));
}
}
}
}
protected void OutputCount(StreamWriter sw, FeatureItemGroup feature, List <string> samples, int offset, bool hasNTA, string indexSuffix, string removeNamePrefix)
{
Func <FeatureSamLocation, bool> acceptOffset = m => MirnaConsts.NO_OFFSET == offset || m.Offset == offset;
if (!feature.Any(l => l.Locations.Any(k => k.SamLocations.Any(g => acceptOffset(g)))))
{
return;
}
var featureName = (from f in feature select f.Name.StringAfter(removeNamePrefix)).Merge(";");
var featureSequences = (from l in feature
select l.Sequence).ToArray();
var sequence = featureSequences.Distinct().Count() == 1 ? featureSequences.First() : featureSequences.Merge(";");
if (!hasNTA)
{
var counts = (from sample in samples
select feature.GetEstimatedCount(m => m.SamLocation.Parent.Sample.Equals(sample) && acceptOffset(m))).ToArray();
if (counts.Any(l => l >= 0.05))
{
sw.WriteLine("{0}{1}\t{2}\t{3}\t{4}", featureName, indexSuffix, feature.DisplayLocations, sequence,
(from count in counts select string.Format("{0:0.#}", count)).Merge("\t"));
}
}
else
{
var ntas = (from m in feature
from mr in m.Locations
from l in mr.SamLocations
where acceptOffset(l)
select l.SamLocation.Parent.ClippedNTA).Distinct().OrderBy(m => m).ToList();
foreach (var nta in ntas)
{
var counts = (from sample in samples
select feature.GetEstimatedCount(m => m.SamLocation.Parent.Sample.Equals(sample) && acceptOffset(m) && m.SamLocation.Parent.ClippedNTA.Equals(nta))).ToArray();
if (counts.Any(l => l >= 0.05))
{
sw.Write("{0}{1}_NTA_{2}\t{3}\t{4}\t{5}", featureName, indexSuffix, nta, feature.DisplayLocations, sequence,
(from count in counts select string.Format("{0:0.#}", count)).Merge("\t"));
}
}
}
}
public static List<FeatureItemGroup> ConvertToGroup(this IEnumerable<FeatureItem> items)
{
var result = new List<FeatureItemGroup>();
foreach (var curItem in items)
{
var group = new FeatureItemGroup();
group.Add(curItem);
result.Add(group);
}
return result;
}
public static List<FeatureItemGroup> GroupByFunction(this IEnumerable<FeatureItem> items, Func<FeatureItem, string> func, bool updateName = false)
{
var result = new List<FeatureItemGroup>();
var dic = items.GroupBy(m => func(m)).ToList();
foreach (var curItems in dic)
{
var group = new FeatureItemGroup();
group.AddRange(from item in curItems orderby item.Name select item);
if (updateName)
{
group.DisplayName = func(curItems.First());
}
result.Add(group);
}
return result;
}
public static Dictionary<string, Dictionary<string, FeatureItemGroup>> GroupByIdenticalQuery(Dictionary<string, Dictionary<string, FeatureItemGroup>> dic)
{
var featureNames = (from d in dic.Values
from fig in d.Values
from fi in fig
select fi.Name).Distinct().ToList();
var map = new Dictionary<string, FeatureItem>();
foreach (var featureName in featureNames)
{
var item = new FeatureItem() { Name = featureName };
item.Locations.Add(new FeatureLocation());
map[featureName] = item;
}
foreach (var d in dic.Values)
{
foreach (var fig in d.Values)
{
foreach (var fi in fig)
{
var item = map[fi.Name];
item.Locations[0].SamLocations.AddRange(from l in fi.Locations from ll in l.SamLocations select ll);
}
}
}
var groups = map.Values.GroupByIdenticalQuery();
var result = new Dictionary<string, Dictionary<string, FeatureItemGroup>>();
foreach (var sample in dic.Keys)
{
var oldfeatures = (from v in dic[sample].Values
from vv in v
select vv).ToDictionary(m => m.Name);
var newdic = new Dictionary<string, FeatureItemGroup>();
result[sample] = newdic;
foreach (var g in groups)
{
var findfeatures = (from item in g
where oldfeatures.ContainsKey(item.Name)
select oldfeatures[item.Name]).ToList();
if (findfeatures.Count > 0)
{
var newgroup = new FeatureItemGroup();
newgroup.AddRange(findfeatures);
newdic[g.DisplayName] = newgroup;
}
}
}
return result;
}
