private void WriteCountNode(
XmlTextWriter writer,
CountItem item)
{
writer.WriteStartElement("counter-item");
WriteElement(writer, "name", item.Name);
WriteElement(writer, "count", item.Count.ToString());
writer.WriteEndElement();
}
public override IEnumerable <string> Process()
{
var countfiles = options.GetCountFiles();
List <CountItem> counts = new List <CountItem>();
foreach (var file in countfiles)
{
Progress.SetMessage("reading " + file.File + " ...");
var count = new CountItem()
{
Dir = file.Name,
Data =
(from line in File.ReadAllLines(file.File).Skip(1)
let parts = line.Split('\t')
where parts.Length >= 6
select parts).ToDictionary(m => m[0])
};
counts.Add(count);
}
var features = (from c in counts
from k in c.Data.Keys
select k).Distinct().OrderBy(m => m).ToList();
var checkSequence = counts.First().Data.First().Value[2];
double value;
var hasSequence = !double.TryParse(checkSequence, out value);
var seqheader = hasSequence ? "\tSequence" : "";
var startIndex = hasSequence ? 3 : 2;
using (StreamWriter sw = new StreamWriter(options.OutputFile))
using (StreamWriter swIso = new StreamWriter(options.IsomirFile))
{
sw.WriteLine("Feature\tLocation{0}\t{1}", seqheader, (from c in counts select c.Dir).Merge("\t"));
swIso.WriteLine("Feature\tLocation{0}\t{1}", seqheader, (from c in counts select c.Dir).Merge("\t"));
foreach (var feature in features)
{
OutputCount(counts, sw, feature, startIndex, "", hasSequence);
OutputCount(counts, swIso, feature, startIndex + 1, "_+_0", hasSequence);
OutputCount(counts, swIso, feature, startIndex + 2, "_+_1", hasSequence);
OutputCount(counts, swIso, feature, startIndex + 3, "_+_2", hasSequence);
}
}
var result = new[] { options.OutputFile, options.IsomirFile }.ToList();
var infofile = Path.ChangeExtension(options.OutputFile, ".info");
if (CountUtils.WriteInfoSummaryFile(infofile, options.GetCountFiles().ToDictionary(m => m.Name, m => m.File)))
{
result.Add(infofile);
}
return(result);
}
public async void init(string did)
{
state = new bool[50];
for (int i = 0; i < 50; i++)
{
state[i] = false;
}
var result = await HttpUtil.GetDuties(did);
if ((bool)result["ok"])
{
JArray duties = (JArray)result["duties"];
JArray counts = (JArray)result["counts"];
for (var i = 0; i < duties.Count; i++)
{
DutyItem D = new DutyItem();
D.cno = (int)duties[i]["dno"];
D.name = (string)duties[i]["name"];
long second = (long)duties[i]["time"];
D.time = new DateTime(second);
D.note = (string)duties[i]["note"];
dutyitems.Add(D);
}
for (var i = 0; i < counts.Count; i++)
{
CountItem C = new CountItem();
C.count = (int)counts[i]["count"];
C.name = (string)counts[i]["name"];
C.no = (int)counts[i]["mno"];
countitems.Add(C);
}
}
else
{
var md = new MessageDialog("duty models init fail!!").ShowAsync();
return;
}
result = await HttpUtil.GetMembers(App.account);
if ((bool)result["ok"])
{
JArray member = (JArray)result["members"];
for (var i = 0; i < member.Count; i++)
{
string mno = (string)member[i]["mno"];
MemberItem m = new MemberItem();
m.name = (string)member[i]["name"];
long second = (long)member[i]["birth"];
m.birth = new System.DateTime(second);
m.pic = new System.Uri("http://www.sysu7s.cn:3000/api/dormitory//get-member-image/" + App.account + "/" + mno);
m.location = (string)member[i]["location"];
memberitems.Add(m);
}
}
}
public override IEnumerable<string> Process()
{
var countfiles = options.GetCountFiles();
List<CountItem> counts = new List<CountItem>();
foreach (var file in countfiles)
{
Progress.SetMessage("reading " + file.File + " ...");
var count = new CountItem()
{
Dir = file.Name,
Data =
(from line in File.ReadAllLines(file.File).Skip(1)
let parts = line.Split('\t')
where parts.Length >= 6
select parts).ToDictionary(m => m[0])
};
counts.Add(count);
}
var features = (from c in counts
from k in c.Data.Keys
select k).Distinct().OrderBy(m => m).ToList();
var checkSequence = counts.First().Data.First().Value[2];
double value;
var hasSequence = !double.TryParse(checkSequence, out value);
var seqheader = hasSequence ? "\tSequence" : "";
var startIndex = hasSequence ? 3 : 2;
using (StreamWriter sw = new StreamWriter(options.OutputFile))
using (StreamWriter swIso = new StreamWriter(options.IsomirFile))
{
sw.WriteLine("Feature\tLocation{0}\t{1}", seqheader, (from c in counts select c.Dir).Merge("\t"));
swIso.WriteLine("Feature\tLocation{0}\t{1}", seqheader, (from c in counts select c.Dir).Merge("\t"));
foreach (var feature in features)
{
OutputCount(counts, sw, feature, startIndex, "", hasSequence);
OutputCount(counts, swIso, feature, startIndex + 1, "_+_0", hasSequence);
OutputCount(counts, swIso, feature, startIndex + 2, "_+_1", hasSequence);
OutputCount(counts, swIso, feature, startIndex + 3, "_+_2", hasSequence);
}
}
var result = new[] { options.OutputFile, options.IsomirFile }.ToList();
var infofile = Path.ChangeExtension(options.OutputFile, ".info");
if (CountUtils.WriteInfoSummaryFile(infofile, options.GetCountFiles().ToDictionary(m => m.Name, m => m.File)))
{
result.Add(infofile);
}
return result;
}
public void CountMaster_Saves_Counts()
{
var sut = new CountMaster("counts.xml");
var input = new CountItem("Casual", 4);
sut.PutItem(input);
var result = (CountItem)sut.TheHt["Casual"];
Assert.True(result.Count == 4);
}
public void RemoveItem(CountItem it)
{
if (it == null)
{
return;
}
if (_eventList.Contains(it))
{
_eventList.Remove(it);
}
}
public void Test_CountItem_Properties()
{
// Arrange
var count = new CountItem();
// Act
count.Id = "a";
count.Key = "b";
// Assert
count.Id.Should().Be("a");
count.Key.Should().Be("b");
}
public void AddItem(CountItem it)
{
if (it.endimeToCall > it.startTimeToCall)
{
Random random = new Random();
it.realTimeToCall = Random.Range(it.startTimeToCall, it.endimeToCall);
}
else
{
it.realTimeToCall = it.startTimeToCall;
}
_eventList.Add(it);
}
public void PutItem(
CountItem item)
{
var name = item.Name;
if (!TheHt.ContainsKey(name))
{
TheHt.Add(
key: name,
value: item);
IsDirty = true;
}
else
{
TheHt[name] = item;
}
}
/// <summary>
/// 進捗表示の更新を実行する
/// </summary>
/// <param name="index">区分インデックスを表す数値</param>
/// <param name="e">イベント引数</param>
private void ChangeProgress(int index, ItemProgressedEventArgs e)
{
ProgressBar pb = index switch
{
1 => _fileProgressBar,
2 => _viewProgressBar,
3 => _itemProgressBar,
_ => null
};
Label nameLabel = index switch
{
1 => _fileNameLabel,
2 => _categoryNameLabel,
3 => _itemNameLabel,
_ => null
};
Label countLabel = index switch
{
1 => _fileCountLabel,
2 => _categoryCountLabel,
3 => _itemCountLabel,
_ => null
};
CountItem item = index switch
{
1 => e.FileCount,
2 => e.ViewCount,
3 => e.DetailCount,
_ => new CountItem()
};
//
Application.DoEvents();
pb.Maximum = item.Items;
pb.Value = item.Counter;
nameLabel.Text = item.Name;
countLabel.Text = $"{item.Counter}/{item.Items}";
int rate = 0;
if (e.DetailCount.Items > 1)
{
rate = 100 * e.DetailCount.Counter / e.DetailCount.Items;
}
Text = $"{GetFormText()}{rate.ToString()}%";
}
/// <summary>
/// 添加回调事件多长时间之后执行回调
/// </summary>
/// <param name="startTime">多长时间</param>
/// <param name="endTime">多长时间</param>
/// <param name="callback">执行回调</param>
/// <param name="repeatCount">重复次数 -1:永久重复</param>
public void AddCallBack(Action callback, float startTime, int repeatCount = 1, float endTime = -1)
{
CountItem it = new CountItem();
it.callback = callback;
it.startTimeToCall = startTime;
it.endimeToCall = endTime;
if (it.endimeToCall > it.startTimeToCall)
{
Random random = new Random();
it.realTimeToCall = Random.Range(it.startTimeToCall, it.endimeToCall);
}
else
{
it.realTimeToCall = it.startTimeToCall;
}
it.totalRepeatCount = repeatCount;
_eventList.Add(it);
}
private void DoProcess(Func <FastqSequence, bool> accept, SmallRNACountMap map, string outputFile, Dictionary <int, CountItem> dic)
{
Progress.SetMessage("Processing " + options.InputFile + " and writing to " + outputFile + "...");
var ccaMap = new MapItemReader(0, 1).ReadFromFile(options.CCAFile).ToDictionary(m => m.Key, m => bool.Parse(m.Value.Value));
var parser = new FastqReader();
var writer = new FastqWriter();
StreamWriter swCount = null;
if (map.HasCountFile)
{
swCount = new StreamWriter(outputFile + ".dupcount");
swCount.WriteLine("Query\tCount\tSequence");
}
try
{
int readcount = 0;
var tmpFile = outputFile + ".tmp";
using (var sr = StreamUtils.GetReader(options.InputFile))
{
using (var sw = StreamUtils.GetWriter(tmpFile, outputFile.ToLower().EndsWith(".gz")))
{
FastqSequence seq;
while ((seq = parser.Parse(sr)) != null)
{
readcount++;
if (readcount % 100000 == 0)
{
Progress.SetMessage("{0} reads processed", readcount);
}
if (!accept(seq))
{
continue;
}
var name = seq.Name;
var sequence = seq.SeqString;
var score = seq.Score;
var len = sequence.Length;
var description = seq.Description;
var count = map.GetCount(seq.Name);
if (map.HasCountFile)
{
swCount.WriteLine("{0}\t{1}\t{2}", seq.Name, count, seq.SeqString);
}
CountItem item;
if (!dic.TryGetValue(sequence.Length, out item))
{
item = new CountItem();
dic[sequence.Length] = item;
}
string clipped;
if (sequence.EndsWith("CCAA"))
{
clipped = "CCAA";
sequence = sequence.Substring(0, sequence.Length - 4);
item.CCAA += count;
}
else if (sequence.EndsWith("CCA"))
{
clipped = "CCA";
sequence = sequence.Substring(0, sequence.Length - 3);
item.CCA += count;
}
else if (sequence.EndsWith("CC"))
{
bool isCCA;
if (ccaMap.TryGetValue(name, out isCCA) && isCCA)
{
clipped = "CC";
sequence = sequence.Substring(0, sequence.Length - 2);
item.CC += count;
}
else
{
clipped = string.Empty;
item.notNTA += count;
}
}
else
{
clipped = string.Empty;
item.notNTA += count;
}
if (!string.IsNullOrEmpty(clipped))
{
var newlen = sequence.Length;
seq.SeqString = sequence;
seq.Score = score.Substring(0, newlen);
seq.Reference = string.Format("{0}{1}{2}", name, SmallRNAConsts.NTA_TAG, clipped);
}
else
{
seq.Reference = string.Format("{0}{1}", name, SmallRNAConsts.NTA_TAG);
}
writer.Write(sw, seq);
if (map.HasCountFile)
{
swCount.WriteLine("{0}\t{1}\t{2}", seq.Name, count, seq.SeqString);
}
}
}
}
File.Move(tmpFile, outputFile);
}
finally
{
if (map.HasCountFile)
{
swCount.Close();
}
}
}
private void AddCount(
CountItem item)
{
PutItem(item);
}
private void DoProcess(Func<FastqSequence, bool> accept, SmallRNACountMap map, string outputFile, Dictionary<int, CountItem> dic)
{
Progress.SetMessage("Processing " + options.InputFile + " and writing to " + outputFile + "...");
var ccaMap = new MapItemReader(0, 1).ReadFromFile(options.CCAFile).ToDictionary(m => m.Key, m => bool.Parse(m.Value.Value));
var parser = new FastqReader();
var writer = new FastqWriter();
StreamWriter swCount = null;
if (map.HasCountFile)
{
swCount = new StreamWriter(outputFile + ".dupcount");
swCount.WriteLine("Query\tCount\tSequence");
}
try
{
int readcount = 0;
var tmpFile = outputFile + ".tmp";
using (var sr = StreamUtils.GetReader(options.InputFile))
{
using (var sw = StreamUtils.GetWriter(tmpFile, outputFile.ToLower().EndsWith(".gz")))
{
FastqSequence seq;
while ((seq = parser.Parse(sr)) != null)
{
readcount++;
if (readcount % 100000 == 0)
{
Progress.SetMessage("{0} reads processed", readcount);
}
if (!accept(seq))
{
continue;
}
var name = seq.Name;
var sequence = seq.SeqString;
var score = seq.Score;
var len = sequence.Length;
var description = seq.Description;
var count = map.GetCount(seq.Name);
if (map.HasCountFile)
{
swCount.WriteLine("{0}\t{1}\t{2}", seq.Name, count, seq.SeqString);
}
CountItem item;
if (!dic.TryGetValue(sequence.Length, out item))
{
item = new CountItem();
dic[sequence.Length] = item;
}
string clipped;
if (sequence.EndsWith("CCAA"))
{
clipped = "CCAA";
sequence = sequence.Substring(0, sequence.Length - 4);
item.CCAA += count;
}
else if (sequence.EndsWith("CCA"))
{
clipped = "CCA";
sequence = sequence.Substring(0, sequence.Length - 3);
item.CCA += count;
}
else if (sequence.EndsWith("CC"))
{
bool isCCA;
if (ccaMap.TryGetValue(name, out isCCA) && isCCA)
{
clipped = "CC";
sequence = sequence.Substring(0, sequence.Length - 2);
item.CC += count;
}
else
{
clipped = string.Empty;
item.notNTA += count;
}
}
else
{
clipped = string.Empty;
item.notNTA += count;
}
if (!string.IsNullOrEmpty(clipped))
{
var newlen = sequence.Length;
seq.SeqString = sequence;
seq.Score = score.Substring(0, newlen);
seq.Reference = string.Format("{0}{1}{2}", name, SmallRNAConsts.NTA_TAG, clipped);
}
else
{
seq.Reference = string.Format("{0}{1}", name, SmallRNAConsts.NTA_TAG);
}
writer.Write(sw, seq);
if (map.HasCountFile)
{
swCount.WriteLine("{0}\t{1}\t{2}", seq.Name, count, seq.SeqString);
}
}
}
}
File.Move(tmpFile, outputFile);
}
finally
{
if (map.HasCountFile)
{
swCount.Close();
}
}
}
