public override IEnumerable<string> Process()
{
List<FeatureItemGroup> groups = new SmallRNAT2CMutationBuilder(options.ExpectRate)
{
Progress = this.Progress
}.Build(options.InputFile);
groups.Sort((m1, m2) => m1[0].Locations[0].PValue.CompareTo(m2[0].Locations[0].PValue));
var unfiltered = Path.ChangeExtension(options.OutputFile, "") + "unfiltered" + Path.GetExtension(options.OutputFile);
new FeatureItemGroupT2CWriter(options.ExpectRate).WriteToFile(unfiltered, groups);
new FeatureItemGroupXmlFormat(true).WriteToFile(unfiltered + ".xml", groups);
groups.RemoveByLocation(m =>
{
return !Accept(m.PValue, m.QueryCountBeforeFilter, m.QueryCount, options.Pvalue, options.MinimumCount, options.ExpectRate);
});
Progress.SetMessage("There are {0} groups containing T2C mutation with pValue < {1} or T2C/Not T2C reads less than {2} with expect error rate {3}", groups.Count, options.Pvalue, options.MinimumCount, options.ExpectRate);
new FeatureItemGroupT2CWriter(options.ExpectRate).WriteToFile(options.OutputFile, groups);
new FeatureItemGroupXmlFormat(true).WriteToFile(options.OutputFile + ".xml", groups);
return new string[] { options.OutputFile, options.OutputFile + ".xml" };
}
public override IEnumerable <string> Process()
{
var sampleInfos = new List <SampleCount>();
using (var sw = new StreamWriter(options.OutputFile))
using (var swUnfiltered = new StreamWriter(Path.ChangeExtension(options.OutputFile, ".unfiltered.tsv")))
{
var header = "File\tCategory\tName\tUniqueRead\tUniqueT2CRead\tUniqueT2CRate\tAvergeT2CIn10BasesOfUniqueRead\tAvergeT2COfUniqueRead\tTotalRead\tTotalT2CRead\tTotalT2CRate\tT2C_pvalue\tAverageT2CIn10BasesOfTotalRead\tAverageT2COfTotalRead";
swUnfiltered.WriteLine(header);
sw.WriteLine(header);
var inputFiles = options.GetCountXmlFiles();
foreach (var file in inputFiles)
{
var sc = new SampleCount();
sc.Name = file.Name;
sampleInfos.Add(sc);
var subjects = new FeatureItemGroupXmlFormat().ReadFromFile(file.File);
var group = subjects.GroupBy(m => m[0].Name.StringBefore(":")).ToList();
foreach (var g in group)
{
var items = g.ToList();
foreach (var item in items)
{
var queries = new HashSet <string>(item.GetAlignedLocations().ConvertAll(l => l.Parent.Qname));
List <FeatureSamLocation> locs = new List <FeatureSamLocation>();
foreach (var l in item)
{
foreach (var loc in l.Locations)
{
foreach (var sl in loc.SamLocations)
{
if (queries.Contains(sl.SamLocation.Parent.Qname))
{
locs.Add(sl);
queries.Remove(sl.SamLocation.Parent.Qname);
}
}
}
}
var t2c = locs.Where(m => m.NumberOfNoPenaltyMutation > 0).ToList();
var ave_t2c_uniquereads = (t2c.Count > 0) ? t2c.ConvertAll(m => m.NumberOfNoPenaltyMutation * 10.0 / m.SamLocation.Parent.Sequence.Length).Average() : 0.0;
var ave_t2c_perread_uniquereads = (t2c.Count > 0) ? t2c.ConvertAll(m => m.NumberOfNoPenaltyMutation).Average() : 0.0;
double ave_t2c_allreads = 0.0;
double ave_t2c_perread_allreads = 0.0;
if (t2c.Count > 0)
{
List <double> values = new List <double>();
List <double> perread_values = new List <double>();
foreach (var t2citem in t2c)
{
var v = t2citem.NumberOfNoPenaltyMutation * 10.0 / t2citem.SamLocation.Parent.Sequence.Length;
for (int i = 0; i < t2citem.SamLocation.Parent.QueryCount; i++)
{
values.Add(v);
perread_values.Add(t2citem.NumberOfNoPenaltyMutation);
}
}
ave_t2c_allreads = values.Average();
ave_t2c_perread_allreads = perread_values.Average();
}
var totalCount = locs.Sum(l => l.SamLocation.Parent.QueryCount);
var totalT2CCount = t2c.Sum(l => l.SamLocation.Parent.QueryCount);
var pvalue = SmallRNAT2CMutationBuilder.CalculateT2CPvalue(totalCount, totalT2CCount, options.ExpectRate);
var t2crate = totalT2CCount == 0 ? 0 : totalT2CCount * 1.0 / totalCount;
var value = string.Format("{0}\t{1}\t{2}\t{3:0.###}\t{4:0.###}\t{5:0.###}\t{6:0.###}\t{7:0.###}\t{8:0.###}\t{9:0.###}\t{10:0.###}\t{11:0.###E+0}\t{12:0.###}\t{13:0.###}",
file.Name,
g.Key,
item.Name,
locs.Count,
t2c.Count,
t2c.Count * 1.0 / locs.Count,
ave_t2c_uniquereads,
ave_t2c_perread_uniquereads,
totalCount,
totalT2CCount,
t2crate,
pvalue,
ave_t2c_allreads,
ave_t2c_perread_allreads);
swUnfiltered.WriteLine(value);
if (!ParclipSmallRNAT2CBuilder.Accept(pvalue, totalCount, totalT2CCount, options.Pvalue, options.MinimumCount, options.ExpectRate))
{
continue;
}
sw.WriteLine(value);
sc.GoodReadCount += totalCount;
sc.GoodT2CReadCount += totalT2CCount;
if (g.Key.Equals(SmallRNAConsts.miRNA))
{
sc.MiRNACount++;
}
else if (g.Key.Equals(SmallRNAConsts.tRNA))
{
sc.TRNACount++;
}
else
{
sc.OtherSmallRNACount++;
}
}
}
}
}
using (var sw = new StreamWriter(options.OutputFile + ".summary"))
{
sw.WriteLine("File\tTotalRead\tT2CRead\tT2CRate\tSmallRNA\tMicroRNA\ttRNA\tOtherSmallRNA");
foreach (var si in sampleInfos)
{
sw.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}",
si.Name,
si.GoodReadCount,
si.GoodT2CReadCount,
si.GoodT2CRate,
si.SmallRNACount,
si.MiRNACount,
si.TRNACount,
si.OtherSmallRNACount);
}
}
return(new[] { Path.GetFullPath(options.OutputFile), Path.GetFullPath(options.OutputFile + ".summary") });
}