public virtual SmallRNACountMap GetCountMap()
{
if (cm == null)
{
cm = new SmallRNACountMap(this.CountFile);
}
return cm;
}
public virtual SmallRNACountMap GetCountMap()
{
if (cm == null)
{
cm = new SmallRNACountMap(this.CountFile);
}
return(cm);
}
public override SmallRNACountMap GetCountMap()
{
if (cm == null)
{
cm = new SmallRNACountMap(this.CountFile);
var keys = cm.Counts.Keys.Where(m => m.Contains(SmallRNAConsts.NTA_TAG)).ToArray();
foreach (var key in keys)
{
var purekey = key.StringBefore(SmallRNAConsts.NTA_TAG);
cm.Counts[purekey] = cm.Counts[key];
}
}
return(cm);
}
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();
}
}
}
public int Extract(string sourceFile, string targetFile, IEnumerable<string> exceptQueryNames, string countFile)
{
int result = 0;
var except = new HashSet<string>(exceptQueryNames);
SmallRNACountMap cm = new SmallRNACountMap();
StreamWriter swCount = null;
if (File.Exists(countFile))
{
var oldCm = new SmallRNACountMap(countFile);
foreach (var c in oldCm.Counts)
{
cm.Counts[c.Key.StringBefore(SmallRNAConsts.NTA_TAG)] = c.Value;
}
swCount = new StreamWriter(targetFile + ".dupcount");
}
try
{
using (var sw = StreamUtils.GetWriter(targetFile, targetFile.ToLower().EndsWith(".gz")))
{
using (var sr = SAMFactory.GetReader(sourceFile, true))
{
string line;
var count = 0;
while ((line = sr.ReadLine()) != null)
{
count++;
if (count % 100000 == 0)
{
Progress.SetMessage("{0} reads", count);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
var ss = SAMUtils.Parse<SAMItemSlim>(line);
ss.Qname = ss.Qname.StringBefore(SmallRNAConsts.NTA_TAG);
if (except.Contains(ss.Qname))
{
continue;
}
if (Filter != null && !Filter.Accept(ss))
{
continue;
}
except.Add(ss.Qname);
ss.WriteFastq(sw);
if (swCount != null)
{
swCount.WriteLine("{0}\t{1}", ss.Qname, cm.Counts[ss.Qname]);
}
result++;
}
}
}
}
finally
{
if (swCount != null)
{
swCount.Close();
}
}
return result;
}
public override IEnumerable <string> Process()
{
var baminfofiles = Directory.GetFiles(options.RootDirectory, "*.bam.info", SearchOption.AllDirectories);
var baminfogroup = baminfofiles.GroupBy(m => Path.GetDirectoryName(Path.GetDirectoryName(m))).ToList();
bool singleDirectory = false;
string singleDirectoryPath = "";
var result = new List <string>();
if (baminfogroup.Count == 1)
{
Progress.SetMessage("Single directory mode");
singleDirectory = true;
singleDirectoryPath = baminfogroup.First().Key;
baminfogroup = baminfofiles.GroupBy(m => Path.GetDirectoryName(m)).ToList();
result.Add(singleDirectoryPath);
}
else
{
Progress.SetMessage("Multiple directories mode");
}
Progress.SetMessage("Total {0} info files in {1} directory/directories found.", baminfofiles.Length, singleDirectory ? 1 : baminfogroup.Count);
var files = new List <string>();
int count = 0;
foreach (var group in baminfogroup)
{
count++;
var file = group.First();
Progress.SetMessage("{0}/{1} : Checking {2} ...", count, baminfogroup.Count, file);
var lines = File.ReadAllLines(file);
var countfileline = lines.FirstOrDefault(m => m.StartsWith("#countFile"));
if (string.IsNullOrWhiteSpace(countfileline))
{
Progress.SetMessage(" not count file used, ignore.");
continue;
}
var countfile = countfileline.StringAfter("\t");
if (!File.Exists(countfile))
{
Progress.SetMessage(" count file {0} not exist, ignore.", countfile);
continue;
}
var countIndex = lines.ToList().FindIndex(m => m.StartsWith("TotalReads"));
var totalCountInInfoFile = int.Parse(lines[countIndex].StringAfter("\t"));
var totalCountInCountFile = new SmallRNACountMap(countfile).GetTotalCount();
if (totalCountInInfoFile != totalCountInCountFile)
{
Progress.SetMessage(" Failed : {0} : {1} => {2}", file, totalCountInInfoFile, totalCountInCountFile);
foreach (var f in group)
{
files.Add(f);
}
if (!singleDirectory)
{
result.Add(group.Key);
}
if (options.PerformUpdate && singleDirectory)
{
lines[countIndex] = "TotalReads\t" + totalCountInCountFile.ToString();
File.WriteAllLines(file, lines);
}
}
}
if (options.PerformUpdate)
{
if (!singleDirectory)
{
Progress.SetMessage("Updating {0} info files from {1} groups ...", files.Count, result.Count);
count = 0;
foreach (var file in files)
{
count++;
Progress.SetMessage("{0}/{1}: updating {2} ...", count, files.Count, file);
var lines = File.ReadAllLines(file);
var countfileline = lines.FirstOrDefault(m => m.StartsWith("#countFile"));
var countfile = countfileline.StringAfter("\t");
var countIndex = lines.ToList().FindIndex(m => m.StartsWith("TotalReads"));
var totalCountInInfoFile = int.Parse(lines[countIndex].StringAfter("\t"));
var totalCountInCountFile = new SmallRNACountMap(countfile).GetTotalCount();
if (totalCountInInfoFile != totalCountInCountFile)
{
lines[countIndex] = "TotalReads\t" + totalCountInCountFile.ToString();
File.WriteAllLines(file, lines);
}
}
Progress.SetMessage("Please redo the category analysis which uses the information from following directoris :");
foreach (var dir in result)
{
Progress.SetMessage(" " + dir);
}
}
else
{
Progress.SetMessage("Please redo the category analysis which uses the information from following directory :");
Progress.SetMessage(" " + singleDirectoryPath);
}
}
else
{
if (files.Count > 0)
{
Progress.SetMessage("Total {0} info files from {1} groups need to be updated.", files.Count, result.Count);
foreach (var dir in result)
{
Progress.SetMessage(" " + dir);
}
Progress.SetMessage("Please redo the smallrna_baminfo_fix with option --update in each directory and redo corresponding category analysis");
}
else
{
Progress.SetMessage("No failed counting found.");
}
}
return(result);
}
public override SmallRNACountMap GetCountMap()
{
if (cm == null)
{
cm = new SmallRNACountMap(this.CountFile);
var keys = cm.Counts.Keys.Where(m => m.Contains(SmallRNAConsts.NTA_TAG)).ToArray();
foreach (var key in keys)
{
var purekey = key.StringBefore(SmallRNAConsts.NTA_TAG);
cm.Counts[purekey] = cm.Counts[key];
}
}
return cm;
}
public override IEnumerable <string> Process()
{
var result = new List <string>();
var except = new HashSet <string>();
if (File.Exists(options.XmlFile))
{
//exclude the reads mapped to features no matter how many number of mismatch it has
var allmapped = new FeatureItemGroupXmlFormat().ReadFromFile(options.XmlFile);
except.UnionWith(from g in allmapped
from f in g
from l in f.Locations
from sl in l.SamLocations
select sl.SamLocation.Parent.Qname.StringBefore(SmallRNAConsts.NTA_TAG));
}
if (File.Exists(options.ExcludeFile))
{
except.UnionWith(from l in File.ReadAllLines(options.ExcludeFile)
select l.StringBefore(SmallRNAConsts.NTA_TAG));
}
SmallRNACountMap cm = options.GetCountMap();
var keys = cm.Counts.Keys.Where(m => m.Contains(SmallRNAConsts.NTA_TAG)).ToArray();
foreach (var key in keys)
{
cm.Counts[key.StringBefore(SmallRNAConsts.NTA_TAG)] = cm.Counts[key];
}
StreamWriter swCount = null;
if (File.Exists(options.CountFile))
{
swCount = new StreamWriter(options.OutputFile + ".dupcount");
}
Progress.SetMessage("output unmapped query...");
try
{
using (var sw = StreamUtils.GetWriter(options.OutputFile, options.OutputFile.ToLower().EndsWith(".gz")))
{
using (var sr = StreamUtils.GetReader(options.InputFile))
{
FastqReader reader = new FastqReader();
FastqWriter writer = new FastqWriter();
FastqSequence ss;
var count = 0;
while ((ss = reader.Parse(sr)) != null)
{
count++;
if (count % 100000 == 0)
{
Progress.SetMessage("{0} reads", count);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
ss.Reference = ss.Name.StringBefore(SmallRNAConsts.NTA_TAG) + " " + ss.Description;
if (except.Contains(ss.Name))
{
continue;
}
if (Accept != null && !Accept(ss))
{
continue;
}
except.Add(ss.Name);
writer.Write(sw, ss);
if (swCount != null)
{
int cmcount;
if (!cm.Counts.TryGetValue(ss.Name, out cmcount))
{
throw new Exception(string.Format("Cannot find {0} in count map", ss.Name));
}
swCount.WriteLine("{0}\t{1}", ss.Name, cmcount);
}
}
}
}
}
finally
{
if (swCount != null)
{
swCount.Close();
}
}
Progress.End();
return(result);
}
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();
}
}
}
public override IEnumerable<string> Process()
{
var baminfofiles = Directory.GetFiles(options.RootDirectory, "*.bam.info", SearchOption.AllDirectories);
var baminfogroup = baminfofiles.GroupBy(m => Path.GetDirectoryName(Path.GetDirectoryName(m))).ToList();
bool singleDirectory = false;
string singleDirectoryPath = "";
var result = new List<string>();
if (baminfogroup.Count == 1)
{
Progress.SetMessage("Single directory mode");
singleDirectory = true;
singleDirectoryPath = baminfogroup.First().Key;
baminfogroup = baminfofiles.GroupBy(m => Path.GetDirectoryName(m)).ToList();
result.Add(singleDirectoryPath);
}
else
{
Progress.SetMessage("Multiple directories mode");
}
Progress.SetMessage("Total {0} info files in {1} directory/directories found.", baminfofiles.Length, singleDirectory ? 1 : baminfogroup.Count);
var files = new List<string>();
int count = 0;
foreach (var group in baminfogroup)
{
count++;
var file = group.First();
Progress.SetMessage("{0}/{1} : Checking {2} ...", count, baminfogroup.Count, file);
var lines = File.ReadAllLines(file);
var countfileline = lines.FirstOrDefault(m => m.StartsWith("#countFile"));
if (string.IsNullOrWhiteSpace(countfileline))
{
Progress.SetMessage(" not count file used, ignore.");
continue;
}
var countfile = countfileline.StringAfter("\t");
if (!File.Exists(countfile))
{
Progress.SetMessage(" count file {0} not exist, ignore.", countfile);
continue;
}
var countIndex = lines.ToList().FindIndex(m => m.StartsWith("TotalReads"));
var totalCountInInfoFile = int.Parse(lines[countIndex].StringAfter("\t"));
var totalCountInCountFile = new SmallRNACountMap(countfile).GetTotalCount();
if (totalCountInInfoFile != totalCountInCountFile)
{
Progress.SetMessage(" Failed : {0} : {1} => {2}", file, totalCountInInfoFile, totalCountInCountFile);
foreach (var f in group)
{
files.Add(f);
}
if (!singleDirectory)
{
result.Add(group.Key);
}
if (options.PerformUpdate && singleDirectory)
{
lines[countIndex] = "TotalReads\t" + totalCountInCountFile.ToString();
File.WriteAllLines(file, lines);
}
}
}
if (options.PerformUpdate)
{
if (!singleDirectory)
{
Progress.SetMessage("Updating {0} info files from {1} groups ...", files.Count, result.Count);
count = 0;
foreach (var file in files)
{
count++;
Progress.SetMessage("{0}/{1}: updating {2} ...", count, files.Count, file);
var lines = File.ReadAllLines(file);
var countfileline = lines.FirstOrDefault(m => m.StartsWith("#countFile"));
var countfile = countfileline.StringAfter("\t");
var countIndex = lines.ToList().FindIndex(m => m.StartsWith("TotalReads"));
var totalCountInInfoFile = int.Parse(lines[countIndex].StringAfter("\t"));
var totalCountInCountFile = new SmallRNACountMap(countfile).GetTotalCount();
if (totalCountInInfoFile != totalCountInCountFile)
{
lines[countIndex] = "TotalReads\t" + totalCountInCountFile.ToString();
File.WriteAllLines(file, lines);
}
}
Progress.SetMessage("Please redo the category analysis which uses the information from following directoris :");
foreach (var dir in result)
{
Progress.SetMessage(" " + dir);
}
}
else
{
Progress.SetMessage("Please redo the category analysis which uses the information from following directory :");
Progress.SetMessage(" " + singleDirectoryPath);
}
}
else
{
if (files.Count > 0)
{
Progress.SetMessage("Total {0} info files from {1} groups need to be updated.", files.Count, result.Count);
foreach (var dir in result)
{
Progress.SetMessage(" " + dir);
}
Progress.SetMessage("Please redo the smallrna_baminfo_fix with option --update in each directory and redo corresponding category analysis");
}
else
{
Progress.SetMessage("No failed counting found.");
}
}
return result;
}
public override IEnumerable<string> Process()
{
PileupCountList pc = new PileupCountList();
var format = options.GetSAMFormat();
var cm = new SmallRNACountMap(options.CountFile);
var srItems = SequenceRegionUtils.GetSequenceRegions(options.CoordinateFile, "miRNA", options.BedAsGtf);
srItems.ForEach(m =>
{
m.Seqname = m.Seqname.StringAfter("chr");
});
var srmap = srItems.GroupBy(m => m.Seqname).ToDictionary(m => m.Key, m => m.ToList());
StreamWriter swScript = null;
try
{
if (options.ExportIgvScript)
{
swScript = new StreamWriter(options.OutputFile + ".igv");
swScript.WriteLine("snapshotDirectory {0}", Path.GetDirectoryName(options.OutputFile).Replace('\\', '/'));
}
using (StreamWriter sw = new StreamWriter(options.OutputFile))
{
sw.WriteLine(@"##fileformat=VCFv4.2
##fileDate={0:yyyyMMdd}
##source={1}
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description=""Number of Samples With Data"">
##INFO=<ID=DP,Number=1,Type=Integer,Description=""Total Depth"">
##INFO=<ID=AF,Number=A,Type=Float,Description=""Allele Frequency"">
##INFO=<ID=FP,Number=1,Type=Float,Description=""Fisher Exact Test P-Value"">
##INFO=<ID=MN,Number=.,Type=String,Description=""miRNA name contains this position"">
##FILTER=<ID=FisherET,Description=""Fisher exact test Pvalue less than {2}"">
##FILTER=<ID=AltAlleFreq,Description=""Alternative allele frequency less than {3}"">
##FILTER=<ID=notMiRNA,Description=""Position not located in miRNA locus"">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description=""Read Depth"">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description=""Allelic Depth"">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT {4}",
DateTime.Now,
"PileupCountBuilder",
options.FisherPValue,
options.MinimumAlternativeAlleleFrequency,
Path.GetFileNameWithoutExtension(options.InputFile));
using (var sr = SAMFactory.GetReader(options.InputFile, true))
{
int count = 0;
string line;
while ((line = sr.ReadLine()) != null)
{
count++;
if (count % 100 == 0)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
if (count % 100000 == 0)
{
Progress.SetMessage("{0} reads processed", count);
}
var parts = line.Split('\t');
var qname = parts[SAMFormatConst.QNAME_INDEX];
var seq = parts[SAMFormatConst.SEQ_INDEX];
//too short
if (seq.Length < options.MinimumReadLength)
{
continue;
}
SAMFlags flag = (SAMFlags)int.Parse(parts[SAMFormatConst.FLAG_INDEX]);
//unmatched
if (flag.HasFlag(SAMFlags.UnmappedQuery))
{
continue;
}
var cigar = parts[SAMFormatConst.CIGAR_INDEX];
//insertion/deletion
if (cigar.Any(m => m == 'I' || m == 'D'))
{
continue;
}
var sam = new SAMAlignedItem()
{
Qname = qname,
};
bool isReversed = flag.HasFlag(SAMFlags.QueryOnReverseStrand);
char strand;
if (isReversed)
{
strand = '-';
sam.Sequence = SequenceUtils.GetReverseComplementedSequence(seq);
}
else
{
strand = '+';
sam.Sequence = seq;
}
var loc = new SAMAlignedLocation(sam)
{
Seqname = parts[SAMFormatConst.RNAME_INDEX].StringAfter("chr"),
Start = int.Parse(parts[SAMFormatConst.POS_INDEX]),
Strand = strand,
Cigar = parts[SAMFormatConst.CIGAR_INDEX],
MismatchPositions = format.GetMismatchPositions(parts),
NumberOfMismatch = format.GetNumberOfMismatch(parts),
Sequence = seq
};
loc.ParseEnd(sam.Sequence);
sam.AddLocation(loc);
if (format.HasAlternativeHits)
{
format.ParseAlternativeHits(parts, sam);
}
var finished = pc.Add(sam, cm.GetCount(sam.Qname));
if (null == finished || 0 == finished.Count)
{
continue;
}
foreach (var fin in finished)
{
//if (fin.Chromosome.Equals("1") && fin.Position == 5160725)
//{
// Console.WriteLine(fin);
//}
var ft = fin.FisherExactTest();
if (ft.PValue <= options.FisherPValue)
{
var total = fin.Sum(m => m.Value);
var minallele = total * options.MinimumAlternativeAlleleFrequency;
if (ft.Sample2.Failed >= minallele)
{
List<GtfItem> srs;
List<string> ranges = new List<string>();
if (srmap.TryGetValue(sam.Locations[0].Seqname, out srs))
{
foreach (var seqr in srs)
{
if (seqr.Contains(fin.Position))
{
ranges.Add(seqr.GetNameLocation());
}
}
}
var alter = (from r in fin
where r.Key != fin.Reference
orderby r.Key
select r).ToList();
var str = string.Format("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\tNS={7};DP={8};AF={9};FP={10:0.##E0}{11}\tDP:AD\t{12}:{13},{14}",
fin.Chromosome,
fin.Position,
".",
fin.Reference,
(from r in alter
select r.Key.ToString()).Merge(","),
0,
ranges.Count == 0 ? "notMiRNA" : "PASS",
1,
total,
(from r in alter
select string.Format("{0:0.###}", r.Value * 1.0 / total)).Merge(","),
ft.PValue,
ranges.Count == 0 ? "" : ";" + ranges.Merge(","),
total,
ft.Sample2.Succeed,
(from r in alter
select r.Value.ToString()).Merge(","));
sw.WriteLine(str);
//Console.WriteLine(str);
if (swScript != null && ranges.Count > 0)
{
swScript.WriteLine(@"goto {0}:{1}
sort position
snapshot {0}_{2}_{1}.png", fin.Chromosome, fin.Position, ranges[0].Replace('(', '_').Replace(')', '_').Replace(':', '_'));
}
}
}
}
finished.Clear();
}
}
}
}
finally
{
if (swScript != null)
{
swScript.Close();
}
}
return new string[] { options.OutputFile };
}
