public int AddByScore(SAMAlignedItem item, int count, int minScore)
{
int result = 0;
string align, score;
item.GetSequenceScore(out align, out score);
for (int i = 0; i < align.Length; i++)
{
if (minScore > 0)
{
var bq = (int)(score[i]) - 33;
if (bq < minScore)
{
result++;
continue;
}
}
var c = align[i];
var dic = Count[(int)(item.Pos) + i];
int curcount = 0;
if (dic.TryGetValue(c, out curcount))
{
dic[c] = curcount + count;
}
else
{
dic[c] = count;
}
}
return result;
}
public static List <SAMAlignedItem> ToSAMAlignedItems(this XElement root)
{
var result = new List <SAMAlignedItem>();
foreach (var queryEle in root.Element("queries").Elements("query"))
{
var query = new SAMAlignedItem();
query.Qname = queryEle.Attribute("name").Value;
query.Sequence = queryEle.Attribute("sequence").Value;
query.QueryCount = int.Parse(queryEle.Attribute("count").Value);
query.Sample = queryEle.GetAttributeValue("sample", null);
result.Add(query);
foreach (var locEle in queryEle.Elements("location"))
{
var loc = new SAMAlignedLocation(query);
loc.ParseLocation(locEle);
loc.Cigar = locEle.Attribute("cigar").Value;
loc.AlignmentScore = int.Parse(locEle.Attribute("score").Value);
loc.MismatchPositions = locEle.Attribute("mdz").Value;
loc.NumberOfMismatch = int.Parse(locEle.Attribute("nmi").Value);
var nnmpattr = locEle.Attribute("nnpm");
if (nnmpattr != null)
{
loc.NumberOfNoPenaltyMutation = int.Parse(nnmpattr.Value);
}
}
}
return(result);
}
public void TestParseAlternativeHits()
{
var bwaformat = new BwaFormat();
var sam = new SAMAlignedItem();
Assert.IsTrue(bwaformat.HasAlternativeHits);
var parts = "HWI-ST508:275:D2A2JACXX:3:1105:21234:49676\t0\t1_hsa\t564952\t0\t36M\t*\t0\t0\tAGTAAGGTCAGCTAATTAAGCTATCGGGCCCATAAA\t@@?DDFF?FFFDBHIIJIJIJJGJJJJJJJJJJJJJ\tRG:Z:2570-KCV-01-19\tXT:A:R\tNM:i:3\tX0:i:4\tX1:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tMD:Z:15A18C0C0\tXA:Z:M_hsa,+4403,36M,3;17_hsa,+19506660,36M,3;X_hsa,-55206629,36M,3;".Split('\t');
bwaformat.ParseAlternativeHits(parts, sam);
}
public SAMAlignedLocation(SAMAlignedItem parent)
{
this.Features = new List<ISequenceRegion>();
if (parent != null)
{
parent.AddLocation(this);
}
}
public SAMAlignedLocation(SAMAlignedItem parent)
{
this.Features = new List <ISequenceRegion>();
if (parent != null)
{
parent.AddLocation(this);
}
}
public List<PileupCount> Add(SAMAlignedItem item, int count)
{
List<PileupCount> result = null;
if (!item.Locations[0].Seqname.Equals(this.Chromosome))
{
result = Count;
Count = new List<PileupCount>();
}
else if (this.Position != -1)
{
if (item.Pos > this.Count.Last().Position)
{
result = Count;
Count = new List<PileupCount>();
}
else
{
int finishedCount = (int)(item.Pos - this.Position);
if (finishedCount > 0)
{
result = new List<PileupCount>();
result.AddRange(Count.Take(finishedCount));
Count.RemoveRange(0, finishedCount);
}
}
}
string align, refer;
item.GetSequences(out align, out refer);
for (int i = Count.Count; i < align.Length; i++)
{
Count.Add(new PileupCount()
{
Chromosome = item.Locations[0].Seqname,
Position = item.Locations[0].Start + i,
Reference = refer[i]
});
}
for (int i = 0; i < align.Length; i++)
{
var c = align[i];
var dic = Count[i];
int curcount = 0;
if (dic.TryGetValue(c, out curcount))
{
dic[c] = curcount + count;
}
else
{
dic[c] = count;
}
}
return result;
}
public void TestGetGetSequences()
{
SAMAlignedItem item = new SAMAlignedItem();
item.AddLocation(new SAMAlignedLocation(item)
{
Cigar = "5S18M2D19M5S",
Start = 39979942,
MismatchPositions = "18^CA10T8",
Sequence = "aaaaaGTAGTACCAACTGTAAGTCCTTATCTTCATACTTTGTaaaaa"
});
string align, refer;
item.GetSequences(out align, out refer);
Assert.AreEqual("GTAGTACCAACTGTAAGT CCTTATCTTCATACTTTGT", align);
Assert.AreEqual("GTAGTACCAACTGTAAGTCACCTTATCTTCTTACTTTGT", refer);
}
public static List <SAMAlignedItem> ReadFrom(XmlReader source)
{
var result = new List <SAMAlignedItem>();
source.ReadToFollowing("queries");
if (source.ReadToDescendant("query"))
{
do
{
var query = new SAMAlignedItem();
result.Add(query);
query.Qname = source.GetAttribute("name");
query.Sequence = source.GetAttribute("sequence");
query.QueryCount = int.Parse(source.GetAttribute("count"));
query.Sample = source.GetAttribute("sample");
if (source.ReadToDescendant("location"))
{
do
{
var loc = new SAMAlignedLocation(query);
loc.Seqname = source.GetAttribute("seqname");
loc.Start = long.Parse(source.GetAttribute("start"));
loc.End = long.Parse(source.GetAttribute("end"));
loc.Strand = source.GetAttribute("strand")[0];
loc.Cigar = source.GetAttribute("cigar");
loc.AlignmentScore = int.Parse(source.GetAttribute("score"));
loc.MismatchPositions = source.GetAttribute("mdz");
loc.NumberOfMismatch = int.Parse(source.GetAttribute("nmi"));
var nnmpattr = source.GetAttribute("nnpm");
if (nnmpattr != null)
{
loc.NumberOfNoPenaltyMutation = int.Parse(nnmpattr);
}
} while (source.ReadToNextSibling("location"));
}
} while (source.ReadToNextSibling("query"));
}
return(result);
}
public static List<SAMAlignedItem> ReadFrom(XmlReader source)
{
var result = new List<SAMAlignedItem>();
source.ReadToFollowing("queries");
if (source.ReadToDescendant("query"))
{
do
{
var query = new SAMAlignedItem();
result.Add(query);
query.Qname = source.GetAttribute("name");
query.Sequence = source.GetAttribute("sequence");
query.QueryCount = int.Parse(source.GetAttribute("count"));
query.Sample = source.GetAttribute("sample");
if (source.ReadToDescendant("location"))
{
do
{
var loc = new SAMAlignedLocation(query);
loc.Seqname = source.GetAttribute("seqname");
loc.Start = long.Parse(source.GetAttribute("start"));
loc.End = long.Parse(source.GetAttribute("end"));
loc.Strand = source.GetAttribute("strand")[0];
loc.Cigar = source.GetAttribute("cigar");
loc.AlignmentScore = int.Parse(source.GetAttribute("score"));
loc.MismatchPositions = source.GetAttribute("mdz");
loc.NumberOfMismatch = int.Parse(source.GetAttribute("nmi"));
var nnmpattr = source.GetAttribute("nnpm");
if (nnmpattr != null)
{
loc.NumberOfNoPenaltyMutation = int.Parse(nnmpattr);
}
} while (source.ReadToNextSibling("location"));
}
} while (source.ReadToNextSibling("query"));
}
return result;
}
public void Add(SAMAlignedItem item, int count)
{
string align, refer;
item.GetSequences(out align, out refer);
for (int i = 0; i < align.Length; i++)
{
var c = align[i];
var dic = Count[(int)(item.Pos) + i];
int curcount = 0;
if (dic.TryGetValue(c, out curcount))
{
dic[c] = curcount + count;
}
else
{
dic[c] = count;
}
}
}
public override void ParseAlternativeHits(string[] parts, SAMAlignedItem item)
{
var countstr = GetOptionValue(parts, "X0:i:", false);
if (string.IsNullOrEmpty(countstr))
{
return;
}
var count = int.Parse(countstr) - 1;
if (count == 0)
{
return;
}
var xaz = GetOptionValue(parts, "XA:Z:", false);
if (string.IsNullOrEmpty(xaz))
{
return;
}
var match = _reg.Match(xaz);
for (var i = 0; i < count; i++)
{
var loc = new SAMAlignedLocation(item)
{
Seqname = match.Groups[1].Value,
Strand = match.Groups[2].Value[0],
Start = long.Parse(match.Groups[3].Value)
};
loc.End = loc.Start + item.Locations[0].Length - 1;
loc.Cigar = match.Groups[4].Value;
loc.NumberOfMismatch = int.Parse(match.Groups[5].Value);
item.AddLocation(loc);
}
}
public virtual void ParseAlternativeHits(string[] parts, SAMAlignedItem target)
{
}
public override void ParseAlternativeHits(string[] parts, SAMAlignedItem item)
{
var countstr = GetOptionValue(parts, "X0:i:", false);
if (string.IsNullOrEmpty(countstr))
{
return;
}
var count = int.Parse(countstr) - 1;
if (count == 0)
{
return;
}
var xaz = GetOptionValue(parts, "XA:Z:", false);
if (string.IsNullOrEmpty(xaz))
{
return;
}
var match = _reg.Match(xaz);
for (var i = 0; i < count; i++)
{
var loc = new SAMAlignedLocation(item)
{
Seqname = match.Groups[1].Value,
Strand = match.Groups[2].Value[0],
Start = long.Parse(match.Groups[3].Value)
};
loc.End = loc.Start + item.Locations[0].Length - 1;
loc.Cigar = match.Groups[4].Value;
loc.NumberOfMismatch = int.Parse(match.Groups[5].Value);
item.AddLocation(loc);
}
}
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 };
}
public SAMAlignedItem NextSAMAlignedItem()
{
string line;
while ((line = _file.ReadLine()) != null)
{
var parts = line.Split('\t');
var qname = parts[SAMFormatConst.QNAME_INDEX];
var seq = parts[SAMFormatConst.SEQ_INDEX];
var flag = (SAMFlags) int.Parse(parts[SAMFormatConst.FLAG_INDEX]);
//unmatched
if (flag.HasFlag(SAMFlags.UnmappedQuery))
{
continue;
}
//check map quality
var mapq = int.Parse(parts[SAMFormatConst.MAPQ_INDEX]);
if (mapq < _options.MinimumReadQuality)
{
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],
Start = int.Parse(parts[SAMFormatConst.POS_INDEX]),
Strand = strand,
Cigar = parts[SAMFormatConst.CIGAR_INDEX],
MismatchPositions = _format.GetMismatchPositions(parts),
NumberOfMismatch = _format.GetNumberOfMismatch(parts),
Sequence = seq,
Qual = parts[SAMFormatConst.QUAL_INDEX]
};
loc.ParseEnd(sam.Sequence);
sam.AddLocation(loc);
if (_format.HasAlternativeHits)
{
_format.ParseAlternativeHits(parts, sam);
}
return sam;
}
return null;
}
/// <summary>
/// Add alignment result and return the completed positions
/// </summary>
/// <param name="item">alignment result</param>
/// <returns>completed positions</returns>
public List<AlignedPositionMap> Add(SAMAlignedItem item)
{
List<AlignedPositionMap> result = null;
//if the alignment result moves to another chromosome, all uncompleted positions
//will be completed.
if (!item.Locations[0].Seqname.Equals(this.Chromosome))
{
result = Positions;
Positions = new List<AlignedPositionMap>();
PositionMap = new Dictionary<long, AlignedPositionMap>();
}
else if (this.Position != -1)
{
//if the alignment result position is larger than the last position in the uncompleted positions,
//all uncompleted positions will be completed.
if (item.Pos > this.Positions.Last().Position)
{
result = Positions;
Positions = new List<AlignedPositionMap>();
PositionMap = new Dictionary<long, AlignedPositionMap>();
}
else
{
//set up the completed list
result = new List<AlignedPositionMap>();
while (Positions[0].Position < item.Pos)
{
result.Add(Positions[0]);
PositionMap.Remove(Positions[0].Position);
Positions.RemoveAt(0);
}
}
}
List<AlignedPosition> align = item.GetAlignedPositions();
foreach (var asp in align)
{
AlignedPositionMap dic;
if (!PositionMap.TryGetValue(asp.Position, out dic))
{
dic = new AlignedPositionMap()
{
Chromosome = item.Locations[0].Seqname,
Position = asp.Position
};
Positions.Add(dic);
PositionMap[dic.Position] = dic;
}
List<AlignedPosition> curcount;
if (!dic.TryGetValue(asp.AlignedEvent, out curcount))
{
curcount = new List<AlignedPosition>();
dic[asp.AlignedEvent] = curcount;
}
curcount.Add(asp);
}
return result;
}
public virtual void ParseAlternativeHits(string[] parts, SAMAlignedItem target)
{
}
public void TestAdd()
{
SAMAlignedItem item1 = new SAMAlignedItem()
{
Sequence = "CTCTTAGATCGATGTGGTGCTCCGGAAAAAA",
};
item1.AddLocation(new SAMAlignedLocation(item1)
{
Seqname ="chr13",
Cigar = "5S21M5S",
MismatchPositions = "10T10",
Start = 39979942,
Sequence = "CTCTTAGATCGATGTGGTGCTCCGGAAAAAA"
});
SAMAlignedItem item2 = new SAMAlignedItem()
{
Sequence = "GATGTAGTGCTCCGGATTTTT"
};
item2.AddLocation(new SAMAlignedLocation(item2)
{
Seqname = "chr13",
Cigar = "21M",
MismatchPositions = "5T15",
Start = 39979947,
Sequence = "GATGTAGTGCTCCGGATTTTT"
});
List<PileupCount> all = new List<PileupCount>();
PileupCountList count = new PileupCountList();
var res1 = count.Add(item1, 2);
Assert.AreEqual(0, res1.Count);
var res2 = count.Add(item2, 3);
Assert.AreEqual(5, res2.Count);
all.AddRange(res2);
for (int i = 0; i < res2.Count; i++)
{
Assert.AreEqual(item1.Sequence[5 + i], res2[i].Reference);
Assert.AreEqual(item1.Sequence[5 + i], res2[i].First().Key);
Assert.AreEqual(2, res2[i].First().Value);
Assert.AreEqual(item1.Locations[0].Seqname, res2[i].Chromosome);
Assert.AreEqual(item1.Pos + i, res2[i].Position);
}
item1.Locations[0].Seqname = "chr14";
var res3 = count.Add(item1, 2);
Assert.AreEqual(21, res3.Count);
all.AddRange(res3);
for (int i = 0; i < 16; i++)
{
if (i == 5)
{
Assert.AreEqual('T', res3[i].Reference);
Assert.True(res3[i].ContainsKey('G'));
Assert.AreEqual(2, res3[i]['G']);
Assert.True(res3[i].ContainsKey('A'));
Assert.AreEqual(3, res3[i]['A']);
}
else
{
Assert.AreEqual(item2.Sequence[i], res3[i].Reference);
Assert.AreEqual(item2.Sequence[i], res3[i].First().Key);
Assert.AreEqual(5, res3[i].First().Value);
}
}
for (int i = 16; i < 21; i++)
{
Assert.AreEqual(item2.Sequence[i], res3[i].First().Key);
Assert.AreEqual(3, res3[i].First().Value);
}
var res4 = count.Count;
Assert.AreEqual(21, res4.Count);
all.AddRange(res4);
for (int i = 0; i < res4.Count; i++)
{
Assert.AreEqual(item1.Sequence[5 + i], res4[i].First().Key);
Assert.AreEqual(2, res4[i].First().Value);
Assert.AreEqual(item1.Locations[0].Seqname, res4[i].Chromosome);
Assert.AreEqual(item1.Pos + i, res4[i].Position);
}
//all.ForEach(m => Output(m));
}
public static List<SAMAlignedItem> ToSAMAlignedItems(this XElement root)
{
var result = new List<SAMAlignedItem>();
foreach (var queryEle in root.Element("queries").Elements("query"))
{
var query = new SAMAlignedItem();
query.Qname = queryEle.Attribute("name").Value;
query.Sequence = queryEle.Attribute("sequence").Value;
query.QueryCount = int.Parse(queryEle.Attribute("count").Value);
query.Sample = queryEle.GetAttributeValue("sample", null);
result.Add(query);
foreach (var locEle in queryEle.Elements("location"))
{
var loc = new SAMAlignedLocation(query);
loc.ParseLocation(locEle);
loc.Cigar = locEle.Attribute("cigar").Value;
loc.AlignmentScore = int.Parse(locEle.Attribute("score").Value);
loc.MismatchPositions = locEle.Attribute("mdz").Value;
loc.NumberOfMismatch = int.Parse(locEle.Attribute("nmi").Value);
var nnmpattr = locEle.Attribute("nnpm");
if (nnmpattr != null)
{
loc.NumberOfNoPenaltyMutation = int.Parse(nnmpattr.Value);
}
}
}
return result;
}