public List <ChromosomeCountSlimItem> Build(string fileName)
{
if (File.Exists(options.CategoryMapFile))
{
Progress.SetMessage("Reading name map file " + options.CategoryMapFile + " ...");
nameMap = new MapItemReader(0, 1).ReadFromFile(options.CategoryMapFile).ToDictionary(m => m.Key, m => m.Value.Value);
}
var result = new List <ChromosomeCountSlimItem>();
var queries = new Dictionary <string, SAMChromosomeItem>();
var chromosomes = new Dictionary <string, ChromosomeCountSlimItem>();
Regex chromosomeRegex = null;
Func <string, bool> acceptChromosome;
if (string.IsNullOrEmpty(options.ChromosomePattern))
{
acceptChromosome = m => true;
}
else
{
chromosomeRegex = new Regex(options.ChromosomePattern);
acceptChromosome = m => chromosomeRegex.Match(m).Success;
}
Progress.SetMessage("Parsing alignment file " + fileName + " ...");
using (var sr = SAMFactory.GetReader(fileName, true))
{
int count = 0;
int waitingcount = 0;
string line;
while ((line = sr.ReadLine()) != null)
{
if (count % 1000 == 0)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
if (count % 100000 == 0 && count > 0)
{
Progress.SetMessage("{0} candidates from {1} reads", waitingcount, count);
}
count++;
var parts = line.Split('\t');
SAMFlags flag = (SAMFlags)int.Parse(parts[SAMFormatConst.FLAG_INDEX]);
//unmatched
if (flag.HasFlag(SAMFlags.UnmappedQuery))
{
continue;
}
var seqname = GetName(parts[SAMFormatConst.RNAME_INDEX]);
if (!acceptChromosome(seqname))
{
continue;
}
var qname = parts[SAMFormatConst.QNAME_INDEX];
SAMChromosomeItem query;
if (!queries.TryGetValue(qname, out query))
{
query = new SAMChromosomeItem();
query.Qname = qname;
queries[qname] = query;
if (options.KeepSequence)
{
query.Sequence = parts[SAMFormatConst.SEQ_INDEX];
if (flag.HasFlag(SAMFlags.QueryOnReverseStrand))
{
query.Sequence = SequenceUtils.GetReverseComplementedSequence(query.Sequence);
}
}
}
query.Chromosomes.Add(seqname);
ChromosomeCountSlimItem item;
if (!chromosomes.TryGetValue(seqname, out item))
{
item = new ChromosomeCountSlimItem();
item.Names.Add(seqname);
chromosomes[seqname] = item;
result.Add(item);
}
item.Queries.Add(query);
waitingcount++;
}
Progress.SetMessage("Finally, there are {0} candidates from {1} reads", waitingcount, count);
}
foreach (var query in queries.Values)
{
query.Chromosomes = query.Chromosomes.Distinct().OrderBy(m => m).ToList();
}
foreach (var sam in chromosomes.Values)
{
sam.Queries = sam.Queries.Distinct().OrderBy(m => m.Qname).ToList();
}
if (!string.IsNullOrEmpty(options.PreferPrefix))
{
foreach (var query in queries.Values)
{
if (query.Chromosomes.Any(l => l.StartsWith(options.PreferPrefix)))
{
var chroms = query.Chromosomes.Where(l => l.StartsWith(options.PreferPrefix)).ToArray();
foreach (var chrom in chroms)
{
chromosomes[chrom].Queries.Remove(query);
query.Chromosomes.Remove(chrom);
}
}
}
result.RemoveAll(l => l.Queries.Count == 0);
}
return(result);
}
public List<ChromosomeCountSlimItem> Build(string fileName)
{
if (File.Exists(options.CategoryMapFile))
{
Progress.SetMessage("Reading name map file " + options.CategoryMapFile + " ...");
nameMap = new MapItemReader(0, 1).ReadFromFile(options.CategoryMapFile).ToDictionary(m => m.Key, m => m.Value.Value);
}
var result = new List<ChromosomeCountSlimItem>();
var queries = new Dictionary<string, SAMChromosomeItem>();
var chromosomes = new Dictionary<string, ChromosomeCountSlimItem>();
Progress.SetMessage("Parsing alignment file " + fileName + " ...");
using (var sr = SAMFactory.GetReader(fileName, true))
{
int count = 0;
int waitingcount = 0;
string line;
while ((line = sr.ReadLine()) != null)
{
if (count % 1000 == 0)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
}
if (count % 100000 == 0 && count > 0)
{
Progress.SetMessage("{0} candidates from {1} reads", waitingcount, count);
}
count++;
var parts = line.Split('\t');
SAMFlags flag = (SAMFlags)int.Parse(parts[SAMFormatConst.FLAG_INDEX]);
//unmatched
if (flag.HasFlag(SAMFlags.UnmappedQuery))
{
continue;
}
var qname = parts[SAMFormatConst.QNAME_INDEX];
SAMChromosomeItem query;
if (!queries.TryGetValue(qname, out query))
{
query = new SAMChromosomeItem();
query.Qname = qname;
queries[qname] = query;
if (options.KeepSequence)
{
query.Sequence = parts[SAMFormatConst.SEQ_INDEX];
if (flag.HasFlag(SAMFlags.QueryOnReverseStrand))
{
query.Sequence = SequenceUtils.GetReverseComplementedSequence(query.Sequence);
}
}
}
var seqname = GetName(parts[SAMFormatConst.RNAME_INDEX]);
query.Chromosomes.Add(seqname);
ChromosomeCountSlimItem item;
if (!chromosomes.TryGetValue(seqname, out item))
{
item = new ChromosomeCountSlimItem();
item.Names.Add(seqname);
chromosomes[seqname] = item;
result.Add(item);
}
item.Queries.Add(query);
waitingcount++;
}
Progress.SetMessage("Finally, there are {0} candidates from {1} reads", waitingcount, count);
}
foreach (var query in queries.Values)
{
query.Chromosomes = query.Chromosomes.Distinct().OrderBy(m => m).ToList();
}
foreach (var sam in chromosomes.Values)
{
sam.Queries = sam.Queries.Distinct().OrderBy(m => m.Qname).ToList();
}
if (!string.IsNullOrEmpty(options.PreferPrefix))
{
foreach (var query in queries.Values)
{
if (query.Chromosomes.Any(l => l.StartsWith(options.PreferPrefix)))
{
var chroms = query.Chromosomes.Where(l => l.StartsWith(options.PreferPrefix)).ToArray();
foreach (var chrom in chroms)
{
chromosomes[chrom].Queries.Remove(query);
query.Chromosomes.Remove(chrom);
}
}
}
result.RemoveAll(l => l.Queries.Count == 0);
}
return result;
}
public List <ChromosomeCountSlimItem> ReadFromFile(string fileName)
{
var result = new List <ChromosomeCountSlimItem>();
using (XmlReader source = XmlReader.Create(fileName))
{
//Progress.SetMessage("read queries ...");
var queries = new List <SAMChromosomeItem>();
source.ReadToFollowing("queries");
if (source.ReadToDescendant("query"))
{
do
{
var query = new SAMChromosomeItem();
queries.Add(query);
query.Qname = source.GetAttribute("name");
query.QueryCount = int.Parse(source.GetAttribute("count"));
var seqAtrr = source.GetAttribute("seq");
if (seqAtrr != null)
{
query.Sequence = seqAtrr;
}
var sampleAtrr = source.GetAttribute("sample");
if (sampleAtrr != null)
{
query.Sample = sampleAtrr;
}
if (source.ReadToDescendant("location"))
{
do
{
var seqname = source.GetAttribute("seqname");
if (!query.Chromosomes.Contains(seqname))
{
query.Chromosomes.Add(seqname);
}
} while (source.ReadToNextSibling("location"));
}
} while (source.ReadToNextSibling("query"));
}
Progress.SetMessage("{0} queries read.", queries.Count);
var qmmap = queries.ToDictionary(m => m.Qname);
queries.Clear();
//Progress.SetMessage("read chromosomes ...");
source.ReadToFollowing("subjectResult");
ChromosomeCountSlimItem item = null;
while (source.Read())
{
if (source.NodeType == XmlNodeType.Element)
{
if (source.Name.Equals("subjectGroup"))
{
item = new ChromosomeCountSlimItem();
result.Add(item);
}
else if (source.Name.Equals("subject"))
{
item.Names.Add(source.GetAttribute("name"));
}
else if (source.Name.Equals("query"))
{
var q = qmmap[source.GetAttribute("qname")];
item.Queries.Add(q);
}
}
}
qmmap.Clear();
Progress.SetMessage("{0} subject groups read.", result.Count);
result.ForEach(l =>
{
if (l.Names.Count > 1)
{
l.Names = l.Names.Distinct().ToList();
}
});
return(result);
}
}
