public void TestReadWrite()
{
var format = new ChromosomeCountSlimItemXmlFormat(false);
var expectFile = @"../../../data/CMS-306.bam.count.mapped.xml";
var items = TestFile(format, expectFile);
var tempFile = expectFile + ".tmp";
format.WriteToFile(tempFile, items);
TestFile(format, tempFile);
File.Delete(tempFile);
}
public void Test()
{
var items = new ChromosomeCountSlimItemXmlFormat().ReadFromFile(@"../../../data/CMS-306.bam.count.mapped.xml");
var queries = items.GetQueries();
Assert.AreEqual("NB501087:31:HTGWLBGXX:1:21112:13668:5159", queries[1].Qname);
Assert.AreEqual(3, queries[1].Chromosomes.Count);
items.MergeCalculateSortByEstimatedCount();
Assert.AreEqual(1, items.Count);
Assert.AreEqual(2, items[0].Queries.Count);
Assert.AreEqual(2, items[0].Names.Count);
Assert.IsTrue(items[0].Names.Contains("gma-miR166k"));
Assert.IsTrue(items[0].Names.Contains("gma-miR166h-3p"));
Assert.AreEqual(2, queries[1].Chromosomes.Count);
Assert.AreEqual(28, items[0].EstimatedCount);
}
private static List<ChromosomeCountSlimItem> TestFile(ChromosomeCountSlimItemXmlFormat format, string expectFile)
{
var result = format.ReadFromFile(expectFile);
Assert.AreEqual(3, result.Count);
Assert.AreEqual(2, result[0].Queries.Count);
Assert.AreEqual(1, result[0].Names.Count);
Assert.AreEqual("gma-miR166k", result[0].Names.First());
Assert.AreEqual(2, result[1].Queries.Count);
Assert.AreEqual(1, result[1].Names.Count);
Assert.AreEqual("gma-miR166h-3p", result[1].Names.First());
Assert.AreEqual(1, result[2].Queries.Count);
Assert.AreEqual(1, result[2].Names.Count);
Assert.AreEqual("gma-miR166u", result[2].Names.First());
return result;
}
public override IEnumerable<string> Process()
{
var result = new List<string>();
var countFiles = options.GetCountFiles();
countFiles.Sort((m1, m2) => m1.Name.CompareTo(m2.Name));
var format = new ChromosomeCountSlimItemXmlFormat(outputSample: true);
var countMap = new Dictionary<string, ChromosomeCountSlimItem>();
int fileIndex = 0;
foreach (var file in countFiles)
{
fileIndex++;
Progress.SetMessage("Reading {0}/{1}: {2} ...", fileIndex, countFiles.Count, file.File);
var curcounts = format.ReadFromFile(file.File);
if (curcounts.Count > 0 && string.IsNullOrEmpty(curcounts[0].Queries[0].Sequence))
{
Console.WriteLine("Didn't read in the sequence of query " + curcounts[0].Queries[0].Qname);
}
curcounts.ForEach(m =>
{
foreach (var q in m.Queries)
{
q.Sample = file.Name;
}
});
foreach (var c in curcounts)
{
var name = c.Names.First();
ChromosomeCountSlimItem item;
if (countMap.TryGetValue(name, out item))
{
item.Queries.AddRange(c.Queries);
}
else
{
countMap[name] = c;
}
}
}
var counts = countMap.Values.ToList();
WriteOutput(options.OutputFile, countFiles, format, counts);
result.Add(options.OutputFile);
if (File.Exists(options.CategoryMapFile))
{
Progress.SetMessage("Reading category map ...");
var categoryMap = new MapItemReader(0, 1).ReadFromFile(options.CategoryMapFile);
var queries = new HashSet<SAMChromosomeItem>(from c in counts
from q in c.Queries
select q);
var dic = new Dictionary<string, ChromosomeCountSlimItem>();
foreach (var q in queries)
{
q.Chromosomes = (from chrom in q.Chromosomes
select categoryMap[chrom].Value).Distinct().OrderBy(m => m).ToList();
foreach (var chrom in q.Chromosomes)
{
ChromosomeCountSlimItem item;
if (!dic.TryGetValue(chrom, out item))
{
item = new ChromosomeCountSlimItem();
item.Names.Add(chrom);
dic[chrom] = item;
}
item.Queries.Add(q);
}
}
var catFile = Path.ChangeExtension(options.OutputFile, ".category" + Path.GetExtension(options.OutputFile));
WriteOutput(catFile, countFiles, format, dic.Values.ToList());
result.Add(catFile);
}
if (options.OutputReadTable || options.OutputReadContigTable)
{
Progress.SetMessage("Building sequence map...");
var reads = SmallRNASequenceUtils.ConvertFrom(counts);
if (options.OutputReadTable)
{
Progress.SetMessage("Saving read file...");
var readOutput = Path.ChangeExtension(options.OutputFile, ".read" + Path.GetExtension(options.OutputFile));
new SmallRNASequenceFormat(int.MaxValue, false).WriteToFile(readOutput, reads);
result.Add(readOutput);
}
if (options.OutputReadContigTable)
{
Progress.SetMessage("Building sequence contig by similarity ...");
var contigs = SmallRNASequenceUtils.BuildContigByIdenticalSimilarity(reads, options.MinimumOverlapRate, options.MaximumExtensionBase, progress: Progress);
Progress.SetMessage("Contig number = {0}", contigs.Count);
Progress.SetMessage("Saving contig file...");
var contigOutput = Path.ChangeExtension(options.OutputFile, ".contig" + Path.GetExtension(options.OutputFile));
new SmallRNASequenceContigFormat().WriteToFile(contigOutput, contigs);
result.Add(contigOutput);
Progress.SetMessage("Saving sequence contig details...");
new SmallRNASequenceContigDetailFormat().WriteToFile(contigOutput + ".details", contigs);
result.Add(contigOutput + ".details");
}
}
Progress.End();
return result;
}
private void WriteOutput(string outputFile, List<FileItem> countFiles, ChromosomeCountSlimItemXmlFormat format, List<ChromosomeCountSlimItem> counts)
{
Progress.SetMessage("Sorting queries in each chromosome for merging ...");
counts.ForEach(l => l.Queries.Sort((m1, m2) => m1.Qname.CompareTo(m2.Qname)));
Progress.SetMessage("Merging, calculating and sorting ...");
counts.MergeCalculateSortByEstimatedCount();
Progress.SetMessage("Writing xml file {0} ...", outputFile + ".xml");
format.WriteToFile(outputFile + ".xml", counts);
Progress.SetMessage("Writing count file {0} ...", outputFile);
using (var sw = new StreamWriter(outputFile))
{
sw.WriteLine("Name\t{0}", countFiles.ConvertAll(m => m.Name).Merge("\t"));
foreach (var count in counts)
{
var individualCounts = (from f in countFiles
let estimatedCount = count.Queries.Where(m => m.Sample.Equals(f.Name)).Sum(m => m.GetEstimatedCount()) * count.Names.Count
select string.Format("{0:0.##}", estimatedCount)).Merge("\t");
sw.WriteLine("{0}\t{1}", (from m in count.Names orderby m select m).Merge(";"), individualCounts);
}
}
}
