public virtual IEnumerable <string> WriteToFile(string outputFile, List <FeatureItemGroup> features, string removeNamePrefix)
{
Dictionary <string, Dictionary <string, SmallRNASequence> > sequences = new Dictionary <string, Dictionary <string, SmallRNASequence> >();
foreach (var fig in features)
{
foreach (var sam in fig)
{
foreach (var loc in sam.Locations)
{
foreach (var samloc in loc.SamLocations)
{
var aligned = samloc.SamLocation.Parent;
var seq = new SmallRNASequence()
{
Sample = aligned.Sample,
Sequence = aligned.Sequence,
Count = aligned.QueryCount
};
Dictionary <string, SmallRNASequence> ssList;
if (!sequences.TryGetValue(seq.Sample, out ssList))
{
ssList = new Dictionary <string, SmallRNASequence>();
sequences[seq.Sample] = ssList;
ssList[seq.Sequence] = seq;
}
else
{
if (!ssList.ContainsKey(seq.Sequence))
{
ssList[seq.Sequence] = seq;
}
}
}
}
}
}
var counts = sequences.ToDictionary(m => m.Key, m => m.Value.Values.ToList());
var samples = sequences.Keys.OrderBy(m => m).ToArray();
List <SmallRNASequenceContig> mergedSequences = SmallRNASequenceUtils.BuildContigByIdenticalSimilarity(counts, minOverlapRate, maxExtensionBase, topNumber);
new SmallRNASequenceContigFormat().WriteToFile(outputFile, mergedSequences);
new SmallRNASequenceContigDetailFormat().WriteToFile(outputFile + ".details", mergedSequences);
return(new[] { outputFile });
}
private void OutputGroup(List <string> result, Dictionary <string, List <SmallRNASequence> > counts, string[] samples)
{
var outputFile = options.OutputFile;
Progress.SetMessage("Building sequence contig...");
var mergedSequences = SmallRNASequenceUtils.BuildContigByIdenticalSimilarity(counts, options.MinimumOverlapRate, options.MaximumExtensionBase, options.TopNumber);
Progress.SetMessage("Saving sequence contig...");
new SmallRNASequenceContigFormat().WriteToFile(options.OutputFile, mergedSequences);
result.Add(options.OutputFile);
if (options.ExportContigDetails)
{
Progress.SetMessage("Saving sequence contig details...");
new SmallRNASequenceContigDetailFormat().WriteToFile(options.OutputFile + ".details", mergedSequences);
result.Add(options.OutputFile + ".details");
}
var miniContigFile = Path.ChangeExtension(options.OutputFile, ".minicontig.count");
Progress.SetMessage("Saving mini sequence contig...");
var miniContig = SmallRNASequenceUtils.BuildMiniContig(mergedSequences, options.TopNumber);
new SmallRNASequenceContigFormat().WriteToFile(miniContigFile, miniContig);
result.Add(miniContigFile);
if (options.ExportContigDetails)
{
Progress.SetMessage("Saving mini sequence contig details...");
new SmallRNASequenceContigDetailFormat().WriteToFile(miniContigFile + ".details", miniContig);
result.Add(miniContigFile + ".details");
}
if (options.ExportFasta)
{
var fastaFile = options.OutputFile + ".fasta";
Progress.SetMessage("Saving " + fastaFile + " ...");
new SmallRNASequenceContigFastaFormat(options.TopNumber).WriteToFile(fastaFile, mergedSequences);
result.Add(fastaFile);
var miniContigFastaFile = miniContigFile + ".fasta";
Progress.SetMessage("Saving " + miniContigFastaFile + " ...");
new SmallRNASequenceContigFastaFormat(options.TopNumber).WriteToFile(miniContigFastaFile, miniContig);
result.Add(miniContigFastaFile);
}
}