public override IEnumerable <string> Process()
{
var countfiles = options.GetCountFiles();
List <CountItem> counts = new List <CountItem>();
foreach (var file in countfiles)
{
Progress.SetMessage("reading " + file.File + " ...");
var count = new CountItem()
{
Dir = file.Name,
Data =
(from line in File.ReadAllLines(file.File).Skip(1)
let parts = line.Split('\t')
where parts.Length >= 6
select parts).ToDictionary(m => m[0])
};
counts.Add(count);
}
var features = (from c in counts
from k in c.Data.Keys
select k).Distinct().OrderBy(m => m).ToList();
var checkSequence = counts.First().Data.First().Value[2];
double value;
var hasSequence = !double.TryParse(checkSequence, out value);
var seqheader = hasSequence ? "\tSequence" : "";
var startIndex = hasSequence ? 3 : 2;
using (StreamWriter sw = new StreamWriter(options.OutputFile))
using (StreamWriter swIso = new StreamWriter(options.IsomirFile))
{
sw.WriteLine("Feature\tLocation{0}\t{1}", seqheader, (from c in counts select c.Dir).Merge("\t"));
swIso.WriteLine("Feature\tLocation{0}\t{1}", seqheader, (from c in counts select c.Dir).Merge("\t"));
foreach (var feature in features)
{
OutputCount(counts, sw, feature, startIndex, "", hasSequence);
OutputCount(counts, swIso, feature, startIndex + 1, "_+_0", hasSequence);
OutputCount(counts, swIso, feature, startIndex + 2, "_+_1", hasSequence);
OutputCount(counts, swIso, feature, startIndex + 3, "_+_2", hasSequence);
}
}
var result = new[] { options.OutputFile, options.IsomirFile }.ToList();
var infofile = Path.ChangeExtension(options.OutputFile, ".info");
if (CountUtils.WriteInfoSummaryFile(infofile, options.GetCountFiles().ToDictionary(m => m.Name, m => m.File)))
{
result.Add(infofile);
}
return(result);
}
public override IEnumerable <string> Process()
{
var countfiles = options.GetCountFiles();
var dic = new Dictionary <string, Dictionary <string, MappedMirnaGroup> >();
foreach (var file in countfiles)
{
Progress.SetMessage("Reading miRNA mapped file " + file.File + " ...");
var mirnas = new MappedMirnaGroupXmlFileFormat().ReadFromFile(file.File);
dic[file.Name] = mirnas.ToDictionary(m => m.DisplayName);
}
var features = (from c in dic.Values
from k in c.Keys
select k).Distinct().OrderBy(m => m).ToList();
var names = dic.Keys.OrderBy(m => m).ToList();
using (StreamWriter sw = new StreamWriter(options.OutputFile))
using (StreamWriter swNTA = new StreamWriter(options.NTAFile))
using (StreamWriter swIso = new StreamWriter(options.IsomirFile))
using (StreamWriter swIsoNTA = new StreamWriter(options.IsomirNTAFile))
{
sw.WriteLine("Feature\tLocation\tSequence\t{0}", names.Merge("\t"));
swNTA.WriteLine("Feature\tLocation\tSequence\t{0}", names.Merge("\t"));
swIso.WriteLine("Feature\tLocation\tSequence\t{0}", names.Merge("\t"));
swIsoNTA.WriteLine("Feature\tLocation\tSequence\t{0}", names.Merge("\t"));
foreach (var feature in features)
{
OutputCount(sw, dic, feature, names, MirnaConsts.NO_OFFSET, false, "");
OutputCount(swNTA, dic, feature, names, MirnaConsts.NO_OFFSET, true, "");
OutputCount(swIso, dic, feature, names, 0, false, "_+_0");
OutputCount(swIso, dic, feature, names, 1, false, "_+_1");
OutputCount(swIso, dic, feature, names, 2, false, "_+_2");
OutputCount(swIsoNTA, dic, feature, names, 0, true, "_+_0");
OutputCount(swIsoNTA, dic, feature, names, 1, true, "_+_1");
OutputCount(swIsoNTA, dic, feature, names, 2, true, "_+_2");
}
}
var result = new[] { options.OutputFile, options.IsomirFile, options.NTAFile, options.IsomirNTAFile }.ToList();
return(result);
}