private static void Main(string[] args)
{
var @out = Console.Out;
//var @out = new StreamWriter("output.json");
var error = Console.Error;
if (args.Length != 3)
{
error.WriteLine("Invalid arguments parameters");
Environment.Exit(-1);
}
var fileName = args[0];
var path = args[1];
var value = args[2];
var source = JArray.Parse(File.ReadAllText(path));
var dictionary = JsonConvert.DeserializeObject<Dictionary<string, object>>(value);
var source2 =
from c in source
where c["Tag"] != null
select new TagInfo
{
Accession = c["Accession"].ToObject<string>(),
Tag = c["Tag"].ToObject<string>(),
BeginIndex = c["LocationBegin"].ToObject<int>(),
EndIndex = c["LocationEnd"].ToObject<int>()
};
var source3 = (from c in source2
orderby c.Accession, c.BeginIndex
group c by c.Accession into g
select g).ToList();
var uniprot = Biosek.Formats.UniProt.uniprot.LoadFromFile(fileName);
var workspace = new Workspace();
foreach (var site in dictionary)
{
var list = (from accession in source3
let proteinsInAccession = accession.ToList()
from index in Enumerable.Range(1, proteinsInAccession.Count - 1)
let proteinA = proteinsInAccession[index - 1]
let proteinB = proteinsInAccession[index]
where proteinA.EndIndex == proteinB.BeginIndex - 1 &&
string.Concat(proteinA.Tag, "-", proteinB.Tag) == site.Key
select Tuple.Create(proteinA, proteinB)).ToList();
error.WriteLine("Found {0} cleavage sites for {1}", list.Count, site.Key);
if (site.Value is JArray)
{
foreach (var current in site.Value as JArray)
{
var windowString = current.ToObject<string>();
Sample(site.Key, uniprot, list, windowString, workspace);
}
}
else
{
Sample(site.Key, uniprot, list, site.Value as string, workspace);
}
}
var jsonSerializer = new JsonSerializer();
var value2 = from c in workspace.Dataset
select new
{
tag = c.Class,
positives = from d in c.Positives.Entries
select new { i = d.Begin, c = d.Samples },
negatives = from d in c.Negatives.Entries
select new { i = d.Begin, c = d.Samples }
};
//jsonSerializer.Formatting = Formatting.Indented;
jsonSerializer.Serialize(@out, new { buffer = workspace.ReadBuffer(0, workspace.BufferLength), samples = value2 });
@out.Close();
}
