protected bool Equals(Metabolite obj)
{
if (obj.HMDB != null && this.HMDB != null)
{
return(this.HMDB.Equals(obj.HMDB));
}
return(false);
}
static void Main(string[] args)
{
if (args.Length != 1)
{
Console.WriteLine("Invalid number of arguments.");
Console.ReadLine();
}
else
{
List <Metabolite> metabolites = new List <Metabolite>();
string path = Environment.CurrentDirectory;
//Read in metabolite database to match against
using (StreamReader reader = new StreamReader(@"MetaboliteOntology.txt"))
{
var map = ColumnMap(reader.ReadLine());
string line;
while ((line = reader.ReadLine()) != null)
{
var m = new Metabolite();
var split = line.Split('\t', '\n');
if (map.ContainsKey(HMDB))
{
m.HMDB = split[map[HMDB]];
}
if (map.ContainsKey(Pubchem))
{
m.Pubchem = split[map[Pubchem]];
}
if (map.ContainsKey(CAS))
{
m.CAS = split[map[CAS]];
}
if (map.ContainsKey(KEGG))
{
m.KEGG = split[map[KEGG]];
}
if (map.ContainsKey(ChEBI))
{
m.ChEBI = split[map[ChEBI]];
}
if (map.ContainsKey(InChI))
{
m.InChI = split[map[InChI]];
}
if (map.ContainsKey(InChIKey))
{
m.InChIKey = split[map[InChIKey]];
}
if (map.ContainsKey(CommonName))
{
m.CommonName = split[map[CommonName]];
}
if (map.ContainsKey(SYNONYMS))
{
m.Synonyms = split[map[SYNONYMS]];
}
if (map.ContainsKey(SuperClass))
{
m.SuperClass = split[map[SuperClass]];
}
if (map.ContainsKey(Class))
{
m.Class = split[map[Class]];
}
if (map.ContainsKey(DirectParent))
{
m.DirectParent = split[map[DirectParent]];
}
if (map.ContainsKey(Pathways))
{
m.Pathways = split[map[Pathways]];
}
metabolites.Add(m);
}
reader.Close();
}
//Read metabolite names to search for
string queryPath = args[0];
using (StreamReader reader = new StreamReader(queryPath))
{
StreamWriter writer = new StreamWriter(Path.GetFullPath(queryPath).Replace(".txt", "_MetFound.txt"));
writer.WriteLine("Query\tHMDB\tPubChem CID\tCAS\tKEGG\tChEBI\tInChI\tInChIKey\tCommon Name\tSynonyms\tSuper Class\tClass\tDirect Parent\tPathways");
string line;
while ((line = reader.ReadLine()) != null)
{
var m = line.Split('\t', '\n')[0];
/*
* var matches = new List<Metabolite>();
* foreach (var metabolite in metabolites)
* {
* foreach (var syn in metabolite.Synonyms)
* {
* if (syn.ToUpper().Contains(m.ToUpper()))
* {
* matches.Add(metabolite);
* }
* }
* }*/
//var matches = (from metabolite in metabolites from syn in metabolite.Synonyms where syn.ToUpper().Contains(m.ToUpper()) select metabolite).ToList();
string mstring = m.ToUpper().Replace(" ", "");
var matches = (from metabolite in metabolites from syn in metabolite.AllNames where syn.ToUpper().Replace(" ", "").Equals(m.ToUpper().Replace(" ", "")) select metabolite).Distinct().ToList();
if (matches.Any())
{
foreach (var match in matches)
{
string synString = match.Synonyms.Aggregate("", (current, syn) => current + (syn + ", "));
writer.WriteLine(
String.Format(
"{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}\t{13}",
m, match.HMDB, match.Pubchem, match.CAS, match.KEGG, match.ChEBI, match.InChI, match.InChIKey, match.CommonName, match.Synonyms, match.SuperClass,
match.Class, match.DirectParent, match.Pathways));
}
}
else
{
writer.WriteLine(String.Format("{0}\t{1}\t{1}\t{1}\t{1}\t{1}\t{1}\t{1}\t{1}\t{1}\t{1}\t{1}\t{1}\t{1}", m, "NA"));
}
}
reader.Close();
writer.Close();
}
}
}
