public void GenerateMimToGeneSymbolFile(GeneSymbolUpdater geneSymbolUpdater)
{
using StreamWriter writer = new StreamWriter(_mimToSymbolStream);
using var response = _httpClient.GetAsync(Mim2GeneUrl).Result;
using var reader = new StreamReader(response.Content.ReadAsStreamAsync().Result);
writer.WriteLine("#MIM number\tGene symbol");
string line;
while ((line = reader.ReadLine()) != null)
{
if (line.OptimizedStartsWith('#'))
{
continue;
}
var fields = line.OptimizedSplit('\t');
var geneSymbol = fields[3];
if (string.IsNullOrEmpty(geneSymbol))
{
continue;
}
var mimNumber = fields[0];
var entrezGeneId = fields[2];
var ensemblGeneId = fields[4];
var updatedGeneSymbol = geneSymbolUpdater.UpdateGeneSymbol(geneSymbol, ensemblGeneId, entrezGeneId);
if (string.IsNullOrEmpty(updatedGeneSymbol))
{
continue;
}
writer.WriteLine($"{mimNumber}\t{updatedGeneSymbol}");
}
}
public IDictionary <string, string> GenerateMimToGeneSymbol(GeneSymbolUpdater geneSymbolUpdater)
{
var mimNumberToGeneSymbol = new Dictionary <string, string>();
using (StreamWriter writer = new StreamWriter(_minToSymbolStream))
using (var response = _httpClient.GetAsync(Mim2GeneUrl).Result)
using (var reader = new StreamReader(response.Content.ReadAsStreamAsync().Result))
{
writer.WriteLine("#MIM number\tGene symbol");
string line;
while ((line = reader.ReadLine()) != null)
{
if (line.OptimizedStartsWith('#'))
{
continue;
}
var fields = line.OptimizedSplit('\t');
string geneSymbol = fields[3];
if (string.IsNullOrEmpty(geneSymbol))
{
continue;
}
string mimNumber = fields[0];
string entrezGeneId = fields[2];
string ensemblGeneId = fields[4];
string updatedGeneSymbol = geneSymbolUpdater.UpdateGeneSymbol(geneSymbol, ensemblGeneId, entrezGeneId);
if (string.IsNullOrEmpty(updatedGeneSymbol))
{
continue;
}
writer.WriteLine($"{mimNumber}\t{updatedGeneSymbol}");
mimNumberToGeneSymbol[mimNumber] = updatedGeneSymbol;
}
}
return(mimNumberToGeneSymbol);
}
private IDictionary <string, string> GetMimNumberToGeneSymbol(HttpClient httpClient, string mim2GeneUrl, ZipArchive zipArchive)
{
var mimNumberToGeneSymbol = new Dictionary <string, string>();
using (StreamWriter writer = zipArchive == null ? null : new StreamWriter(zipArchive.CreateEntry("mim2gene.txt").Open()))
using (var response = httpClient.GetAsync(mim2GeneUrl).Result)
using (var reader = new StreamReader(response.Content.ReadAsStreamAsync().Result))
{
string line;
while ((line = reader.ReadLine()) != null)
{
writer?.WriteLine(line);
if (line.OptimizedStartsWith('#'))
{
continue;
}
var fields = line.OptimizedSplit('\t');
string geneSymbol = fields[3];
if (string.IsNullOrEmpty(geneSymbol))
{
continue;
}
string mimNumber = fields[0];
string entrezGeneId = fields[2];
string ensemblGeneId = fields[4];
string updatedGeneSymbol = _geneSymbolUpdater.UpdateGeneSymbol(geneSymbol, ensemblGeneId, entrezGeneId);
if (string.IsNullOrEmpty(updatedGeneSymbol))
{
continue;
}
mimNumberToGeneSymbol[mimNumber] = updatedGeneSymbol;
}
}
return(mimNumberToGeneSymbol);
}