/// <summary>
/// Search sequence online in the corresponding DB
/// </summary>
public void RetrieveSequences()
{
WSDBFetchServerService db = new WSDBFetchServerService();
foreach (PSIPIanalysissearchDBSequenceType p in ListProteins)
{
if (p.seq != null)
{
continue;
}
if (p.SearchDatabase_ref.ToUpper() != "SDB_SWISSPROT")
{
throw new ApplicationException("DB " + p.SearchDatabase_ref + " not supported");
}
Console.WriteLine("Retrieving " + p.accession + " ...");
string fasta = db.fetchData("UNIPROT:" + p.accession, "fasta", "raw");
fasta = fasta.Remove(0, fasta.IndexOf('\n'));
string seq = "";
foreach (string str in fasta.Split('\n'))
{
seq += str;
}
p.seq = seq; //seq.ToUpper();
}
}
public string GetFASTA(string accessionNumber)
{
WSDBFetchServerService fetch = new WSDBFetchServerService();
try
{
string result = fetch.fetchData("UniProtKB: Accession: " + accessionNumber, "FASTA", "RAW");
return(result);
}
catch (Exception e)
{
string problem = "There was a Problem with your request. Please check that your accession number is correct and that the record is on the UNIprotKB database.";
return(problem);
}
}
/// <summary>
/// Search sequence online in the corresponding DB
/// </summary>
public void RetrieveSequences()
{
WSDBFetchServerService db = new WSDBFetchServerService();
foreach( DBSequenceType p in ListProteins ) {
if( p.Seq!= null )
continue;
if( p.searchDatabase_ref.ToUpper() != "SDB_SWISSPROT" )
throw new ApplicationException( "DB " + p.searchDatabase_ref + " not supported" );
Console.WriteLine( "Retrieving " + p.accession + " ..." );
string fasta = db.fetchData("UNIPROT:"+p.accession, "fasta", "raw");
fasta = fasta.Remove(0,fasta.IndexOf('\n'));
string seq = "";
foreach( string str in fasta.Split('\n') )
seq += str;
p.Seq = seq;//seq.ToUpper();
}
}
