public static void runEnsembl( string file ) { StreamReader rd = new StreamReader(new GZipStream(new FileStream(file,FileMode.Open), CompressionMode.Decompress)); string line; char[] sep1 = new char[]{','}; char[] sep2 = new char[]{':'}; string[] fields, fields2; String mut, prot; Variant v; Fasta f; List<string> ids = new List<string>(); SortedList<string,Fasta> fasta = new SortedList<string, Fasta>(); eFetchSnpService ssrv = new eFetchSnpService(); EhuBio.Database.Ncbi.eFetch.Snp.MessageEFetchRequest sreq = new EhuBio.Database.Ncbi.eFetch.Snp.MessageEFetchRequest(); EhuBio.Database.Ncbi.eFetch.Snp.MessageEFetchResult sres; eFetchSequenceService psrv = new eFetchSequenceService(); EhuBio.Database.Ncbi.eFetch.Sequences.MessageEFetchRequest preq = new EhuBio.Database.Ncbi.eFetch.Sequences.MessageEFetchRequest(); EhuBio.Database.Ncbi.eFetch.Sequences.MessageEFetchResult pres; //int count = 1; while( (line=rd.ReadLine()) != null ) { fields = line.Split(sep1); if( !fields[2].Contains("/") || fields[3].Length == 0 || fields[3] != fields[4] ) continue; v = new Variant(); if( ids.Contains(fields[0]) ) continue; ids.Add(fields[0]); sreq.id = fields[0]; sres = ssrv.run_eFetch( sreq ); if( sres == null || sres.ExchangeSet.Rs == null || sres.ExchangeSet.Rs.Length == 0 ) continue; Console.WriteLine( fields[0] + "..." ); foreach( string str in sres.ExchangeSet.Rs[0].hgvs ) { if( !str.StartsWith("NP_") ) continue; Console.Write( str + " " ); v = new Variant(); v.id = str; fields2 = str.Split(sep2); mut = fields2[1]; prot = fields2[0]; try { v.orig = AminoAcid.Get(mut.Substring(2,3)).Letter; v.mut = AminoAcid.Get(mut.Substring(mut.Length-3,3)).Letter; v.pos = ulong.Parse(mut.Substring(5,mut.Length-8))-1; } catch { Console.WriteLine( "(filtered)" ); continue; } if( fasta.ContainsKey(prot) ) { Console.WriteLine( "(cached)" ); f = fasta[prot]; } else { preq.db = "protein"; preq.id = prot; pres = psrv.run_eFetch( preq ); f = new Fasta(Fasta.Type.Protein,prot+"|"+pres.GBSet[0].GBSeq_definition,pres.GBSet[0].GBSeq_sequence); fasta.Add( prot, f ); Console.WriteLine( "(downloaded)" ); } f.mVariants.Add( v ); } /*if( --count == 0 ) break;*/ } foreach( Fasta fas in fasta.Values ) fas.Dump( true ); }
public static void runEnsembl(string file) { StreamReader rd = new StreamReader(new GZipStream(new FileStream(file, FileMode.Open), CompressionMode.Decompress)); string line; char[] sep1 = new char[] { ',' }; char[] sep2 = new char[] { ':' }; string[] fields, fields2; String mut, prot; Variant v; Fasta f; List <string> ids = new List <string>(); SortedList <string, Fasta> fasta = new SortedList <string, Fasta>(); eFetchSnpService ssrv = new eFetchSnpService(); EhuBio.Database.Ncbi.eFetch.Snp.MessageEFetchRequest sreq = new EhuBio.Database.Ncbi.eFetch.Snp.MessageEFetchRequest(); EhuBio.Database.Ncbi.eFetch.Snp.MessageEFetchResult sres; eFetchSequenceService psrv = new eFetchSequenceService(); EhuBio.Database.Ncbi.eFetch.Sequences.MessageEFetchRequest preq = new EhuBio.Database.Ncbi.eFetch.Sequences.MessageEFetchRequest(); EhuBio.Database.Ncbi.eFetch.Sequences.MessageEFetchResult pres; //int count = 1; while ((line = rd.ReadLine()) != null) { fields = line.Split(sep1); if (!fields[2].Contains("/") || fields[3].Length == 0 || fields[3] != fields[4]) { continue; } v = new Variant(); if (ids.Contains(fields[0])) { continue; } ids.Add(fields[0]); sreq.id = fields[0]; sres = ssrv.run_eFetch(sreq); if (sres == null || sres.ExchangeSet.Rs == null || sres.ExchangeSet.Rs.Length == 0) { continue; } Console.WriteLine(fields[0] + "..."); foreach (string str in sres.ExchangeSet.Rs[0].hgvs) { if (!str.StartsWith("NP_")) { continue; } Console.Write(str + " "); v = new Variant(); v.id = str; fields2 = str.Split(sep2); mut = fields2[1]; prot = fields2[0]; try { v.orig = AminoAcid.Get(mut.Substring(2, 3)).Letter; v.mut = AminoAcid.Get(mut.Substring(mut.Length - 3, 3)).Letter; v.pos = ulong.Parse(mut.Substring(5, mut.Length - 8)) - 1; } catch { Console.WriteLine("(filtered)"); continue; } if (fasta.ContainsKey(prot)) { Console.WriteLine("(cached)"); f = fasta[prot]; } else { preq.db = "protein"; preq.id = prot; pres = psrv.run_eFetch(preq); f = new Fasta(Fasta.Type.Protein, prot + "|" + pres.GBSet[0].GBSeq_definition, pres.GBSet[0].GBSeq_sequence); fasta.Add(prot, f); Console.WriteLine("(downloaded)"); } f.mVariants.Add(v); } /*if( --count == 0 ) * break;*/ } foreach (Fasta fas in fasta.Values) { fas.Dump(true); } }