protected bool Equals(InterfaceFragment other)
{
return(FragmentLength == other.FragmentLength && string.Equals(PdbId, other.PdbId) && ReceptorChainId == other.ReceptorChainId && ReceptorResSeq == other.ReceptorResSeq && ReceptorIndex == other.ReceptorIndex && string.Equals(ReceptorAminoAcidSequence, other.ReceptorAminoAcidSequence) && string.Equals(ReceptorSecondaryStructure, other.ReceptorSecondaryStructure) && LigandChainId == other.LigandChainId && LigandResSeq == other.LigandResSeq && LigandIndex == other.LigandIndex && string.Equals(LigandAminoAcidSequence, other.LigandAminoAcidSequence) && string.Equals(LigandSecondaryStructure, other.LigandSecondaryStructure));
}
static void Main(string[] args)
{
//var requiredInterfaceLengths = new int[] { 7, 9, 11, 13, 15 };
var requiredInterfaceLengths = new int[] { 9 };
var sequenceFilename = @"C:\pdbe\pdb_seqres.fasta";
var dsspFilename = @"C:\pdbe\ss.txt";
var sequenceListFromFastaFile = Sequence.LoadSequenceFile(sequenceFilename, new string[] { null, "", "protein" });
var dsspList = Sequence.LoadSequenceFile(dsspFilename, new string[] { null, "", "protein" });
dsspList = dsspList.Where(a => a.IdSplit.Description == "secstr").ToList();
//var pdbIdList = new List<string>(); {"1a00"};
var pdbFiles = Directory.GetFiles(@"c:\pdbe\contacts_all\", "????.pdb", SearchOption.TopDirectoryOnly).ToList();
var pdbFileLengths = pdbFiles.Select(a => new Tuple <string, long>(a, new FileInfo(a).Length)).ToList();
pdbFileLengths = pdbFileLengths.Where(a => a.Item2 > 0).ToList();
pdbFileLengths = pdbFileLengths.OrderBy(a => a.Item2).ToList();
var ifList = InterfaceFragment.Load(@"c:\r\if.csv");
ifList = ifList.Where(a => requiredInterfaceLengths.Contains(a.FragmentLength)).ToList();
if (ifList.Count == 0)
{
var pdbIdList = pdbFileLengths.Select(a => a.Item1).Select(Path.GetFileNameWithoutExtension).Select(a => a.ToUpperInvariant()).ToList();
//pdbIdList = pdbIdList.GetRange(0, 100);
//var result = new List<InterfaceFragment>();
var taskList1 = new List <Task <List <InterfaceFragment> > >();
foreach (var pdbId1 in pdbIdList)
{
var pdbId = pdbId1;
Console.WriteLine(pdbId + " " + (pdbIdList.IndexOf(pdbId) + 1) + "/" + pdbIdList.Count);
while (taskList1.Count(a => !a.IsCompleted) >= Environment.ProcessorCount)
{
Task.WaitAny(taskList1.Where(a => !a.IsCompleted).ToArray <Task>());
}
taskList1.Add(Task.Run(() =>
{
var pdbResult = new List <InterfaceFragment>();
var atomsFilename = @"c:\pdbe\atoms_all\" + pdbId + ".pdb";
var contactsFilename = @"c:\pdbe\contacts_all\" + pdbId + ".pdb";
var interfaceCsv = @"c:\r\interface_9\" + pdbId + @".csv";
if (File.Exists(interfaceCsv))
{
return(InterfaceFragment.Load(interfaceCsv));
}
if (!File.Exists(atomsFilename) || !File.Exists(contactsFilename))
{
return(null); // new List<InterfaceFragment>(); // continue;
}
if (new FileInfo(atomsFilename).Length == 0 || new FileInfo(contactsFilename).Length == 0)
{
return(null); //new List<InterfaceFragment>(); // continue;
}
var contacts = ProteinBioClass.AtomPair.LoadAtomPairList(contactsFilename);
var contactChainIds = contacts.SelectMany(a => new char[] { a.Atom1.chainID.FieldValue[0], a.Atom2.chainID.FieldValue[0] }).Distinct().ToList();
var proteinFileChains = ProteinBioClass.PdbAtomicChains(atomsFilename, contactChainIds.ToArray(), -1, -1, false);
var sequenceListFromPdbFile = proteinFileChains.ChainList.Select(pdbChain => Sequence.LoadStructureFile(atomsFilename, new[] { pdbChain.ChainId }, true, null, null, '-', '-')).ToList();
var dsspFromFastaFile = proteinFileChains.ChainList.Select(pdbChain => dsspList.FirstOrDefault(a => a.IdSplit.PdbId.ToUpperInvariant() == pdbId.Substring(0, a.IdSplit.PdbId.Length).ToUpperInvariant() && a.IdSplit.ChainId == pdbChain.ChainId)?.FullSequence).ToList();
var sequenceFromFastaFile = proteinFileChains.ChainList.Select(pdbChain => sequenceListFromFastaFile.FirstOrDefault(a => a.IdSplit.PdbId.ToUpperInvariant() == pdbId.Substring(0, a.IdSplit.PdbId.Length).ToUpperInvariant() && a.IdSplit.ChainId == pdbChain.ChainId)?.FullSequence).ToList();
var sequenceFromPdbFile = proteinFileChains.ChainList.Select((pdbChain, i) => sequenceListFromPdbFile[i].FirstOrDefault(a => (string.IsNullOrWhiteSpace(a.IdSplit.PdbId) || a.IdSplit.PdbId.ToUpperInvariant() == pdbId.Substring(0, a.IdSplit.PdbId.Length).ToUpperInvariant()) && a.IdSplit.ChainId == pdbChain.ChainId)?.FullSequence).ToList();
var structureToSequenceAlignmentResult = proteinFileChains.ChainList.Select((pdbChain, i) => ProteinBioClass.StructureToSequenceAlignment.Align(pdbChain.AtomList, sequenceFromFastaFile[i], sequenceFromPdbFile[i])).ToList();
if (structureToSequenceAlignmentResult.Any(a => a == null))
{
return(null);
}
for (var chainIndex3 = 0; chainIndex3 < proteinFileChains.ChainList.Count; chainIndex3++)
{
for (var i = 0; i < structureToSequenceAlignmentResult[chainIndex3].FastaSequenceAligned.Length; i++)
{
if (structureToSequenceAlignmentResult[chainIndex3].FastaSequenceAligned[i] == '-')
{
dsspFromFastaFile[chainIndex3] = dsspFromFastaFile[chainIndex3].Insert(i, "-");
}
}
}
foreach (var contactChainId1 in contactChainIds)
{
var chainIndex1 = proteinFileChains.ChainList.FindIndex(g => g.ChainId == contactChainId1);
if (structureToSequenceAlignmentResult[chainIndex1] == null)
{
continue;
}
if (string.IsNullOrWhiteSpace(sequenceFromPdbFile[chainIndex1]) || string.IsNullOrWhiteSpace(sequenceFromFastaFile[chainIndex1]) || string.IsNullOrWhiteSpace(dsspFromFastaFile[chainIndex1]))
{
continue;
}
var chainResult = new List <InterfaceFragment>();
//var pdbChain = proteinFileChains.ChainList.First(a => a.ChainId == contactChainId).AtomList;
var chainContacts = contacts.Where(a => a.Atom1.chainID.FieldValue[0] == contactChainId1 || a.Atom2.chainID.FieldValue[0] == contactChainId1).Select(a => a.Atom1.chainID.FieldValue[0] == contactChainId1 ? a : a.SwapAtoms()).ToList();
//chainContacts = chainContacts.GroupBy(a => int.Parse(a.resSeq.FieldValue)).ToList().Select(a => a.First()).ToList();
//chainContacts = chainContacts.Distinct().ToList();
chainContacts = chainContacts.OrderBy(a => int.Parse(a.Atom1.resSeq.FieldValue)).ThenBy(a => int.Parse(a.Atom1.serial.FieldValue)).ToList();
foreach (var atomPair in chainContacts)
{
foreach (var requiredInterfaceLength in requiredInterfaceLengths)
{
var contactChainId2 = atomPair.Atom2.chainID.FieldValue[0];
var chainIndex2 = proteinFileChains.ChainList.FindIndex(g => g.ChainId == contactChainId2);
if (structureToSequenceAlignmentResult[chainIndex2] == null)
{
continue;
}
if (string.IsNullOrWhiteSpace(sequenceFromPdbFile[chainIndex2]) || string.IsNullOrWhiteSpace(sequenceFromFastaFile[chainIndex2]) || string.IsNullOrWhiteSpace(dsspFromFastaFile[chainIndex2]))
{
continue;
}
var interfaceLength1 = requiredInterfaceLength;
var interfaceLength2 = requiredInterfaceLength;
var resSeq1 = int.Parse(atomPair.Atom1.resSeq.FieldValue);
var resSeq2 = int.Parse(atomPair.Atom2.resSeq.FieldValue);
var resSeqIndex1a = structureToSequenceAlignmentResult[chainIndex1].AlignmentMap.ToList().FindIndex(a => a == resSeq1);
var resSeqIndex2a = structureToSequenceAlignmentResult[chainIndex2].AlignmentMap.ToList().FindIndex(a => a == resSeq2);
if (structureToSequenceAlignmentResult[chainIndex1].FastaSequenceAligned.Length < interfaceLength1)
{
interfaceLength1 = structureToSequenceAlignmentResult[chainIndex1].FastaSequenceAligned.Length;
}
if (structureToSequenceAlignmentResult[chainIndex2].FastaSequenceAligned.Length < interfaceLength2)
{
interfaceLength2 = structureToSequenceAlignmentResult[chainIndex2].FastaSequenceAligned.Length;
}
var resSeqIndex1 = resSeqIndex1a - (interfaceLength1 / 2);
var resSeqIndex2 = resSeqIndex2a - (interfaceLength2 / 2);
if (resSeqIndex1 < 0)
{
resSeqIndex1 = 0;
}
if (resSeqIndex2 < 0)
{
resSeqIndex2 = 0;
}
if (resSeqIndex1 + interfaceLength1 > structureToSequenceAlignmentResult[chainIndex1].FastaSequenceAligned.Length)
{
resSeqIndex1 = (structureToSequenceAlignmentResult[chainIndex1].FastaSequenceAligned.Length - interfaceLength1);
}
if (resSeqIndex2 + interfaceLength2 > structureToSequenceAlignmentResult[chainIndex2].FastaSequenceAligned.Length)
{
resSeqIndex2 = (structureToSequenceAlignmentResult[chainIndex2].FastaSequenceAligned.Length - interfaceLength2);
}
var interfaceSuper1 = structureToSequenceAlignmentResult[chainIndex1].FastaSequenceAligned.Substring(resSeqIndex1, interfaceLength1);
var interfaceSuper2 = structureToSequenceAlignmentResult[chainIndex2].FastaSequenceAligned.Substring(resSeqIndex2, interfaceLength2);
var dsspSuper1 = dsspFromFastaFile[chainIndex1].Substring(resSeqIndex1, interfaceLength1);
var dsspSuper2 = dsspFromFastaFile[chainIndex2].Substring(resSeqIndex2, interfaceLength2);
if (interfaceSuper1.Length != requiredInterfaceLength || dsspSuper1.Length != requiredInterfaceLength)
{
continue;
}
if (interfaceSuper2.Length != requiredInterfaceLength || dsspSuper2.Length != requiredInterfaceLength)
{
continue;
}
var interfaceFragment = new InterfaceFragment()
{
FragmentLength = requiredInterfaceLength,
PdbId = pdbId,
ReceptorChainId = contactChainId1,
ReceptorResSeq = resSeq1,
ReceptorIndex = resSeqIndex1a,
ReceptorAminoAcidSequence = interfaceSuper1,
ReceptorSecondaryStructure = dsspSuper1,
LigandChainId = contactChainId2,
LigandResSeq = resSeq2,
LigandIndex = resSeqIndex2a,
LigandAminoAcidSequence = interfaceSuper2,
LigandSecondaryStructure = dsspSuper2
};
chainResult.Add(interfaceFragment);
}
}
pdbResult.AddRange(chainResult);
}
InterfaceFragment.Save(interfaceCsv, pdbResult.Distinct().ToList());
return(null); // return pdbResult;
}));
//result.AddRange(pdbResult);
}
//try
//{
Task.WaitAll(taskList1.ToArray <Task>());
//}
//catch (AggregateException ae)
//{
// throw ae.Flatten();
//}
ifList = taskList1.Where(a => a.Result != null).SelectMany(a => a.Result).ToList();
ifList = ifList.Distinct().ToList();
InterfaceFragment.Save(@"c:\r\if.csv", ifList);
}
var pairs1 = ifList.Select(a => new Tuple <string, string>(a.ReceptorAminoAcidSequence, a.ReceptorSecondaryStructure)).Distinct().ToList();
sequenceFilename = null;
dsspFilename = null;
sequenceListFromFastaFile.Clear(); sequenceListFromFastaFile = null;
dsspList.Clear(); dsspList = null;
pdbFiles.Clear(); pdbFiles = null;
pdbFileLengths.Clear(); pdbFileLengths = null;
//ifList.Clear(); ifList = null;
var similarAA = new string[] { "LAGVIP", "DE", "ST", "RKH", "FYW", "NQ", "CM", "BJOUXZ", "-" };
var simAaList = similarAA.SelectMany(a => a.ToList()).ToList();
var simAaDict = new Dictionary <char, string>();
foreach (var s in simAaList)
{
simAaDict.Add(s, similarAA.First(a => a.Contains(s)));
}
DateTime startTime = DateTime.Now;
var simList = new List <Tuple <string, string, string, string, decimal, decimal, decimal> >(); // aa, ss, aa-sim, aa-evo-sim, ss-sim
// compare without alignments, as aligments takes too long, also allow for insertion/deletions with index pos -1/+1.
for (int i = 0; i < pairs1.Count; i++)
{
TimeSpan timeRemaining = TimeSpan.FromTicks(DateTime.Now.Subtract(startTime).Ticks *(pairs1.Count - (i + 1)) / (i + 1));
Console.WriteLine((i + 1) + " / " + pairs1.Count + " " + timeRemaining.ToString("d'd 'h'h 'm'm 's's'"));
var a = pairs1[i];
for (int j = 0; j < pairs1.Count; j++)
{
if (j <= i)
{
continue;
}
var b = pairs1[j];
if (a.Item1.Length != b.Item1.Length)
{
continue;
}
var scoreAa = 0;
var scoreSs = 0;
var scoreAaEvo = 0;
for (var x = 0; x < a.Item1.Length; x++)
{
if (a.Item1[x] == b.Item1[x])
{
scoreAa++;
}
else if (x > 0 && (a.Item1[x - 1] == b.Item1[x] || a.Item1[x] == b.Item1[x - 1]))
{
scoreAa++;
}
else if (x < a.Item1.Length - 1 && (a.Item1[x + 1] == b.Item1[x] || a.Item1[x] == b.Item1[x + 1]))
{
scoreAa++;
}
if (simAaDict[a.Item1[x]].Contains(b.Item1[x]))
{
scoreAaEvo++;
}
else if (x > 0 && (simAaDict[a.Item1[x - 1]].Contains(b.Item1[x]) || simAaDict[a.Item1[x]].Contains(b.Item1[x - 1])))
{
scoreAaEvo++;
}
else if (x < a.Item1.Length - 1 && (simAaDict[a.Item1[x + 1]].Contains(b.Item1[x]) || simAaDict[a.Item1[x]].Contains(b.Item1[x + 1])))
{
scoreAaEvo++;
}
if (a.Item2[x] == b.Item2[x])
{
scoreSs++;
}
else if (x > 0 && (a.Item2[x - 1] == b.Item2[x] || a.Item2[x] == b.Item2[x - 1]))
{
scoreSs++;
}
else if (x < a.Item2.Length - 1 && (a.Item2[x + 1] == b.Item2[x] || a.Item2[x] == b.Item2[x + 1]))
{
scoreSs++;
}
}
decimal scoreAaPct = (decimal)scoreAa / (decimal)a.Item1.Length;
decimal scoreAaEvoPct = (decimal)scoreAaEvo / (decimal)a.Item1.Length;
decimal scoreSsPct = (decimal)scoreSs / (decimal)a.Item2.Length;
simList.Add(new Tuple <string, string, string, string, decimal, decimal, decimal>(a.Item1, a.Item2, b.Item1, b.Item2, scoreAaPct, scoreAaEvoPct, scoreSsPct));
//simList.Add(new Tuple<string, string, string, string, decimal, decimal, decimal>(b.AminoAcidSequence, b.SecondaryStructure, a.AminoAcidSequence, a.SecondaryStructure, scoreAaPct, scoreAaEvoPct, scoreSsPct));
}
}
//var if2 = simList.SelectMany(a => new List<string>() { string.Join(",", new string[] { a.Item1, a.Item2, a.Item3, a.Item4, "" + a.Item5, "" + a.Item6, "" + a.Item7 }) /*,
// string.Join(",", new string[] { a.Item3, a.Item4, a.Item1, a.Item2, "" + a.Item5, "" + a.Item6, "" + a.Item7 })*/ }).ToList();
var taskList3 = new List <Task>();
for (int i = 0; i < pairs1.Count; i++)
{
TimeSpan timeRemaining = TimeSpan.FromTicks(DateTime.Now.Subtract(startTime).Ticks *(pairs1.Count - (i + 1)) / (i + 1));
Console.WriteLine((i + 1) + " / " + pairs1.Count + " " + timeRemaining.ToString("d'd 'h'h 'm'm 's's'"));
while (taskList3.Count(a => !a.IsCompleted) >= Environment.ProcessorCount)
{
Task.WaitAny(taskList3.Where(a => !a.IsCompleted).ToArray <Task>());
}
var i1 = i;
var t = Task.Run(() =>
{
var a = pairs1[i1];
// find all instances of this pair with good simple alignment
var cluster = simList.Where(c => (c.Item1 == a.Item1 || c.Item3 == a.Item1) && (c.Item2 == a.Item2 || c.Item4 == a.Item2) && (c.Item5 >= 0.4m && c.Item6 >= 0.8m && c.Item7 >= 0.9m) && (c.Item5 < 1.0m /*&& c.Item6 < 1.0m && c.Item7 < 1.0m*/)).ToList();
if (cluster.Count < 5)
{
return;
}
var clusterPdbs = ifList.Where(c => cluster.Any(d => (d.Item1 == c.ReceptorAminoAcidSequence || d.Item3 == c.ReceptorAminoAcidSequence) && (d.Item2 == c.ReceptorSecondaryStructure || d.Item4 == c.ReceptorSecondaryStructure))).Select(e => new Tuple <string, char>(e.PdbId, e.ReceptorChainId)).ToList();
if (clusterPdbs.Count < 5)
{
return;
}
List <string> o = new List <string>();
o.Add("delete *");
o.AddRange(clusterPdbs.Select(e => @"load c:\pdbe\" + e.Item1 + ".pdb").ToList());
o.Add("hide all");
o.Add("show cartoon");
o.AddRange(clusterPdbs.Select((e, w) => w == 0 ? "" : @"super /" + e.Item1 + @"//" + e.Item2 + @", /" + clusterPdbs[0].Item1 + @"//" + clusterPdbs[0].Item2).ToList());
File.WriteAllLines(@"c:\r\cluster_" + (i1 + 1) + ".txt", o);
});
taskList3.Add(t);
}
Task.WaitAll(taskList3.ToArray <Task>());
//File.WriteAllLines(@"c:\r\if2.csv", if2);
Console.WriteLine("Calculating aa/ss sequence identities - part 1");
var taskList2 = new List <Task <InterfaceFragmentData> >();
//var interfaceFragmentLengths = new int[] { 15, 13, 11, 9, 7, 5, 3 };
//var interfaceFragmentLengths = new int[] { requiredInterfaceLengths[0] };
var interfaceFragmentLengths = new int[] { 11 };
for (int index = 0; index < interfaceFragmentLengths.Length; index++)
{
var index1 = index;
var interfaceFragmentLength = interfaceFragmentLengths[index1];
taskList2.Add(Task.Run(() =>
{
var pairs = ifList.Where(a => a.FragmentLength == interfaceFragmentLength).Select(a => new Tuple <string, string>(a.ReceptorAminoAcidSequence.Substring(index1, interfaceFragmentLength), a.ReceptorSecondaryStructure.Substring(index1, interfaceFragmentLength))).Distinct().ToList();
var aassList = new List <Tuple <string, string, string, string, decimal, decimal, decimal> >();
var aaSequenceList = pairs.Select(a => a.Item1).Distinct().ToList();
var aaAlignmentList = Align(aaSequenceList);
var ssSequenceList = pairs.Select(a => a.Item2).Distinct().ToList();
var ssAlignmentList = Align(ssSequenceList);
for (int i = 0; i < pairs.Count; i++)
{
Console.WriteLine((i + 1) + " / " + pairs.Count);
var pair1 = pairs[i];
for (int j = 0; j < pairs.Count; j++)
{
if (j < i)
{
continue;
}
var pair2 = pairs[j];
var aaSid = aaAlignmentList.First(alignment => alignment.Item1 == pair1.Item1 && alignment.Item2 == pair2.Item1).Item3;
var ssSid = ssAlignmentList.First(alignment => alignment.Item1 == pair1.Item2 && alignment.Item2 == pair2.Item2).Item3;
var weighted = (aaSid * 0.5m) + (ssSid * 0.5m);
aassList.Add(new Tuple <string, string, string, string, decimal, decimal, decimal>(pair1.Item1, pair1.Item2, pair2.Item1, pair2.Item2, aaSid, ssSid, weighted));
aassList.Add(new Tuple <string, string, string, string, decimal, decimal, decimal>(pair2.Item1, pair2.Item2, pair1.Item1, pair1.Item2, aaSid, ssSid, weighted));
}
}
var r = new InterfaceFragmentData();
r.AaSsData = aassList;
r.AaData = aaAlignmentList;
r.SsData = ssAlignmentList;
return(r);
}));
}
Task.WaitAll(taskList2.ToArray <Task>());
Console.WriteLine("Calculating aa/ss sequence identities - part 2");
var sids = new decimal[] { 1.0m, 0.9m, 0.8m, 0.7m, 0.6m, 0.5m, 0.4m, 0.3m, 0.2m, 0.1m, 0.0m };
//aa count non-transivity clusters
var aaData = taskList2.SelectMany(a => a.Result.AaData).ToList();
var aaDistinct = aaData.Select(a => a.Item1).Distinct().ToList();
var aaNeighbours = new List <Tuple <string, decimal, decimal> >();
foreach (var aa in aaDistinct)
{
var subset = aaData.Where(a => a.Item1 == aa).ToList();
foreach (var sid in sids)
{
aaNeighbours.Add(new Tuple <string, decimal, decimal>(aa, sid, subset.Count(b => b.Item3 >= sid)));
}
}
File.WriteAllLines(@"c:\r\aa.csv", aaData.Select(a => string.Join(",", new string[] { "" + a.Item1.Length, a.Item1, a.Item2, "" + a.Item3 })));
File.WriteAllLines(@"c:\r\aa-clusters-1.csv", aaDistinct.Select(a => a + "," + string.Join(",", aaNeighbours.Where(d => d.Item1 == a).Select(d => "" + d.Item3).ToArray())));
//ss count non-transivity clusters
var ssData = taskList2.SelectMany(a => a.Result.SsData).ToList();
var ssDistinct = ssData.Select(a => a.Item1).Distinct().ToList();
var ssNeighbours = new List <Tuple <string, decimal, decimal> >();
foreach (var ss in ssDistinct)
{
var subset = ssData.Where(a => a.Item1 == ss).ToList();
foreach (var sid in sids)
{
ssNeighbours.Add(new Tuple <string, decimal, decimal>(ss, sid, subset.Count(b => b.Item3 >= sid)));
}
}
File.WriteAllLines(@"c:\r\ss.csv", ssData.Select(a => string.Join(",", new string[] { "" + a.Item1.Length, a.Item1, a.Item2, "" + a.Item3 })));
File.WriteAllLines(@"c:\r\ss-clusters-1.csv", ssDistinct.Select(a => a + "," + string.Join(",", ssNeighbours.Where(d => d.Item1 == a).Select(d => "" + d.Item3).ToList())));
//aa-ss count non-transivity clusters
var aaSsData = taskList2.SelectMany(a => a.Result.AaSsData).ToList();
var aaSsDistinct = aaSsData.Select(a => new Tuple <string, string>(a.Item1, a.Item2)).Distinct().ToList();
var aaSsNeighbours = new List <Tuple <string, string, decimal, decimal> >();
foreach (var aaSs in aaSsDistinct)
{
var subset = aaSsData.Where(a => a.Item1 == aaSs.Item1 && a.Item2 == aaSs.Item2).ToList();
foreach (var sid in sids)
{
aaSsNeighbours.Add(new Tuple <string, string, decimal, decimal>(aaSs.Item1, aaSs.Item2, sid, subset.Count(b => b.Item5 >= sid)));
}
}
File.WriteAllLines(@"c:\r\aa-ss.csv", aaSsData.Select(a => string.Join(",", new string[] { "" + a.Item1.Length, a.Item1, a.Item2, a.Item3, a.Item4, "" + a.Item5, "" + a.Item6, "" + a.Item7 })));
File.WriteAllLines(@"c:\r\aa-ss-clusters-1.csv", aaSsDistinct.Select(a => a.Item1 + "," + a.Item2 + "," + string.Join(",", aaSsNeighbours.Where(d => d.Item1 == a.Item1 && d.Item2 == a.Item2).Select(d => "" + d.Item4).ToList())));
// cluster by transivity
//var aaSsPairList = aaSsData.Select(a => new Tuple<string, string>(a.Item1, a.Item2)).Distinct().ToList();
var aaSsPairClusters = aaSsData.Select(a => new Tuple <string, string>(a.Item1, a.Item2)).Distinct().Select(a => new List <Tuple <string, string> >()
{
a
}).ToList();
var aaClusters = aaSsData.Select(a => a.Item1).Distinct().Select(a => new List <string>()
{
a
}).ToList();
var ssClusters = aaSsData.Select(a => a.Item2).Distinct().Select(a => new List <string>()
{
a
}).ToList();
decimal minTransivitySid = 0.3m;
foreach (var x in aaSsDistinct)
{
foreach (var y in aaSsDistinct)
{
if (x == y)
{
continue;
}
if (x.Item1.Length != y.Item1.Length)
{
continue; //items have not been sequence aligned if not the same length
}
var z = aaSsData.First(a => a.Item1 == x.Item1 && a.Item2 == x.Item2 && a.Item3 == y.Item1 && a.Item4 == y.Item2);
if (z.Item5 >= minTransivitySid)
{
var c1 = aaClusters.First(a => a.Any(b => b == x.Item1));
var c2 = aaClusters.First(a => a.Any(b => b == y.Item1));
if (c1 != c2)
{
c1.AddRange(c2);
aaClusters.Remove(c2);
}
}
if (z.Item6 >= minTransivitySid)
{
var c1 = ssClusters.First(a => a.Any(b => b == x.Item2));
var c2 = ssClusters.First(a => a.Any(b => b == y.Item2));
if (c1 != c2)
{
c1.AddRange(c2);
ssClusters.Remove(c2);
}
}
if (z.Item7 >= minTransivitySid)
{
var c1 = aaSsPairClusters.First(a => a.Any(b => b.Item1 == x.Item1 && b.Item2 == x.Item2));
var c2 = aaSsPairClusters.First(a => a.Any(b => b.Item1 == y.Item1 && b.Item2 == y.Item2));
if (c1 != c2)
{
c1.AddRange(c2);
aaSsPairClusters.Remove(c2);
}
}
}
}
var aaSsPairClusters2 = aaSsPairClusters.SelectMany((a, i) => a.Select(b => new Tuple <int, string, string>(i + 1, b.Item1, b.Item2))).ToList();
aaSsPairClusters2 = aaSsPairClusters2.OrderByDescending(a => aaSsPairClusters2.Count(b => b.Item1 == a.Item1)).ToList();
File.WriteAllLines(@"c:\r\aa-ss-clusters-2.csv", aaSsPairClusters2.Select(a => string.Join(",", new string[] { "" + a.Item1, a.Item2, a.Item3 })));
var aaClusters2 = aaClusters.SelectMany((a, i) => a.Select(b => new Tuple <int, string>(i + 1, b))).ToList();
aaClusters2 = aaClusters2.OrderByDescending(a => aaClusters2.Count(b => b.Item1 == a.Item1)).ToList();
File.WriteAllLines(@"c:\r\aa-clusters-2.csv", aaClusters2.Select(a => string.Join(",", new string[] { "" + a.Item1, a.Item2 })));
var ssClusters2 = ssClusters.SelectMany((a, i) => a.Select(b => new Tuple <int, string>(i + 1, b))).ToList();
ssClusters2 = ssClusters2.OrderByDescending(a => ssClusters2.Count(b => b.Item1 == a.Item1)).ToList();
File.WriteAllLines(@"c:\r\ss-clusters-2.csv", ssClusters2.Select(a => string.Join(",", new string[] { "" + a.Item1, a.Item2 })));
//File.WriteAllLines(@"c:\r\clusters-ss.csv", ssClusters2.Select(a => string.Join(",", new string[] { "" + a.Item1, a.Item2 })));
// clusters by aa sid, ss sid, aa-ss sid
}
