/// <summary>
///
/// </summary>
/// <param name="alignInfo"></param>
private void FindEndPosition(ref AlignSeqInfo alignInfo)
{
string noGapAlignSequence = GetNonGapAlignedString(alignInfo.alignSequence);
string sequenceInCoord = GetChainSequenceInCoordinates(alignInfo.pdbId, Convert.ToInt32(alignInfo.asymChainId));
string noGapCoordSeq = "";
Hashtable coordSeqIdSeqIdHash = GetCoordSeqToSeqHash(sequenceInCoord, out noGapCoordSeq, alignInfo.alignStart);
int alignStartIdx = noGapCoordSeq.IndexOf(noGapAlignSequence);
if (alignStartIdx > -1)
{
int alignEndIdx = alignStartIdx + noGapAlignSequence.Length;
// get the XML sequential id
int alignEnd = (int)coordSeqIdSeqIdHash[alignEndIdx];
alignInfo.alignEnd = alignEnd;
}
}
/// <summary>
/// the aligned seqeuence only for those with coordinates
/// Fatcat don't provide the end position which is in the PDB file
/// have to find the real start and end positions in XML residue sequential number
/// </summary>
/// <param name="pdbId"></param>
/// <param name="asymChain"></param>
/// <param name="startPos"></param>
/// <param name="alignInfo"></param>
private void FindStartEndPosition(string pdbId, int entityID, int startPos, ref AlignSeqInfo alignInfo)
{
string noGapAlignSequence = GetNonGapAlignedString(alignInfo.alignSequence);
string sequenceInCoord = GetChainSequenceInCoordinates(pdbId, entityID);
string noGapCoordSeq = "";
Hashtable coordSeqIdSeqIdHash = GetCoordSeqToSeqHash(sequenceInCoord, out noGapCoordSeq, startPos);
int alignStartIdx = noGapCoordSeq.IndexOf(noGapAlignSequence);
if (alignStartIdx > -1)
{
alignInfo.alignStart = (int)coordSeqIdSeqIdHash[alignStartIdx + 1];
int alignEndIdx = alignStartIdx + noGapAlignSequence.Length;
// get the XML sequential id
int alignEnd = (int)coordSeqIdSeqIdHash[alignEndIdx];
alignInfo.alignEnd = alignEnd;
}
}
/// <summary>
/// parse one fatcat alignment output file
/// insert data into database
/// </summary>
/// <param name="alignFile"></param>
public void ParsePfamFatcatAlignmentFile(string alignFile, bool isUpdate)
{
StreamReader dataReader = new StreamReader(alignFile);
string line = "";
int scoreIdx = -1;
int alignLenIdx = -1;
int gapIdx = -1;
int gapEndIdx = -1;
string alignSequence1 = "";
string alignSequence2 = "";
int alignStart1 = -1;
int alignEnd1 = -1;
int alignStart2 = -1;
int alignEnd2 = -1;
string[] fields = null;
bool chain1Started = false;
bool chain2Started = false;
AlignSeqInfo alignInfo1 = new AlignSeqInfo();
AlignSeqInfo alignInfo2 = new AlignSeqInfo();
DataRow dataRow = FatcatTables.fatcatAlignTable.NewRow();
string dataLine = "";
// the asymchain and startpos for this domain
Hashtable domainChainInfoHash = new Hashtable();
while ((line = dataReader.ReadLine()) != null)
{
if (line == "")
{
continue;
}
try
{
dataLine += (line + "\r\n");
if (line.IndexOf("Align") > -1 &&
line.Substring(0, "Align".Length) == "Align")
{
fields = ParseHelper.SplitPlus(line, ' ');
// domain 1
string[] domainInfo1 = ParseDomainName(fields[1], ref domainChainInfoHash);
dataRow["QueryEntry"] = domainInfo1[0];
dataRow["QueryDomainID"] = domainInfo1[1];
dataRow["QueryEntity"] = domainInfo1[2];
dataRow["QueryDomainStart"] = domainInfo1[3];
dataRow["QueryLength"] = fields[2];
// domain 2
string[] domainInfo2 = ParseDomainName(fields[4], ref domainChainInfoHash);
dataRow["HitEntry"] = domainInfo2[0];
dataRow["HitDomainID"] = domainInfo2[1];
dataRow["HitEntity"] = domainInfo2[2];
dataRow["HitDomainStart"] = domainInfo2[3];
dataRow["HitLength"] = fields[5];
alignInfo1.pdbId = fields[1].Substring(0, 4);
alignInfo1.asymChainId = domainInfo1[2];
alignInfo2.pdbId = fields[4].Substring(0, 4);
alignInfo2.asymChainId = domainInfo2[2];
alignSequence1 = "";
alignSequence2 = "";
chain1Started = true;
chain2Started = true;
}
scoreIdx = line.IndexOf("Score");
if (scoreIdx > -1)
{
// from opt-equ, equivalent positions
// dataRow["AlignmentLength"] =
alignLenIdx = line.IndexOf("align-len");
gapIdx = line.IndexOf("gaps");
gapEndIdx = line.LastIndexOf("(");
dataRow["Score"] = line.Substring(scoreIdx + "Score".Length + 1, alignLenIdx - scoreIdx - "Score".Length - 1);
dataRow["Align_Len"] = line.Substring(alignLenIdx + "align-len".Length + 1,
gapIdx - alignLenIdx - "align-len".Length - 2);
dataRow["Gaps"] = line.Substring(gapIdx + "gaps".Length + 1, gapEndIdx - gapIdx - "gaps".Length - 2);
}
if (line.IndexOf("P-value") > -1)
{
fields = ParseHelper.SplitPlus(line, ' ');
dataRow["E_Value"] = Convert.ToDouble(fields[1]);
dataRow["Identity"] = fields[5].TrimEnd('%');
dataRow["Similarity"] = fields[7].TrimEnd('%');
}
if (line.IndexOf("Chain 1:") > -1)
{
// contain alignStart and aligned sequence
fields = ParseChainAlignSeqLine(line);
if (chain1Started)
{
alignStart1 = ConvertSeqToInt(fields[0]);
chain1Started = false;
}
alignSequence1 += fields[1];
alignEnd1 = ConvertSeqToInt(fields[0]) + GetNonGapAlignedString(fields[1]).Length - 1;
}
if (line.IndexOf("Chain 2:") > -1)
{
fields = ParseChainAlignSeqLine(line);
if (chain2Started)
{
alignStart2 = ConvertSeqToInt(fields[0]);
chain2Started = false;
}
alignSequence2 += fields[1];
alignEnd2 = ConvertSeqToInt(fields[0]) + GetNonGapAlignedString(fields[1]).Length - 1;
}
if (line.IndexOf("Note:") > -1)
{
if (alignSequence1 == "")
{
continue;
}
alignInfo1.alignStart = alignStart1;
alignInfo1.alignEnd = alignEnd1;
alignInfo1.alignSequence = alignSequence1;
if (alignInfo1.alignStart < 0)
{
FindStartEndPosition(dataRow["QueryEntry"].ToString(),
Convert.ToInt32(dataRow["QueryEntity"].ToString()),
Convert.ToInt16(dataRow["QueryDomainStart"].ToString()), ref alignInfo1);
}
alignInfo2.alignStart = alignStart2;
alignInfo2.alignEnd = alignEnd2;
alignInfo2.alignSequence = alignSequence2;
if (alignInfo2.alignStart < 0)
{
FindStartEndPosition(dataRow["HitEntry"].ToString(),
Convert.ToInt32(dataRow["HitEntity"].ToString()),
Convert.ToInt16(dataRow["HitDomainStart"].ToString()), ref alignInfo2);
}
dataRow["AlignmentLength"] = GetAlignmentLength(alignSequence1, alignSequence2);
dataRow["QuerySequence"] = alignInfo1.alignSequence;
dataRow["HitSequence"] = alignInfo2.alignSequence;
dataRow["QueryStart"] = alignInfo1.alignStart;
dataRow["QueryEnd"] = alignInfo1.alignEnd;
dataRow["HitStart"] = alignInfo2.alignStart;
dataRow["HitEnd"] = alignInfo2.alignEnd;
// delete the previous data
if (isUpdate)
{
DeletePfamAlignment(dataRow["QueryEntry"].ToString(), Convert.ToInt64(dataRow["QueryDomainID"].ToString()),
dataRow["HitEntry"].ToString(), Convert.ToInt64(dataRow["HitDomainID"].ToString()));
}
if (FatcatTables.fatcatAlignTable.Columns.Contains("QuerySeqNumbers"))
{
AddQueryHitSeqNumbers(dataRow);
}
dbInsert.InsertDataIntoDb(AppSettings.alignmentDbConnection, dataRow);
alignSequence1 = "";
alignSequence2 = "";
dataLine = "";
}
if (line.IndexOf("#Time used") > -1)
{
break;
}
}
catch (Exception ex)
{
logWriter.WriteLine(ex.Message);
logWriter.WriteLine(line);
logWriter.WriteLine(dataLine);
logWriter.Flush();
dataLine = "";
}
}
dataReader.Close();
}
