private static void Main(string[] args)
{
try
{
Stopwatch stopWatchMumUtil = Stopwatch.StartNew();
Stopwatch stopWatchInterval = new Stopwatch();
Console.Error.WriteLine(SplashString());
if (args.Length > 0)
{
CommandLineOptions myArgs = ProcessCommandLine(args);
TimeSpan writetime = new TimeSpan();
LongestIncreasingSubsequence lis = new LongestIncreasingSubsequence();
IEnumerable <Match> mums;
if (myArgs.PerformLISOnly)
{
stopWatchInterval.Restart();
IList <Match> parsedMUMs = ParseMums(myArgs.FileList[0]);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed MUM file: {0}", Path.GetFullPath(myArgs.FileList[0]));
Console.Error.WriteLine(" Total MUMs: {0:#,000}", parsedMUMs.Count);
Console.Error.WriteLine(" Read/Processing time: {0}", stopWatchInterval.Elapsed);
}
stopWatchInterval.Restart();
IList <Match> sortedMUMs = lis.SortMum(parsedMUMs);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Sort MUM time: {0}", stopWatchInterval.Elapsed);
}
stopWatchInterval.Restart();
if (sortedMUMs.Count != 0)
{
mums = lis.GetLongestSequence(sortedMUMs);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Perform LIS time: {0}", stopWatchInterval.Elapsed);
}
stopWatchInterval.Restart();
WriteMums(mums);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Write MUM time: {0}", stopWatchInterval.Elapsed);
}
stopWatchMumUtil.Stop();
}
else
{
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Perform LIS time: {0}", stopWatchInterval.Elapsed);
}
stopWatchInterval.Restart();
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Write MUM time: {0}", stopWatchInterval.Elapsed);
}
stopWatchMumUtil.Stop();
}
}
else
{
FileInfo refFileinfo = new FileInfo(myArgs.FileList[0]);
long refFileLength = refFileinfo.Length;
refFileinfo = null;
stopWatchInterval.Restart();
IEnumerable <ISequence> referenceSequences = ParseFastA(myArgs.FileList[0]);
ISequence referenceSequence = referenceSequences.First();
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed Reference FastA file: {0}", Path.GetFullPath(myArgs.FileList[0]));
Console.Error.WriteLine(" Length of first Sequence: {0:#,000}", referenceSequence.Count);
Console.Error.WriteLine(" Read/Processing time: {0}", stopWatchInterval.Elapsed);
Console.Error.WriteLine(" File Size : {0}", refFileLength);
}
FileInfo queryFileinfo = new FileInfo(myArgs.FileList[1]);
long queryFileLength = queryFileinfo.Length;
refFileinfo = null;
stopWatchInterval.Restart();
IEnumerable <ISequence> querySequences = ParseFastA(myArgs.FileList[1]);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed Query FastA file: {0}", Path.GetFullPath(myArgs.FileList[1]));
Console.Error.WriteLine(" Read/Processing time: {0}", stopWatchInterval.Elapsed);
Console.Error.WriteLine(" File Size : {0}", queryFileLength);
}
if (myArgs.ReverseOnly)
{
stopWatchInterval.Restart();
querySequences = ReverseComplementSequenceList(querySequences);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine(" Reverse Complement time: {0}", stopWatchInterval.Elapsed);
}
}
else if (myArgs.Both)
{ // add the reverse complement sequences to the query list too
stopWatchInterval.Restart();
querySequences = AddReverseComplementsToSequenceList(querySequences);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine(" Add Reverse Complement time: {0}", stopWatchInterval.Elapsed);
}
}
TimeSpan mummerTime = new TimeSpan(0, 0, 0);
stopWatchInterval.Restart();
Sequence seq = referenceSequence as Sequence;
if (seq == null)
{
throw new ArgumentException("MUMmer supports only Sequence class");
}
MUMmer mummer = new MUMmer(seq);
stopWatchInterval.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine("Suffix tree construction time: {0}", stopWatchInterval.Elapsed);
}
mummer.LengthOfMUM = myArgs.Length;
mummer.NoAmbiguity = myArgs.NoAmbiguity;
long querySeqCount = 0;
double sumofSeqLength = 0;
if (myArgs.MaxMatch)
{
foreach (ISequence querySeq in querySequences)
{
stopWatchInterval.Restart();
IList <Match> mumList = GetMumsForLIS(mummer.GetMatchesUniqueInReference(querySeq));
if (mumList.Count != 0)
{
mums = lis.GetLongestSequence(lis.SortMum(mumList));
stopWatchInterval.Stop();
mummerTime = mummerTime.Add(stopWatchInterval.Elapsed);
stopWatchInterval.Restart();
WriteMums(mums, referenceSequence, querySeq, myArgs);
stopWatchInterval.Stop();
writetime = writetime.Add(stopWatchInterval.Elapsed);
querySeqCount++;
sumofSeqLength += querySeq.Count;
}
else
{
stopWatchInterval.Stop();
mummerTime = mummerTime.Add(stopWatchInterval.Elapsed);
stopWatchInterval.Restart();
stopWatchInterval.Stop();
writetime = writetime.Add(stopWatchInterval.Elapsed);
querySeqCount++;
sumofSeqLength += querySeq.Count;
}
}
if (myArgs.Verbose)
{
Console.Error.WriteLine(" Number of query Sequences: {0}", querySeqCount);
Console.Error.WriteLine(" Average length of query Sequences: {0}", sumofSeqLength / querySeqCount);
Console.Error.WriteLine(" Compute GetMumsMaxMatch() with LIS time: {0}", mummerTime);
}
}
else if (myArgs.Mum)
{
foreach (ISequence querySeq in querySequences)
{
stopWatchInterval.Restart();
IList <Match> mumList = GetMumsForLIS(mummer.GetMatchesUniqueInReference(querySeq));
if (mumList.Count != 0)
{
mums = lis.GetLongestSequence(lis.SortMum(mumList));
stopWatchInterval.Stop();
mummerTime = mummerTime.Add(stopWatchInterval.Elapsed);
stopWatchInterval.Restart();
WriteMums(mums, referenceSequence, querySeq, myArgs);
stopWatchInterval.Stop();
writetime = writetime.Add(stopWatchInterval.Elapsed);
querySeqCount++;
sumofSeqLength += querySeq.Count;
}
else
{
stopWatchInterval.Stop();
mummerTime = mummerTime.Add(stopWatchInterval.Elapsed);
stopWatchInterval.Restart();
stopWatchInterval.Stop();
writetime = writetime.Add(stopWatchInterval.Elapsed);
querySeqCount++;
sumofSeqLength += querySeq.Count;
}
}
if (myArgs.Verbose)
{
Console.Error.WriteLine(" Number of query Sequences: {0}", querySeqCount);
Console.Error.WriteLine(" Average length of query Sequences: {0}", sumofSeqLength / querySeqCount);
Console.Error.WriteLine(" Compute GetMumsMum() with LIS time: {0}", mummerTime);
}
}
else if (myArgs.Mumreference)
{
// NOTE:
// mum3.GetMUMs() this really implements the GetMumReference() functionality
// mums = mum3.GetMumsReference( referenceSequences[0], querySequences); // should be
foreach (ISequence querySeq in querySequences)
{
stopWatchInterval.Restart();
IList <Match> mumList = GetMumsForLIS(mummer.GetMatchesUniqueInReference(querySeq));
if (mumList.Count != 0)
{
mums = lis.GetLongestSequence(lis.SortMum(mumList));
stopWatchInterval.Stop();
mummerTime = mummerTime.Add(stopWatchInterval.Elapsed);
stopWatchInterval.Restart();
// do sort
// WriteLongestIncreasingSubsequences
WriteMums(mums, referenceSequence, querySeq, myArgs);
stopWatchInterval.Stop();
writetime = writetime.Add(stopWatchInterval.Elapsed);
querySeqCount++;
sumofSeqLength += querySeq.Count;
}
else
{
stopWatchInterval.Stop();
mummerTime = mummerTime.Add(stopWatchInterval.Elapsed);
stopWatchInterval.Restart();
stopWatchInterval.Stop();
writetime = writetime.Add(stopWatchInterval.Elapsed);
querySeqCount++;
sumofSeqLength += querySeq.Count;
}
}
if (myArgs.Verbose)
{
Console.Error.WriteLine(" Number of query Sequences: {0}", querySeqCount);
Console.Error.WriteLine(" Average length of query Sequences: {0}", sumofSeqLength / querySeqCount);
Console.Error.WriteLine(" Compute GetMumsReference() time: {0}", mummerTime);
}
}
else
{
// cannot happen as argument processing already asserted one of the three options must be specified
Console.Error.WriteLine("\nError: one of /maxmatch, /mum, /mumreference options must be specified.");
Environment.Exit(-1);
// kill the error about unitialized use of 'mums' in the next block...the compiler does not recognize
// Environment.Exit() as a no-return function
throw new Exception("Never hit this");
}
}
if (myArgs.Verbose)
{
Console.Error.WriteLine(" WriteMums() time: {0}", writetime);
}
stopWatchMumUtil.Stop();
if (myArgs.Verbose)
{
Console.Error.WriteLine(" Total LisUtil Runtime: {0}", stopWatchMumUtil.Elapsed);
}
}
else
{
Console.WriteLine(Resources.LisUtilHelp);
}
}
catch (Exception ex)
{
DisplayException(ex);
}
}
static void Main(string[] args)
{
try
{
// DateTime dStart = DateTime.Now;
Stopwatch swMumUtil = Stopwatch.StartNew();
Stopwatch swInterval = new Stopwatch();
Console.Error.WriteLine(SplashString());
if (args.Length > 0)
{
CommandLineOptions myArgs = ProcessCommandLine(args);
if (myArgs.help)
{
Console.WriteLine(Resources.MumUtilHelp);
}
else
{
FileInfo refFileinfo = new FileInfo(myArgs.fileList[0]);
long refFileLength = refFileinfo.Length;
refFileinfo = null;
swInterval.Restart();
IEnumerable <ISequence> referenceSequences = ParseFastA(myArgs.fileList[0]);
Sequence referenceSequence = referenceSequences.First() as Sequence;
swInterval.Stop();
if (myArgs.verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed Reference FastA file: {0}", Path.GetFullPath(myArgs.fileList[0]));
Console.Error.WriteLine(" Length of first Sequence: {0:#,000}", referenceSequence.Count);
Console.Error.WriteLine(" Read/Processing time: {0}", swInterval.Elapsed);
Console.Error.WriteLine(" File size : {0:#,000} bytes", refFileLength);
}
FileInfo queryFileinfo = new FileInfo(myArgs.fileList[1]);
long queryFileLength = queryFileinfo.Length;
refFileinfo = null;
IEnumerable <ISequence> parsedQuerySequences = ParseFastA(myArgs.fileList[1]);
IEnumerable <ISequence> querySequences = parsedQuerySequences;
if (myArgs.reverseOnly)
{
// convert to reverse complement sequences
querySequences = ReverseComplementSequenceList(parsedQuerySequences);
}
else if (myArgs.both)
{
// add the reverse complement sequences along with query sequences.
querySequences = AddReverseComplementsToSequenceList(parsedQuerySequences);
}
// DISCUSSION:
// Three possible outputs desired. Globally unique 'mum' (v1), unique in reference sequence (v2),
// or get the maximum matches of length or greater.
//
mummerTime = new TimeSpan();
writetime = new TimeSpan();
IEnumerable <Match> mums;
long memoryAtStart = 0;
long memoryAtEnd = 0;
if (myArgs.verbose)
{
swMumUtil.Stop();
memoryAtStart = GC.GetTotalMemory(true);
swMumUtil.Start();
}
swInterval.Restart();
MultiWaySuffixTree suffixTreee = new MultiWaySuffixTree(referenceSequence);
swInterval.Stop();
if (myArgs.verbose)
{
swMumUtil.Stop();
memoryAtEnd = GC.GetTotalMemory(true);
swMumUtil.Start();
}
MUMmer mummer = new MUMmer(suffixTreee);
if (myArgs.verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine("Suffix tree construction time : {0}", swInterval.Elapsed);
Console.Error.WriteLine("Memory consumed by Suffix tree : {0:#,000}", memoryAtEnd - memoryAtStart);
Console.Error.WriteLine("Total edges created : {0:#,000}", suffixTreee.EdgesCount);
Console.Error.WriteLine("Memory per edge : {0:#,000.00} bytes", (((double)(memoryAtEnd - memoryAtStart)) / suffixTreee.EdgesCount));
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed Query FastA file: {0}", Path.GetFullPath(myArgs.fileList[1]));
Console.Error.WriteLine(" File Size : {0:#,000} bytes", queryFileLength);
}
mummer.LengthOfMUM = myArgs.length;
mummer.NoAmbiguity = myArgs.noAmbiguity;
long querySeqCount = 0;
double sumofSeqLength = 0;
TimeSpan totalTimetakenToProcessQuerySequences = new TimeSpan();
string outputOption = string.Empty;
if (myArgs.maxmatch)
{
outputOption = "GetMumsMaxMatch()";
swInterval.Restart();
foreach (Sequence qSeq in querySequences)
{
// Stop the wath after each query sequence parsed.
swInterval.Stop();
// Add total time to process query sequence.
// if reverse complement option is set, includes reverse complement time also.
totalTimetakenToProcessQuerySequences = totalTimetakenToProcessQuerySequences.Add(swInterval.Elapsed);
mums = mummer.GetMatches(qSeq);
WriteMums(mums, referenceSequence, qSeq, myArgs);
querySeqCount++;
sumofSeqLength += qSeq.Count;
// Start the watch for next query sequence parse.
swInterval.Restart();
}
swInterval.Stop();
}
else if (myArgs.mum)
{
// mums = mum3.GetMumsMum( referenceSequences[0], querySequences);
outputOption = "GetMumsMum()";
swInterval.Restart();
foreach (Sequence qSeq in querySequences)
{
// Stop the wath after each query sequence parsed.
swInterval.Stop();
// Add total time to process query sequence.
// if reverse complement option is set, includes reverse complement time also.
totalTimetakenToProcessQuerySequences = totalTimetakenToProcessQuerySequences.Add(swInterval.Elapsed);
swInterval.Restart();
// TODO: After implementing GetMatchesUniqueInBothReferenceAndQuery() in MUMmer
//// GetMatchesUniqueInReference() with GetMatchesUniqueInBothReferenceAndQuery() in the line below.
mums = mummer.GetMatchesUniqueInReference(qSeq);
swInterval.Stop();
// Add time taken by GetMatchesUniqueInBothReferenceAndQuery().
mummerTime = mummerTime.Add(swInterval.Elapsed);
swInterval.Restart();
WriteMums(mums, referenceSequence, qSeq, myArgs);
swInterval.Stop();
// Add time taken by write matches.
writetime = writetime.Add(swInterval.Elapsed);
querySeqCount++;
sumofSeqLength += qSeq.Count;
// Start the watch for next query sequence parse.
swInterval.Restart();
}
swInterval.Stop();
}
else if (myArgs.mumreference)
{
// NOTE:
// mum3.GetMUMs() this really implements the GetMumReference() functionality
// mums = mum3.GetMumsReference( referenceSequences[0], querySequences); // should be
//swInterval.Restart();
outputOption = "GetMumsReference()";
swInterval.Restart();
foreach (Sequence qSeq in querySequences)
{
// Stop the wath after each query sequence parsed.
swInterval.Stop();
// Add total time to process query sequence.
// if reverse complement option is set, includes reverse complement time also.
totalTimetakenToProcessQuerySequences = totalTimetakenToProcessQuerySequences.Add(swInterval.Elapsed);
swInterval.Restart();
mums = mummer.GetMatchesUniqueInReference(qSeq);
swInterval.Stop();
// Add time taken by GetMatchesUniqueInReference().
mummerTime = mummerTime.Add(swInterval.Elapsed);
swInterval.Restart();
WriteMums(mums, referenceSequence, qSeq, myArgs);
swInterval.Stop();
// Add time taken by write matches.
writetime = writetime.Add(swInterval.Elapsed);
querySeqCount++;
sumofSeqLength += qSeq.Count;
// Start the watch for next query sequence parse.
swInterval.Restart();
}
swInterval.Stop();
}
else
{
// cannot happen as argument processing already asserted one of the three options must be specified
Console.Error.WriteLine("\nError: one of /maxmatch, /mum, /mumreference options must be specified.");
Environment.Exit(-1);
// kill the error about unitialized use of 'mums' in the next block...the compiler does not recognize
// Environment.Exit() as a no-return function
throw new Exception("Never hit this");
}
if (myArgs.verbose)
{
if (myArgs.reverseOnly || myArgs.both)
{
Console.Error.WriteLine(" Read/Processing time : {0}", timeTakenToParseQuerySequences);
Console.Error.WriteLine(" Reverse Complement time : {0}", timeTakenToGetReverseComplement);
Console.Error.WriteLine(" Total time taken to Process reads: {0}", totalTimetakenToProcessQuerySequences);
}
else
{
Console.Error.WriteLine(" Read/Processing time : {0}", totalTimetakenToProcessQuerySequences);
}
Console.Error.WriteLine();
Console.Error.WriteLine(" Number of query Sequences : {0:#,000}", querySeqCount);
Console.Error.WriteLine(" Average length of query Sequences: {0:#,000}", sumofSeqLength / querySeqCount);
Console.Error.WriteLine();
Console.Error.WriteLine("Compute {0,20} time : {1}", outputOption, mummerTime);
Console.Error.WriteLine(" WriteMums() time : {0}", writetime);
}
swMumUtil.Stop();
if (myArgs.verbose)
{
Console.Error.WriteLine(" Total MumUtil Runtime : {0}", swMumUtil.Elapsed);
}
}
}
else
{
Console.WriteLine(Resources.MumUtilHelp);
}
}
catch (Exception ex)
{
DisplayException(ex);
}
}
