static void Main( string[] args )
{
// Write program headers to the command line
Console.WriteLine( "IDPickerReport " + Version + " (" + LastModified.ToShortDateString() + ")" );
Console.WriteLine( "IDPickerWorkspace " + Workspace.Version + " (" + Workspace.LastModified.ToShortDateString() + ")" );
Console.WriteLine( "IDPickerPresentation " + Presentation.Version + " (" + Presentation.LastModified.ToShortDateString() + ")" );
Console.WriteLine( IDPREPORT_LICENSE );
// Process the command line
List<string> argsList = new List<string>( args );
if( InitProcess( ref argsList ) )
{
return;
}
// Init the IDPicker workspace
long start;
Workspace ws = new Workspace( rtConfig );
ws.setStatusOutput( Console.Out );
// Initialize the modifications that can and can not appear in distinct peptides
ws.distinctPeptideSettings = new Workspace.DistinctPeptideSettings(
rtConfig.ModsAreDistinctByDefault, rtConfig.DistinctModsOverride, rtConfig.IndistinctModsOverride );
// Read the spectra export from a previous search, if given
if( rtConfig.SpectraExport != string.Empty && rtConfig.SearchScoreNames != string.Empty )
{
string[] scores = rtConfig.SearchScoreNames.Split( new char[] { ' ' } );
ws.spectraExport = new ImportSpectraExport( rtConfig.SpectraExport, scores );
}
#region SNP Annotation stuff (TODO: simplify this logic, i.e. use a bool instead of testing for empty string)
// Read the unimod modification database, if provided
if( rtConfig.UnimodXMLPath != string.Empty )
{
try
{
Console.WriteLine( "Reading modification annotations from unimod xml file path: " + rtConfig.UnimodXMLPath );
ws.readUniModXML( rtConfig.UnimodXMLPath );
Console.WriteLine( "Finished reading modification annotations." );
//ws.printUnimodObjects( 57.03f );
//Environment.Exit( 1 );
} catch( Exception e )
{
Console.Error.WriteLine( e.StackTrace.ToString() );
Console.Error.WriteLine( "Error reading unimod xml at : " + rtConfig.UnimodXMLPath );
}
}
// Read the CanProVar database, if provided
if( rtConfig.ProCanVarFasta != string.Empty && rtConfig.ProCanVarMap != string.Empty )
{
Console.WriteLine( "Reading ProCanVar SNP data....." );
ws.snpAnntoations = new SNPMetaDataGenerator();
ws.snpAnntoations.getVariantDataFromProCanVarFlatFile( rtConfig.ProCanVarFasta, rtConfig.ProCanVarMap );
Console.WriteLine( "Finished reading ProCanVar SNP data." );
/*SNPMetaDataGenerator snpData = new SNPMetaDataGenerator();
snpData.getVariantDataFromProCanVarFlatFile( rtConfig.ProCanVarFasta, rtConfig.ProCanVarMap );
Console.WriteLine( "Finished reading ProCanVar SNP data." );
SNPMetaDataGenerator.SNP test = new SNPMetaDataGenerator.SNP( "Y", "H", "24" );
string str = snpData.getSNPAnnotationFromProCanVar( "ENSP00000368054", test, "EGFYAVVIFLSIFVIIVTCLMILYR" );
Console.WriteLine( str );
Environment.Exit( 1 );*/
}
#endregion
#region Read input idpXML files
List<string> inputFilepaths = new List<string>();
for( int i = 1; i < argsList.Count; ++i )
{
try
{
string path = Path.GetDirectoryName(argsList[i]);
if (path.Length < 1)
{
path = "." + Path.DirectorySeparatorChar;
}
//Console.WriteLine( path + " : " + Path.GetFileName( args[i] ) );
inputFilepaths.AddRange(Directory.GetFiles(path, Path.GetFileName(argsList[i])));
foreach( string inputFilepath in inputFilepaths )
{
try
{
if( !Util.TestFileType( inputFilepath, "idpickerpeptides" ) )
continue;
start = DateTime.Now.Ticks;
Console.WriteLine( "Reading and parsing IDPicker XML from filepath: " + inputFilepath );
StreamReader inputStream = new StreamReader( inputFilepath );
// Read each file and assign them to the root group.
ws.readPeptidesXml( inputStream, "", rtConfig.MaxFDR, rtConfig.MaxResultRank );
inputStream.Close();
Console.WriteLine( "\nFinished reading and parsing IDPicker XML; " + new TimeSpan( DateTime.Now.Ticks - start ).TotalSeconds + " seconds elapsed." );
} catch( Exception e )
{
Console.Error.WriteLine( e.StackTrace.ToString() );
Console.Error.WriteLine( "Error reading input filepath \"" + inputFilepath + "\": " + e.Message );
continue;
}
}
} catch( Exception e )
{
Console.Error.WriteLine( "Error parsing input filemask \"" + argsList[i] + "\": " + e.Message );
continue;
}
}
if( ws.groups.Count == 0 )
{
Console.Error.WriteLine( "Error: no input files read; nothing to report." );
return;
}
#endregion
// Generate a processing event for the idpReport.
ProcessingEvent presentationEvent = new ProcessingEvent();
presentationEvent.type = "presentation/filtration";
presentationEvent.startTime = DateTime.Now;
ProcessingParam presentationParam = new ProcessingParam();
presentationParam.name = "software name";
presentationParam.value = "idpReport";
presentationEvent.parameters.Add( presentationParam );
presentationParam = new ProcessingParam();
presentationParam.name = "software version";
presentationParam.value = Version + " (" + LastModified.ToShortDateString() + ")";
presentationEvent.parameters.Add( presentationParam );
RunTimeVariableMap presentationVars = rtConfig.getVariables();
foreach( KeyValuePair<string, string> itr in presentationVars )
{
presentationParam = new ProcessingParam();
presentationParam.name = itr.Key;
presentationParam.value = itr.Value;
presentationEvent.parameters.Add( presentationParam );
}
#region Pre-filtering validation
{ ws.validate( rtConfig.MaxFDR, 0, 100 ); }
#endregion
#region Apply filtering criteria and assemble proteins
start = DateTime.Now.Ticks;
Console.WriteLine( "Filtering out peptides shorter than " + rtConfig.MinPeptideLength + " residues..." );
ws.filterByMinimumPeptideLength( rtConfig.MinPeptideLength );
Console.WriteLine( "\nFinished filtering by minimum peptide length; " + new TimeSpan( DateTime.Now.Ticks - start ).TotalSeconds + " seconds elapsed." ); { ws.validate( rtConfig.MaxFDR, 0, 100 ); }
start = DateTime.Now.Ticks;
Console.WriteLine( "Filtering out results with more than " + rtConfig.MaxAmbiguousIds + " ambiguous ids..." );
ws.filterByResultAmbiguity( rtConfig.MaxAmbiguousIds );
Console.WriteLine( "\nFinished filtering by maximum ambiguous ids; " + new TimeSpan( DateTime.Now.Ticks - start ).TotalSeconds + " seconds elapsed." ); { ws.validate( rtConfig.MaxFDR, 0, rtConfig.MaxAmbiguousIds ); }
start = DateTime.Now.Ticks;
Console.WriteLine( "Filtering out proteins with less than " + rtConfig.MinDistinctPeptides + " distinct peptides..." );
ws.filterByDistinctPeptides( rtConfig.MinDistinctPeptides );
Console.WriteLine( "\nFinished filtering by minimum distinct peptides; " + new TimeSpan( DateTime.Now.Ticks - start ).TotalSeconds + " seconds elapsed." ); { ws.validate( rtConfig.MaxFDR, rtConfig.MinDistinctPeptides, rtConfig.MaxAmbiguousIds ); }
start = DateTime.Now.Ticks;
Console.WriteLine( "Filtering out proteins with less than " + rtConfig.MinSpectraPerProtein + " spectra..." );
ws.filterBySpectralCount( rtConfig.MinSpectraPerProtein );
Console.WriteLine( "\nFinished filtering by minimum protein spectral counts; " + new TimeSpan( DateTime.Now.Ticks - start ).TotalSeconds + " seconds elapsed." ); { ws.validate( rtConfig.MaxFDR, rtConfig.MinDistinctPeptides, rtConfig.MaxAmbiguousIds ); }
start = DateTime.Now.Ticks;
Console.WriteLine( "Assembling protein groups..." );
ws.assembleProteinGroups();
Console.WriteLine( "\nFinished assembling protein groups; " + new TimeSpan( DateTime.Now.Ticks - start ).TotalSeconds + " seconds elapsed." ); { ws.validate( rtConfig.MaxFDR, rtConfig.MinDistinctPeptides, rtConfig.MaxAmbiguousIds ); }
start = DateTime.Now.Ticks;
Console.WriteLine( "Assembling peptide groups..." );
ws.assemblePeptideGroups();
Console.WriteLine( "\nFinished assembling peptide groups; " + new TimeSpan( DateTime.Now.Ticks - start ).TotalSeconds + " seconds elapsed." ); { ws.validate( rtConfig.MaxFDR, rtConfig.MinDistinctPeptides, rtConfig.MaxAmbiguousIds ); }
start = DateTime.Now.Ticks;
Console.WriteLine( "Assembling clusters..." );
ws.assembleClusters();
Console.WriteLine( "\nFinished assembling clusters; " + new TimeSpan( DateTime.Now.Ticks - start ).TotalSeconds + " seconds elapsed." ); { ws.validate( rtConfig.MaxFDR, rtConfig.MinDistinctPeptides, rtConfig.MaxAmbiguousIds ); }
start = DateTime.Now.Ticks;
// Determine the minimum number of protein clusters needed
// to explain all the peptides.
Console.WriteLine( "Assembling minimum covering set for clusters..." );
int clusterCount = 0;
foreach( ClusterInfo c in ws.clusters )
{
++clusterCount;
Console.Write( "Assembling minimum covering set for cluster " + clusterCount + " of " + ws.clusters.Count + " (" + c.proteinGroups.Count + " protein groups, " + c.results.Count + " results) \r" );
ws.assembleMinimumCoveringSet( c );
}
Console.WriteLine( "\nFinished assembling minimum covering sets; " + new TimeSpan( DateTime.Now.Ticks - start ).TotalSeconds + " seconds elapsed." ); { ws.validate( rtConfig.MaxFDR, rtConfig.MinDistinctPeptides, rtConfig.MaxAmbiguousIds ); }
if( rtConfig.MinAdditionalPeptides > 0 )
{
start = DateTime.Now.Ticks;
Console.WriteLine( "Filtering workspace by minimum covering set..." );
ws.filterByMinimumCoveringSet( rtConfig.MinAdditionalPeptides );
Console.WriteLine( "\nFinished filtering by minimum covering set; " + new TimeSpan( DateTime.Now.Ticks - start ).TotalSeconds + " seconds elapsed." ); { ws.validate( rtConfig.MaxFDR, rtConfig.MinDistinctPeptides, rtConfig.MaxAmbiguousIds ); }
}
start = DateTime.Now.Ticks;
Console.Write( "Assembling source groups..." );
ws.assembleSourceGroups();
Console.WriteLine( " finished; " + new TimeSpan( DateTime.Now.Ticks - start ).TotalSeconds + " seconds elapsed." );
#endregion
#region Post-filtering validation
// Check to see if the protein, peptides, sources, and the clusters have
// all required fields and satisfy the user-defined criteria.
try
{
ws.validate( rtConfig.MaxFDR, rtConfig.MinDistinctPeptides, rtConfig.MaxAmbiguousIds );
} catch( Exception e )
{
Console.Error.WriteLine( "Error while validating workspace: " + e.Message );
return;
}
#endregion
#region SNP annotation stuff (TODO: move this into a Workspace function)
if( rtConfig.FlagUnknownMods.Length > 0 )
{
string[] toks = rtConfig.FlagUnknownMods.Split( new char[] { ' ' } );
if( toks.Length % 2 == 0 )
{
ws.knownModMasses = new float[toks.Length / 2];
ws.knownModResidues = new char[toks.Length / 2];
int index = 0;
for( int i = 0; i < toks.Length - 1; i = i + 2 )
{
ws.knownModResidues[index] = toks[i][0];
ws.knownModMasses[index] = (float) Convert.ToDouble( toks[i + 1] );
++index;
}
}
}
// If the user wants to annotate the SNPs found in the
// dataset then pull the annotations.
if( rtConfig.AnnotateSNPs.Length > 0 )
{
ws.pullSNPMetaData( rtConfig.AnnotateSNPs );
}
#endregion
// Make an output folder and generate files
Console.WriteLine( "Creating output directory for report: " + rtConfig.outputDir );
if( !Directory.Exists( rtConfig.outputDir ) )
Directory.CreateDirectory( rtConfig.outputDir );
Directory.SetCurrentDirectory( rtConfig.outputDir );
StreamWriter outputStream;
#region Web report
if( rtConfig.OutputWebReport )
{
string reportIndexFilename = "index.html";
string idpickerJavascriptFilename = "idpicker-scripts.js";
string idpickerStylesheetFilename = "idpicker-style.css";
string navFrameFilename = rtConfig.outputPrefix + "-nav.html";
string wsSummaryFilename = rtConfig.outputPrefix + "-summary.html";
string wsDataProcessingDetailsFilename = rtConfig.outputPrefix + "-processing.html";
string wsIndexByProteinFilename = rtConfig.outputPrefix + "-index-by-protein.html";
string wsIndexBySpectrumFilename = rtConfig.outputPrefix + "-index-by-spectrum.html";
string wsIndexByModificationFilename = rtConfig.outputPrefix + "-index-by-modification.html";
string wsGroupsFilename = rtConfig.outputPrefix + "-groups.html";
string wsSequencesPerProteinByGroupFilename = rtConfig.outputPrefix + "-sequences-per-protein-by-group.html";
string wsSpectraPerProteinByGroupFilename = rtConfig.outputPrefix + "-spectra-per-protein-by-group.html";
string wsSpectraPerPeptideByGroupFilename = rtConfig.outputPrefix + "-spectra-per-peptide-by-group.html";
try
{
Console.WriteLine( "Writing report index: " + reportIndexFilename );
outputStream = new StreamWriter( reportIndexFilename );
outputStream.Write( Presentation.assembleReportIndex( rtConfig.outputPrefix, navFrameFilename, wsSummaryFilename ) );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError report index: " + e.Message );
}
try
{
Console.WriteLine( "Writing javascript: " + idpickerJavascriptFilename );
outputStream = new StreamWriter( idpickerJavascriptFilename );
outputStream.Write( Presentation.assembleJavascript() );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing javascript: " + e.Message );
}
try
{
Console.WriteLine( "Writing stylesheet: " + idpickerStylesheetFilename );
outputStream = new StreamWriter( idpickerStylesheetFilename );
outputStream.Write( Presentation.assembleStylesheet() );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing stylesheet: " + e.Message );
}
try
{
Console.WriteLine( "Writing navigation frame: " + navFrameFilename );
Dictionary<string, string> navigationMap = new Dictionary<string, string>();
navigationMap.Add( "Summary", wsSummaryFilename );
navigationMap.Add( "Group association table", wsGroupsFilename );
navigationMap.Add( "Index by protein", wsIndexByProteinFilename );
navigationMap.Add( "Index by spectrum", wsIndexBySpectrumFilename );
navigationMap.Add( "Index by modification", wsIndexByModificationFilename );
navigationMap.Add( "Sequences per protein by group", wsSequencesPerProteinByGroupFilename );
navigationMap.Add( "Spectra per protein by group", wsSpectraPerProteinByGroupFilename );
navigationMap.Add( "Spectra per peptide by group", wsSpectraPerPeptideByGroupFilename );
navigationMap.Add( "Data processing details", wsDataProcessingDetailsFilename );
outputStream = new StreamWriter( navFrameFilename );
Presentation.assembleNavFrameHtml( ws, outputStream, rtConfig.outputPrefix, navigationMap );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing navigation frame: " + e.Message );
}
try
{
Console.WriteLine( "Writing index by protein to filepath: " + wsIndexByProteinFilename );
outputStream = new StreamWriter( wsIndexByProteinFilename );
Presentation.assembleIndexByProteinHtml( ws, outputStream, rtConfig.outputPrefix );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing index by protein: " + e.Message );
}
try
{
Console.WriteLine( "Writing index by spectrum to filepath: " + wsIndexBySpectrumFilename );
outputStream = new StreamWriter( wsIndexBySpectrumFilename );
Presentation.assembleIndexBySpectrumHtml( ws, outputStream, rtConfig.outputPrefix, rtConfig.AllowSharedSourceNames );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing index by spectrum: " + e.Message );
}
try
{
Console.WriteLine( "Writing index by modification to filepath: " + wsIndexByModificationFilename );
outputStream = new StreamWriter( wsIndexByModificationFilename );
Presentation.assembleIndexByModificationHtml( ws, outputStream, rtConfig.outputPrefix );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing index by modification: " + e.Message );
}
try
{
Console.WriteLine( "Writing overall summary to filepath: " + wsSummaryFilename );
outputStream = new StreamWriter( wsSummaryFilename );
Dictionary<string, string> parameterMap = new Dictionary<string, string>();
parameterMap.Add( "Maximum FDR", rtConfig.MaxFDR.ToString( "f2" ) );
parameterMap.Add( "Minimum distinct peptides", rtConfig.MinDistinctPeptides.ToString() );
parameterMap.Add( "Maximum ambiguous IDs", rtConfig.MaxAmbiguousIds.ToString() );
parameterMap.Add( "Minimum peptide length", rtConfig.MinPeptideLength.ToString() );
parameterMap.Add( "Minimum additional peptides", rtConfig.MinAdditionalPeptides.ToString() );
parameterMap.Add( "Minimum spectra per protein", rtConfig.MinSpectraPerProtein.ToString() );
if( rtConfig.ModsAreDistinctByDefault )
parameterMap.Add( "Indistinct modifications", rtConfig.IndistinctModsOverride );
else
parameterMap.Add( "Distinct modifications", rtConfig.DistinctModsOverride );
Presentation.assembleSummaryHtml( ws, outputStream, rtConfig.outputPrefix, parameterMap );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing overall summary: " + e.Message );
}
presentationEvent.endTime = DateTime.Now;
foreach( SourceInfo source in ws.groups["/"].getSources( true ) )
source.processingEvents.Add( presentationEvent );
try
{
Console.WriteLine( "Writing data processing details to filepath: " + wsDataProcessingDetailsFilename );
outputStream = new StreamWriter( wsDataProcessingDetailsFilename );
Presentation.assembleDataProcessingDetailsHtml( ws, outputStream, rtConfig.outputPrefix );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing data processing details: " + e.Message );
}
try
{
Console.WriteLine( "Writing source groups summary to filepath: " + wsGroupsFilename );
outputStream = new StreamWriter( wsGroupsFilename );
Presentation.assembleGroupAssociationHtml( ws, outputStream, rtConfig.outputPrefix );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing source groups summary: " + e.Message );
}
Console.WriteLine( "Writing sequences per protein table to filepath: " + wsSequencesPerProteinByGroupFilename );
try
{
outputStream = new StreamWriter( wsSequencesPerProteinByGroupFilename );
Presentation.assembleProteinSequencesTable( ws, outputStream, rtConfig.outputPrefix );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing sequences per protein table: " + e.Message );
}
try
{
Console.WriteLine( "Writing spectra per protein table to filepath: " + wsSpectraPerProteinByGroupFilename );
outputStream = new StreamWriter( wsSpectraPerProteinByGroupFilename );
Presentation.assembleProteinSpectraTable( ws, outputStream, rtConfig.outputPrefix );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing spectra per protein table: " + e.Message );
}
try
{
Console.WriteLine( "Writing spectra per peptide table to filepath: " + wsSpectraPerPeptideByGroupFilename );
outputStream = new StreamWriter( wsSpectraPerPeptideByGroupFilename );
Presentation.assemblePeptideSpectraTable( ws, outputStream, rtConfig.outputPrefix );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing spectra per peptide table: " + e.Message );
}
for( int i = 0; i < ws.clusters.Count; ++i )
{
int cid = i + 1;
string clusterSummaryFilename = rtConfig.outputPrefix + "-cluster" + cid + ".html";
try
{
Console.Write( "Writing summary for cluster " + cid + " of " + ws.clusters.Count + " to filepath: " + clusterSummaryFilename + " \r" );
outputStream = new StreamWriter( clusterSummaryFilename );
Presentation.assembleClusterHtml( ws, outputStream, rtConfig.outputPrefix, i, rtConfig.GenerateBipartiteGraphs,
rtConfig.RawSourceHostURL, rtConfig.RawSourcePath, rtConfig.RawSourceExtension );
outputStream.Close();
} catch( System.Exception e )
{
Console.Error.WriteLine( "\nError writing summary for cluster " + cid + ": " + e.Message );
}
}
Console.WriteLine();
}
#endregion
#region Generate GraphViz files
/*outputStream = new StreamWriter( "workspace.dot" );
outputStream.Write( assembleWorkspaceGraph( ws ) );
outputStream.Close();*/
if( rtConfig.GenerateBipartiteGraphs )
{
for( int i = 0; i < ws.clusters.Count; ++i )
{
int cid = i + 1;
string clusterGraphTextFilename = rtConfig.outputPrefix + "-cluster" + cid + ".dot";
Console.Write( "Writing graph of cluster " + cid + " of " + ws.clusters.Count + " to filepath: " + clusterGraphTextFilename + " \r" );
outputStream = new StreamWriter( clusterGraphTextFilename );
Presentation.assembleClusterGraph( ws, outputStream, i );
outputStream.Close();
}
Console.WriteLine();
for( int i = 0; i < ws.clusters.Count; ++i )
{
int cid = i + 1;
string clusterGraphTextFilename = rtConfig.outputPrefix + "-cluster" + cid + ".dot";
string clusterGraphImageFilename = rtConfig.outputPrefix + "-cluster" + cid + ".gif";
Console.Write( "Graphing cluster " + cid + " of " + ws.clusters.Count + " from filepath: " + clusterGraphTextFilename + " \r" );
string dotCommand = "dot";
string dotArgs = "-Tgif -o" + clusterGraphImageFilename + " " + clusterGraphTextFilename;
Process dotProcess = new Process();
dotProcess.StartInfo.FileName = dotCommand;
dotProcess.StartInfo.Arguments = dotArgs;
dotProcess.StartInfo.CreateNoWindow = true;
dotProcess.StartInfo.UseShellExecute = false;
dotProcess.Start();
dotProcess.WaitForExit();
//File.Delete( clusterGraphTextFilename );
}
Console.WriteLine();
}
#endregion
#region Text report
if( rtConfig.OutputTextReport )
{
string wsSummaryFilename = rtConfig.outputPrefix + "-summary.tsv";
string wsSequencesPerProteinByGroupFilename = rtConfig.outputPrefix + "-sequences-per-protein-by-group.tsv";
string wsSpectraPerProteinByGroupFilename = rtConfig.outputPrefix + "-spectra-per-protein-by-group.tsv";
string wsSpectraPerPeptideByGroupFilename = rtConfig.outputPrefix + "-spectra-per-peptide-by-group.tsv";
string wsSpectraTableFilename = rtConfig.outputPrefix + "-spectra-table.tsv";
string wsProteinGroupToPeptideGroupFilename = rtConfig.outputPrefix + "-protein-to-peptide-table.tsv";
string wsSpectraPerPeptideGroupFilename = rtConfig.outputPrefix + "-spectra-per-peptide-group.tsv";
// Write a protein modification report. This report takes all the modifications
// seen in the dataset and writes out a tab-delimited file of each modification
// and the samples it was identified
/*try
{
string modificationTableFilename = rtConfig.outputPrefix + "-prot-modification-table.csv";
Console.WriteLine( "Writing protein modification report to filepath: " + modificationTableFilename );
outputStream = new StreamWriter( modificationTableFilename );
outputStream.Write( Presentation.assembleDetailedModificationReport( ws ) );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing protein modification report: " + e.Message );
}*/
string rootInputDirectory;
Util.LongestCommonPrefix(inputFilepaths, out rootInputDirectory);
if (String.IsNullOrEmpty(rootInputDirectory))
rootInputDirectory = Directory.GetCurrentDirectory();
else if (!Directory.Exists(rootInputDirectory))
rootInputDirectory = Path.GetDirectoryName(rootInputDirectory);
QuantifyingTransmogrifier.quantify(ws, rootInputDirectory, rtConfig.quantitationMethod);
try
{
Console.WriteLine( "Writing overall summary to filepath: " + wsSummaryFilename );
outputStream = new StreamWriter( wsSummaryFilename );
Presentation.exportSummaryTable( ws, outputStream, rtConfig.outputPrefix, '\t' );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing overall summary: " + e.Message );
}
Console.WriteLine( "Writing sequences per protein table to filepath: " + wsSequencesPerProteinByGroupFilename );
try
{
outputStream = new StreamWriter( wsSequencesPerProteinByGroupFilename );
Presentation.exportProteinSequencesTable( ws, outputStream, rtConfig.outputPrefix, '\t' );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing sequences per protein table: " + e.Message );
}
try
{
Console.WriteLine( "Writing spectra per protein table to filepath: " + wsSpectraPerProteinByGroupFilename );
outputStream = new StreamWriter( wsSpectraPerProteinByGroupFilename );
Presentation.exportProteinSpectraTable( ws, outputStream, rtConfig.outputPrefix, '\t' );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing spectra per protein table: " + e.Message );
}
try
{
Console.WriteLine( "Writing spectra per peptide table to filepath: " + wsSpectraPerPeptideByGroupFilename );
outputStream = new StreamWriter( wsSpectraPerPeptideByGroupFilename );
Presentation.exportPeptideSpectraTable(ws, outputStream, rtConfig.outputPrefix, rtConfig.quantitationMethod, '\t');
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing spectra per peptide table: " + e.Message );
}
try
{
Console.WriteLine( "Writing spectra table to filepath: " + wsSpectraTableFilename );
outputStream = new StreamWriter( wsSpectraTableFilename );
Presentation.exportSpectraTable( ws, outputStream, rtConfig.outputPrefix, rtConfig.quantitationMethod, '\t' );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError writing spectra table: " + e.Message );
}
try
{
Console.WriteLine( "Writing protein group to peptide group table to filepath: " + wsProteinGroupToPeptideGroupFilename );
outputStream = new StreamWriter( wsProteinGroupToPeptideGroupFilename );
Presentation.exportProteinGroupToPeptideGroupTable( ws, outputStream, '\t' );
outputStream.Close();
} catch( Exception e )
{
Console.Error.WriteLine( "\nError protein group to peptide group table: " + e.Message );
}
try
{
Console.WriteLine( "Writing spectra per peptide group table to filepath: " + wsSpectraPerPeptideGroupFilename );
outputStream = new StreamWriter(wsSpectraPerPeptideGroupFilename);
Presentation.exportPeptideGroupSpectraTable(ws, outputStream, rtConfig.outputPrefix, rtConfig.quantitationMethod, '\t');
outputStream.Close();
}
catch (Exception e)
{
Console.Error.WriteLine( "\nError spectra per peptide group table: " + e.Message );
}
}
#endregion
#region Xml report
if( rtConfig.OutputXmlReport )
{
string wsAssembledXmlFilename = rtConfig.outputPrefix + "-assembled.idpXML";
outputStream = new StreamWriter( wsAssembledXmlFilename );
ws.assemblePeptidesXmlToStream( outputStream );
outputStream.Close();
}
#endregion
}
