static void Main(string[] args)
{
if (args.Length == 0)
{
ShowMessage(Resources.Program_Main_Missing_report_file_path_argument_from_Skyline__try_re_installing_TFExport_);
return;
}
var reportFilePath = args[0];
Dictionary <string, List <TransitionRecord> > peptideTransitions;
try
{
peptideTransitions = GetTransitions(reportFilePath);
}
catch (Exception e)
{
ShowMessage(string.Format(Resources.Program_Main_Failure_reading_the_report_file__0__, reportFilePath) +
Environment.NewLine + e.Message);
return;
}
var filePaths = new List <string>(peptideTransitions
.SelectMany(trans => trans.Value).OrderBy(t => t.FileName)
.Select(t => t.FileName).Distinct());
using (var tf = new TFExportDlg(filePaths))
{
if (tf.ShowDialog() != DialogResult.OK)
{
return;
}
_isAutoFill = tf.IsAutoFill(); // if false don't auto fill anything
_isAutoFillAll = tf.IsAutoFillAll(); // auto fill all as 'TargetPeak'
_isAutoFillConfirming = tf.IsAutoFillConfirming(); // auto fill one as 'TargetPeak' and rest as 'Confirming' or 'Fragment'
_internalStandardType = (InternalStandardType)tf.GetStandardType();
_rtFile = tf.GetSelectedRTFile();
_intensityFile = tf.GetSelectedIntensityFile();
_rtWindow = tf.GetRtWindow();
if (_rtFile == null)
{
_useAvgRt = true;
_rtFile = filePaths[0];
}
if (_intensityFile == null)
{
_useAvgIntensity = true;
}
// Strip peptideTransitions to either file or first one
var updatedPeptideTransitions = new Dictionary <string, List <TransitionRecord> >();
foreach (var k in peptideTransitions.Keys)
{
IList <TransitionRecord> values = peptideTransitions[k];
var transitionRecords = new List <TransitionRecord>();
foreach (var v in values)
{
if (v.FileName.Equals(_rtFile))
{
transitionRecords.Add(v);
}
}
var fileAreas = new Dictionary <string, List <double> >();
AddTransitionFileAreas(_useAvgIntensity
? values
: values.Where(tr => Equals(tr.FileName, _intensityFile)), fileAreas);
// even if area from a single file is used will still funnel through this averaging code
// but instead will just have an int array with one value so the average will be that value(value in selected file)
var avgAreas = new Dictionary <string, double>();
foreach (var fileArea in fileAreas)
{
var avg = fileArea.Value.Average();
avgAreas.Add(fileArea.Key, avg);
}
foreach (var avgArea in avgAreas)
{
var keyInfo = GetKeyParts(avgArea.Key);
var seq = keyInfo[0];
var precursorMz = keyInfo[1];
var fragmentIon = keyInfo[2];
var label = keyInfo[3];
var prodMz = keyInfo[4];
foreach (var transitionRecord in transitionRecords)
{
if (transitionRecord.ModifiedSequence.Equals(seq) &&
transitionRecord.PrecursorMz.ToString(CultureInfo.InvariantCulture).Equals(precursorMz) &&
transitionRecord.FragmentIon.Equals(fragmentIon) &&
transitionRecord.IsotopeLabelType.Equals(label) &&
transitionRecord.ProductMz.ToString(CultureInfo.InvariantCulture).Equals(prodMz))
{
transitionRecord.Area = avgArea.Value;
}
}
}
updatedPeptideTransitions.Add(k, transitionRecords); // add the transitions for this peptide
var standards = new List <TransitionRecord>();
var nonStandards = new List <TransitionRecord>();
foreach (var v in updatedPeptideTransitions[k])
{
if (v.IsotopeLabelType.Equals(_internalStandardType.ToString()))
{
standards.Add(v);
}
else
{
nonStandards.Add(v);
}
}
// make non-standards sort same as standards by giving them the same area
// area will not be seen by user but is only used to sort in this case
foreach (var v in nonStandards)
{
if (!v.IsotopeLabelType.Equals(_internalStandardType.ToString()))
{
foreach (var transitionRecord in standards)
{
if (transitionRecord.PeptideModifiedSequence.Equals(v.PeptideModifiedSequence) &&
transitionRecord.ProductCharge == v.ProductCharge &&
transitionRecord.PrecursorCharge == v.PrecursorCharge &&
transitionRecord.FragmentIon.Equals(v.FragmentIon))
{
v.Area = transitionRecord.Area;
}
}
}
}
var all = standards.Concat(nonStandards).ToList();
// Sort final list of transitions by peptide, then label type, then peak area
all.Sort((x, y) =>
{
if (x.IsotopeLabelType != y.IsotopeLabelType)
{
if (_internalStandardType.ToString().Equals(x.IsotopeLabelType))
{
return(-1);
}
if (_internalStandardType.ToString().Equals(y.IsotopeLabelType))
{
return(1);
}
}
return(y.Area.CompareTo(x.Area));
});
updatedPeptideTransitions[k] = all;
}
// EXPORT
using (var saveFileDialog = new SaveFileDialog
{
FileName = @"TFExport.csv", // Not L10N
Filter = Resources.Program_Main_CSV__Comma_delimited_____csv____csv
})
{
if (saveFileDialog.ShowDialog() != DialogResult.OK)
{
return;
}
var saveFileLocation = saveFileDialog.FileName;
try
{
WriteToCsv(saveFileLocation, updatedPeptideTransitions);
ShowMessage(string.Format(Resources.Program_Main_File_saved_to__0__, saveFileLocation));
}
catch (Exception e)
{
ShowMessage(string.Format(Resources.Program_Main_Error___0_, e.Message));
}
}
}
}
static void Main(string[] args)
{
if (args.Length == 0)
{
Console.WriteLine("Error opening report file from Skyline, try re-installing TFExport."); // Not L10N
return;
}
var reportFilePath = args[0];
var peptideTransitions = GetTransitions(reportFilePath);
var filePaths = new List <string>();
foreach (var transitions in peptideTransitions.Values)
{
foreach (var t in transitions)
{
if (!filePaths.Contains(t.FileName))
{
filePaths.Add(t.FileName);
}
}
}
filePaths.Sort();
using (var tf = new TFExportDlg(filePaths))
{
if (tf.ShowDialog() != DialogResult.OK)
{
return;
}
_isAutoFill = tf.IsAutoFill(); // if false don't auto fill anything
_isAutoFillAll = tf.IsAutoFillAll(); // auto fill all as 'TargetPeak'
_isAutoFillConfirming = tf.IsAutoFillConfirming(); // auto fill one as 'TargetPeak' and rest as 'Confirming' or 'Fragment'
_internalStandardType = (InternalStandardType)tf.GetStandardType();
_rtFile = tf.GetSelectedRTFile();
_intensityFile = tf.GetSelectedIntensityFile();
_rtWindow = tf.GetRtWindow();
if (_rtFile == null)
{
_useAvgRt = true;
_rtFile = filePaths[0];
}
if (_intensityFile == null)
{
_useAvgIntensity = true;
}
// Strip peptideTransitions to either file or first one
var updatedPeptideTransitions = new Dictionary <string, List <TransitionRecord> >();
foreach (var k in peptideTransitions.Keys)
{
var values = peptideTransitions[k];
var transitionRecords = new List <TransitionRecord>();
foreach (var v in values)
{
if (v.FileName.Equals(_rtFile))
{
transitionRecords.Add(v);
}
}
var fileAreas = new Dictionary <string, List <double> >();
if (_useAvgIntensity) // if average intensity then calculate values
{
foreach (var v in values)
{
var key = v.ModifiedSequence + "," + v.PrecursorMz + "," + v.FragmentIon + "," +
v.IsotopeLabelType + "," + v.ProductMz;
if (!fileAreas.ContainsKey(key))
{
fileAreas.Add(key, new List <double>());
}
fileAreas[key].Add(v.Area);
}
} // if use intensity from specific file
else
{
foreach (var v in values)
{
if (!v.FileName.Equals(_intensityFile))
{
continue;
}
var key = v.ModifiedSequence + "," + v.PrecursorMz + "," + v.FragmentIon + "," +
v.IsotopeLabelType + "," + v.ProductMz;
if (!fileAreas.ContainsKey(key))
{
fileAreas.Add(key, new List <double>());
}
fileAreas[key].Add(v.Area);
}
}
// even if area from a single file is used will still funnel through this averageing code
// but instead will just have an int array with one value so the average will be that value(value in selected file)
var avgAreas = new Dictionary <string, double>();
foreach (var fileArea in fileAreas)
{
var avg = fileArea.Value.Average();
avgAreas.Add(fileArea.Key, avg);
}
foreach (var avgArea in avgAreas)
{
var keyInfo = avgArea.Key.Split(',');
var seq = keyInfo[0];
var precursorMz = keyInfo[1];
var fragmentIon = keyInfo[2];
var label = keyInfo[3];
var prodMz = keyInfo[4];
foreach (var transitionRecord in transitionRecords)
{
if (transitionRecord.ModifiedSequence.Equals(seq) &&
transitionRecord.PrecursorMz.ToString(CultureInfo.InvariantCulture).Equals(precursorMz) &&
transitionRecord.FragmentIon.Equals(fragmentIon) &&
transitionRecord.IsotopeLabelType.Equals(label) &&
transitionRecord.ProductMz.ToString(CultureInfo.InvariantCulture).Equals(prodMz))
{
transitionRecord.Area = avgArea.Value;
}
}
}
updatedPeptideTransitions.Add(k, transitionRecords); // add the transitions for this peptide
var standards = new List <TransitionRecord>();
var nonStandards = new List <TransitionRecord>();
foreach (var v in updatedPeptideTransitions[k])
{
if (v.IsotopeLabelType.Equals(_internalStandardType.ToString()))
{
standards.Add(v);
}
else
{
nonStandards.Add(v);
}
}
// make non-standards sort same as standards by giving them the same area
// area will not be seen by user but is only used to sort in this case
foreach (var v in nonStandards)
{
if (!v.IsotopeLabelType.Equals(_internalStandardType.ToString()))
{
foreach (var transitionRecord in standards)
{
if (transitionRecord.PeptideModifiedSequence.Equals(v.PeptideModifiedSequence) &&
transitionRecord.ProductCharge == v.ProductCharge &&
transitionRecord.PrecursorCharge == v.PrecursorCharge &&
transitionRecord.FragmentIon.Equals(v.FragmentIon))
{
v.Area = transitionRecord.Area;
}
}
}
}
var all = standards.Concat(nonStandards).ToList();
// Sort final list of transitions by peptide, then label type, then peak area
all.Sort((x, y) =>
{
if (x.IsotopeLabelType == y.IsotopeLabelType)
{
return(y.Area.CompareTo(x.Area));
}
if (_internalStandardType.ToString().Equals(x.IsotopeLabelType))
{
return(-1);
}
if (_internalStandardType.ToString().Equals(y.IsotopeLabelType))
{
return(1);
}
return(y.Area.CompareTo(x.Area));
});
updatedPeptideTransitions[k] = all;
}
// EXPORT
using (var saveFileDialog = new SaveFileDialog
{
FileName = "TFExport.csv", // Not L10N
Filter = "csv files (*.csv)|*.csv" // Not L10N
})
{
if (saveFileDialog.ShowDialog() != DialogResult.OK)
{
return;
}
var saveFileLocation = saveFileDialog.FileName;
var res = WriteToCsv(saveFileLocation, updatedPeptideTransitions);
if (string.IsNullOrEmpty(res))
{
Console.WriteLine("File saved to {0}.", saveFileLocation);
}
else // if not success
{
Console.WriteLine("Error: {0}", res);
}
}
}
}