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Merged
ypriverol merged 30 commits into from
May 9, 2024
Merged

Bugfix/cleanup commandline options #178

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8cceaf9
ZSPACE-12104 Remove reduncant properties.
zhaoheting-zontal Feb 24, 2023
04b1c61
ZSPACE-12104 Remove reduncant properties.
zhaoheting-zontal Feb 24, 2023
ac97343
ZSPACE-12104 Remove reduncant properties.
zhaoheting-zontal Feb 24, 2023
40404df
ZSPACE-12104 Remove reduncant properties.
zhaoheting-zontal Feb 24, 2023
9c1e636
ZSPACE-12104 Solve code review issues.
zhaoheting-zontal Feb 27, 2023
dc22d87
ZSPACE-12104 Solve code review issues.
zhaoheting-zontal Feb 27, 2023
467506b
ZSPACE-12467 Check if the file is MS type
zhaoheting-zontal Mar 3, 2023
65f14e5
ZSPACE-12467 Solve code review issues.
zhaoheting-zontal Mar 9, 2023
bceb3dd
ZSPACE-12467 Fix code review issues.
zhaoheting-zontal Mar 10, 2023
cfa25a2
ZSPACE-12467 Remove ms data for not MS type.
zhaoheting-zontal Mar 14, 2023
a29ac4c
ZSPACE-12467 Solve code review issues.
zhaoheting-zontal Mar 14, 2023
adc3417
ZSPACE-12467 Replace whitespace with underscore.
zhaoheting-zontal Mar 14, 2023
1a4c9a1
cleanup code
wolfgangcolsman Mar 14, 2023
ebacd5a
Merge pull request #3 from zontal/feature/support_non_ms_instruments
wolfgangcolsman Mar 14, 2023
93a5974
handle empty channel name
wolfgangcolsman Mar 20, 2023
878596b
add unitAccession for Volts
wolfgangcolsman Mar 20, 2023
793055f
Merge pull request #4 from zontal/feature/support_non_ms_instruments
wolfgangcolsman Mar 20, 2023
65347bc
Merge pull request #5 from zontal/try_to_close_stream
wolfgangcolsman Apr 4, 2023
6153039
unique channel name
wolfgangcolsman Apr 10, 2023
d240356
Merge pull request #7 from zontal/feature/support_non_ms_instruments
wolfgangcolsman Apr 10, 2023
abc6be5
fix
wolfgangcolsman Apr 10, 2023
c3729b9
Merge pull request #8 from zontal/feature/support_non_ms_instruments
wolfgangcolsman Apr 10, 2023
8530c38
add expected runtime
wolfgangcolsman Jul 10, 2023
46f387d
Merge branch 'zontal' into feature/runtime
wolfgangcolsman Jul 10, 2023
3359fba
Merge pull request #12 from zontal/feature/runtime
wolfgangcolsman Jul 10, 2023
8da0889
Merge branch '1.4.3' into zontal
zhaoheting-zontal Aug 9, 2023
e94cf14
Treat as if it is never set when last spectrum is set as 0.
zhaoheting-zontal Aug 10, 2023
2e4e8c7
Treat as if it is never set when last spectrum is set as 0.
zhaoheting-zontal Aug 10, 2023
be47d3c
Merge pull request #14 from zontal/bugfix/treat-last-spectrum-0
wolfgangcolsman Aug 12, 2023
75934f8
Bugfix command line options
Andre99999999 Mar 17, 2024
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12 changes: 6 additions & 6 deletions MainClass.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -63,15 +63,15 @@ private static void XicParametersParsing(string[] args)
"h|help", "Prints out the options.",
h => parameters.help = h != null
},
{
"i=|input=", "The raw file input (Required). Specify this or an input directory -d",
v => singleFile = v
},
{
"d=|input_directory=",
"The directory containing the raw files (Required). Specify this or an input file -i.",
v => fileDirectory = v
},
{
"i=|input=", "The raw file input (Required). Specify this or an input directory -d",
v => singleFile = v
},
{
"j=|json=",
"The json input file (Required).",
Expand All @@ -83,12 +83,12 @@ private static void XicParametersParsing(string[] args)
v => parameters.printJsonExample = v != null
},
{
"o=|output=",
"o=|output_directory=",
"The output directory. Specify this or an output file. Specifying neither writes to the input directory.",
v => outputDirectory = v
},
{
"b=|output_file",
"b=|output=",
"The output file. Specify this or an output directory. Specifying neither writes to the input directory.",
v => outputFile = v
},
Expand Down
6 changes: 0 additions & 6 deletions RawFileParser.cs
100755 → 100644
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@caetera caetera Mar 22, 2024

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This change cannot be accepted, see #144

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@caetera caetera Mar 27, 2024

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@wolfgangcolsman Could you, please, comment on what was the reason for implementing this change?

Original file line number Diff line number Diff line change
Expand Up @@ -146,12 +146,6 @@ private static void ProcessFile(ParseInput parseInput)
// Get the first and last scan from the RAW file
firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;

// Check for empty file
if (lastScanNumber < 1)
{
throw new RawFileParserException("Empty RAW file, no output will be produced");
}
}

if (parseInput.MetadataFormat != MetadataFormat.NONE)
Expand Down
124 changes: 62 additions & 62 deletions Writer/MetadataWriter.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ public void WriteMetadata(IRawDataPlus rawFile, int firstScanNumber, int lastSca
}
}
}

if (minCharge == 100000000000000)
{
minCharge = 0;
Expand Down Expand Up @@ -178,58 +178,57 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last


// MS Data
foreach (KeyValuePair<string, int> entry in msTypes)
{
if (entry.Key.Equals(MSOrderType.Ms.ToString()))
metadata.addMSData(new CVTerm("PRIDE:0000481", "PRIDE", "Number of MS1 spectra",
entry.Value.ToString()));
if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
metadata.addMSData(new CVTerm("PRIDE:0000482", "PRIDE", "Number of MS2 spectra",
entry.Value.ToString()));
if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
metadata.addMSData(new CVTerm("PRIDE:0000483", "PRIDE", "Number of MS3 spectra",
entry.Value.ToString()));
}

metadata.addMSData(new CVTerm("PRIDE:0000472", "PRIDE", "MS min charge",
minCharge.ToString(CultureInfo.InvariantCulture)));
metadata.addMSData(new CVTerm("PRIDE:0000473", "PRIDE", "MS max charge",
maxCharge.ToString(CultureInfo.InvariantCulture)));

metadata.addMSData(new CVTerm("PRIDE:0000474", "PRIDE", "MS min RT",
minTime.ToString(CultureInfo.InvariantCulture)));
metadata.addMSData(new CVTerm("PRIDE:0000475", "PRIDE", "MS max RT",
maxTime.ToString(CultureInfo.InvariantCulture)));

metadata.addMSData(new CVTerm("PRIDE:0000476", "PRIDE", "MS min MZ",
minMz.ToString(CultureInfo.InvariantCulture)));
metadata.addMSData(new CVTerm("PRIDE:0000477", "PRIDE", "MS max MZ",
maxMz.ToString(CultureInfo.InvariantCulture)));

// Scan Settings
// Get the start and end time from the RAW file

if (rawFile.SelectMsData())
{
var runHeader = rawFile.RunHeader;
var runHeaderEx = rawFile.RunHeaderEx;
var startTime = runHeaderEx.StartTime;
var endTime = runHeaderEx.EndTime;
foreach (KeyValuePair<string, int> entry in msTypes)
{
if (entry.Key.Equals(MSOrderType.Ms.ToString()))
metadata.addMSData(new CVTerm("PRIDE:0000481", "PRIDE", "Number of MS1 spectra",
entry.Value.ToString()));
if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
metadata.addMSData(new CVTerm("PRIDE:0000482", "PRIDE", "Number of MS2 spectra",
entry.Value.ToString()));
if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
metadata.addMSData(new CVTerm("PRIDE:0000483", "PRIDE", "Number of MS3 spectra",
entry.Value.ToString()));
}

metadata.addMSData(new CVTerm("PRIDE:0000472", "PRIDE", "MS min charge",
minCharge.ToString(CultureInfo.InvariantCulture)));
metadata.addMSData(new CVTerm("PRIDE:0000473", "PRIDE", "MS max charge",
maxCharge.ToString(CultureInfo.InvariantCulture)));

metadata.addMSData(new CVTerm("PRIDE:0000474", "PRIDE", "MS min RT",
minTime.ToString(CultureInfo.InvariantCulture)));
metadata.addMSData(new CVTerm("PRIDE:0000475", "PRIDE", "MS max RT",
maxTime.ToString(CultureInfo.InvariantCulture)));

metadata.addMSData(new CVTerm("PRIDE:0000476", "PRIDE", "MS min MZ",
minMz.ToString(CultureInfo.InvariantCulture)));
metadata.addMSData(new CVTerm("PRIDE:0000477", "PRIDE", "MS max MZ",
maxMz.ToString(CultureInfo.InvariantCulture)));

// Scan Settings
// Get the start and end time from the RAW file
var startTime = rawFile.RunHeaderEx.StartTime;
var endTime = rawFile.RunHeaderEx.EndTime;
metadata.addScanSetting(new CVTerm("MS:1000016", "MS", "scan start time",
startTime.ToString(CultureInfo.InvariantCulture)));
metadata.addScanSetting(new CVTerm("", "", "expected runtime",
rawFile.RunHeader.ExpectedRuntime.ToString(CultureInfo.InvariantCulture)));
metadata.addScanSetting(new CVTerm("MS:1000011", "MS", "mass resolution",
runHeaderEx.MassResolution.ToString(CultureInfo.InvariantCulture)));
rawFile.RunHeaderEx.MassResolution.ToString(CultureInfo.InvariantCulture)));
metadata.addScanSetting(new CVTerm("UO:0000002", "MS", "mass unit",
rawFile.GetInstrumentData().Units.ToString()));
metadata.addScanSetting(new CVTerm("PRIDE:0000478", "PRIDE", "Number of scans",
runHeaderEx.SpectraCount.ToString()));
rawFile.RunHeaderEx.SpectraCount.ToString()));
metadata.addScanSetting(new CVTerm("PRIDE:0000479", "PRIDE", "MS scan range",
firstScanNumber + ":" + lastScanNumber));
metadata.addScanSetting(new CVTerm("PRIDE:0000484", "PRIDE", "Retention time range",
startTime + ":" + endTime));
metadata.addScanSetting(new CVTerm("PRIDE:0000485", "PRIDE", "Mz range",
runHeaderEx.LowMass + ":" + runHeaderEx.HighMass));
rawFile.RunHeaderEx.LowMass + ":" + rawFile.RunHeaderEx.HighMass));
metadata.addScanSetting(fragmentationTypes);
metadata.addScanSetting(new CVTerm("PRIDE:0000479", "PRIDE", "MS scan range",
firstScanNumber + ":" + lastScanNumber));
}

// Sample Data
Expand Down Expand Up @@ -373,31 +372,31 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
}

// MS Data
output.Add("#MsData");
foreach (KeyValuePair<string, int> entry in msTypes)
if (rawFile.SelectMsData())
{
if (entry.Key.Equals(MSOrderType.Ms.ToString()))
output.Add("Number of MS1 spectra=" + entry.Value);
if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
output.Add("Number of MS2 spectra=" + entry.Value);
if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
output.Add("Number of MS3 spectra=" + entry.Value);
}

output.AddRange(new List<string>
output.Add("#MsData");
foreach (KeyValuePair<string, int> entry in msTypes)
{
"MS min charge=" + minCharge.ToString(CultureInfo.InvariantCulture),
"MS max charge=" + maxCharge.ToString(CultureInfo.InvariantCulture),
$"MS min RT={minTime.ToString(CultureInfo.InvariantCulture)}",
$"MS max RT={maxTime.ToString(CultureInfo.InvariantCulture)}",
$"MS min MZ={minMz.ToString(CultureInfo.InvariantCulture)}",
$"MS max MZ={maxMz.ToString(CultureInfo.InvariantCulture)}"
if (entry.Key.Equals(MSOrderType.Ms.ToString()))
output.Add("Number of MS1 spectra=" + entry.Value);
if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
output.Add("Number of MS2 spectra=" + entry.Value);
if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
output.Add("Number of MS3 spectra=" + entry.Value);
}
);

// Scan Settings
if (rawFile.SelectMsData())
{
output.AddRange(new List<string>
{
"MS min charge=" + minCharge.ToString(CultureInfo.InvariantCulture),
"MS max charge=" + maxCharge.ToString(CultureInfo.InvariantCulture),
$"MS min RT={minTime.ToString(CultureInfo.InvariantCulture)}",
$"MS max RT={maxTime.ToString(CultureInfo.InvariantCulture)}",
$"MS min MZ={minMz.ToString(CultureInfo.InvariantCulture)}",
$"MS max MZ={maxMz.ToString(CultureInfo.InvariantCulture)}"
}
);

// Scan Settings
// Get the start and end time from the RAW file
var startTime = rawFile.RunHeaderEx.StartTime;
var endTime = rawFile.RunHeaderEx.EndTime;
Expand All @@ -415,6 +414,7 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
}
);
}

// Sample Data
output.Add("#SampleData");

Expand Down
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