def main():
drivers = [psmtopeptable.MzidTSVPeptableDriver(),
isoquant.AddIsobaricQuantDriver(),
model_qvals.ModelQValuesDriver(),
merge.BuildPeptideTableDriver(),
]
startup.start_msstitch(drivers, sys.argv)
def main():
drivers = [
psmtopeptable.MzidTSVPeptableDriver(),
isoquant.AddIsobaricQuantDriver(),
model_qvals.ModelQValuesDriver(),
merge.BuildPeptideTableDriver(),
]
startup.start_msstitch(drivers, sys.argv)
def main():
drivers = [splitmerge.SplitTDDriver(),
splitmerge.SplitProteinDriver(),
splitmerge.MergeDriver(),
filters.FilterUniquePeptides(),
filters.FilterPeptideLength(),
filters.FilterWholeProteinSequence(),
filters.FilterPeptideSequence(),
qvality.QvalityDriver(),
stats.ReassignmentDriver(),
]
startup.start_msstitch(drivers, sys.argv)
def main():
drivers = [spectra.TSVSpectraDriver(),
percolator.MzidPercoTSVDriver(),
splitmerge.MzidTSVConcatenateDriver(),
splitmerge.MzidTSVSplitDriver(),
filter_confidence.ConfidenceFilterDriver(),
quant.TSVQuantDriver(),
proteingrouping.ProteinGroupDriver(),
prot2gene.TSVGeneFromProteinDriver(),
isonormalize.PSMIsoquantRatioDriver(),
isonormalize.PSMIsoquantNormalizeDriver(),
]
startup.start_msstitch(drivers, sys.argv)
def main():
drivers = [biosets.BioSetLookupDriver(),
spectra.SpectraLookupDriver(),
psms.PSMLookupDriver(),
quant.IsobaricQuantLookupDriver(),
quant.PrecursorQuantLookupDriver(),
proteingroups.ProteinGroupLookupDriver(),
pepquant.PeptideQuantLookupDriver(),
proteinquant.ProteinQuantLookupDriver(),
seqspace.SeqspaceLookupDriver(),
seqspace.WholeProteinSeqspaceLookupDriver(),
]
startup.start_msstitch(drivers, sys.argv)
def main():
drivers = [
splitmerge.SplitTDDriver(),
splitmerge.SplitProteinDriver(),
splitmerge.MergeDriver(),
filters.FilterUniquePeptides(),
filters.FilterPeptideLength(),
filters.FilterWholeProteinSequence(),
filters.FilterPeptideSequence(),
qvality.QvalityDriver(),
stats.ReassignmentDriver(),
]
startup.start_msstitch(drivers, sys.argv)
def main():
drivers = [info.AddProteinInfoDriver(),
merge.BuildProteinTableDriver(),
isoquant.AddIsobaricQuantDriver(),
precursorarea.AddPrecursorAreaDriver(),
probability.AddProteinProbability(),
create_empty.CreateEmptyDriver(),
bestpeptide.BestPeptidePerProtein(),
fdr.ProttableFDRDriver(),
fdr.PickedFDRDriver(),
fdr.ProttableAddFDRDriver(),
]
startup.start_msstitch(drivers, sys.argv)
def main():
drivers = [
info.AddProteinInfoDriver(),
merge.BuildProteinTableDriver(),
isoquant.AddIsobaricQuantDriver(),
precursorarea.AddPrecursorAreaDriver(),
probability.AddProteinProbability(),
create_empty.CreateEmptyDriver(),
bestpeptide.BestPeptidePerProtein(),
fdr.ProttableFDRDriver(),
fdr.PickedFDRDriver(),
fdr.ProttableAddFDRDriver(),
]
startup.start_msstitch(drivers, sys.argv)
def main():
drivers = [
spectra.TSVSpectraDriver(),
percolator.MzidPercoTSVDriver(),
splitmerge.MzidTSVConcatenateDriver(),
splitmerge.MzidTSVSplitDriver(),
filter_confidence.ConfidenceFilterDriver(),
quant.TSVQuantDriver(),
proteingrouping.ProteinGroupDriver(),
prot2gene.TSVGeneFromProteinDriver(),
isonormalize.PSMIsoquantRatioDriver(),
isonormalize.PSMIsoquantNormalizeDriver(),
]
startup.start_msstitch(drivers, sys.argv)
def main():
drivers = [
lookups.SpectraLookupDriver(),
lookups.QuantLookupDriver(),
lookups.SequenceLookupDriver(),
sequence.DecoySeqDriver(),
sequence.TrypsinizeDriver(),
psmtable.TSVConcatenateDriver(),
psmtable.TSVSplitDriver(),
psmtable.Perco2PSMDriver(),
psmtable.ConfidenceFilterDriver(),
psmtable.PSMTableRefineDriver(),
psmtable.IsoSummarizeDriver(),
psmtable.DeleteSetDriver(),
percolator.FilterSequences(),
percolator.SplitProteinDriver(),
peptable.CreatePeptableDriver(),
prottable.ProteinsDriver(),
prottable.GenesDriver(),
prottable.ENSGDriver(),
merge.MergeDriver(),
]
startup.start_msstitch(drivers, sys.argv)