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Feature/mq #29

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919f2d8
modified column names
Apr 21, 2020
660db22
Merge branch 'feature/mq' of https://github.com/Roestlab/dia-pasef in…
Apr 21, 2020
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9 changes: 6 additions & 3 deletions src/diapysef/diapysef/conversions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -183,13 +183,16 @@ def pasef_to_tsv(evidence, msms,
if irt.shape[1] > 2:
irt_colnames = irt.columns.values.tolist()
# allowing different formats for reading iRTs
irt_mod = ['ModifiedPeptideSequence','Modified sequence', 'FullUniModPeptideName', 'FullPeptideName']
irt_mod = ['ModifiedPeptideSequence','Modified sequence', 'FullUniModPeptideName', 'FullPeptideName', 'ModifiedSequence']
irt_mod = [name for name in irt_colnames if name in irt_mod]
irt_mod = irt_mod[0]
irt_rt = ['NormalizedRetentionTime', 'iRT', 'RetentionTime', 'Tr_recalibrated']
irt_rt = ['NormalizedRetentionTime', 'iRT', 'RetentionTime', 'Tr_recalibrated', 'RetentionTimeCalculatorScore']
irt_rt = [name for name in irt_colnames if name in irt_rt]
irt_rt = irt_rt[0]
irt = irt.loc[:, [irt_mod, irt_rt, "PrecursorIonMobility","PrecursorCharge"]]
irt_im = ['PrecursorIonMobility', 'Ion Mobility MS1']
irt_im = [name for name in irt_colnames if name in irt_im]
irt_im = irt_im[0]
irt = irt.loc[:, [irt_mod, irt_rt, irt_im,"PrecursorCharge"]]
irt = irt.drop_duplicates()
irt.columns = ["sequence","irt", "iim", "charge"]
irt = reformat_mods(irt, 'sequence')
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