From 919f2d81d7dfa53f2b9e1e843f02d5673e31b0e4 Mon Sep 17 00:00:00 2001 From: Annie Ha Date: Tue, 21 Apr 2020 17:32:36 -0400 Subject: [PATCH] modified column names --- src/diapysef/diapysef/conversions.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/diapysef/diapysef/conversions.py b/src/diapysef/diapysef/conversions.py index 9ca1c83..d708c2d 100755 --- a/src/diapysef/diapysef/conversions.py +++ b/src/diapysef/diapysef/conversions.py @@ -172,13 +172,16 @@ 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')