From 51946a4bf16533353c3f3eb5f0804e4c1a3f6fa2 Mon Sep 17 00:00:00 2001 From: Marie Locard-Paulet <8386272+mlocardpaulet@users.noreply.github.com> Date: Mon, 18 Sep 2023 17:10:12 +0200 Subject: [PATCH] fix direct Proline import - issue #42 --- .../parse_settings_proline.toml | 26 +++++++++---------- proteobench/modules/dda_quant/module.py | 2 +- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/proteobench/modules/dda_quant/io_parse_settings/parse_settings_proline.toml b/proteobench/modules/dda_quant/io_parse_settings/parse_settings_proline.toml index c7be525e..86e4cdb7 100644 --- a/proteobench/modules/dda_quant/io_parse_settings/parse_settings_proline.toml +++ b/proteobench/modules/dda_quant/io_parse_settings/parse_settings_proline.toml @@ -2,24 +2,24 @@ "samesets_accessions" = "Proteins" sequence = "Sequence" "modifications" = "Modifications" -charge = "Charge" +"master_quant_peptide_ion_charge" = "Charge" [replicate_mapper] -abundance_LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01 = 1 -abundance_LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02 = 1 -abundance_LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03 = 1 -abundance_LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01 = 2 -abundance_LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02 = 2 -abundance_LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03 = 2 +abundance_DDA_Condition_A_Sample_Alpha_01 = 1 +abundance_DDA_Condition_A_Sample_Alpha_02 = 1 +abundance_DDA_Condition_A_Sample_Alpha_03 = 1 +abundance_DDA_Condition_B_Sample_Alpha_01 = 2 +abundance_DDA_Condition_B_Sample_Alpha_02 = 2 +abundance_DDA_Condition_B_Sample_Alpha_03 = 2 [run_mapper] -"abundance_LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01" = "LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01" -"abundance_LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02" = "LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02" -"abundance_LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03" = "LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03" -"abundance_LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01" = "LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01" -"abundance_LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02" = "LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02" -"abundance_LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03" = "LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03" +"abundance_DDA_Condition_A_Sample_Alpha_01" = "LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01" +"abundance_DDA_Condition_A_Sample_Alpha_02" = "LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02" +"abundance_DDA_Condition_A_Sample_Alpha_03" = "LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03" +"abundance_DDA_Condition_B_Sample_Alpha_01" = "LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01" +"abundance_DDA_Condition_B_Sample_Alpha_02" = "LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02" +"abundance_DDA_Condition_B_Sample_Alpha_03" = "LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03" [species_dict] "YEAST" = "_YEAST" diff --git a/proteobench/modules/dda_quant/module.py b/proteobench/modules/dda_quant/module.py index 937d6efb..2cdd3388 100644 --- a/proteobench/modules/dda_quant/module.py +++ b/proteobench/modules/dda_quant/module.py @@ -157,7 +157,7 @@ def load_input_file(self, input_csv: str, input_format: str) -> pd.DataFrame: self.strip_sequence_wombat ) elif input_format == "Proline": - input_data_frame = pd.read_excel(input_csv, sheet_name="Best PSM from protein sets") + input_data_frame = pd.read_csv(input_csv, low_memory=False, sep="\t") elif input_format == "Custom": input_data_frame = pd.read_csv(input_csv, low_memory=False, sep="\t")