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Merge pull request #101 from daichengxin/master
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add acquisition column
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@ypriverol
ypriverol authored Mar 10, 2022
2 parents be0f2e1 + 36b8219 commit 837af51
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Showing 3 changed files with 42 additions and 31 deletions.
15 changes: 13 additions & 2 deletions sdrf_pipelines/openms/openms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -706,7 +706,8 @@ def writeOneTableExperimentalDesign(self, output_filename, legacy, sdrf, file2te

def save_search_settings_to_file(self, output_filename, sdrf, f2c):
f = open(output_filename, "w+")
open_ms_search_settings_header = ["URI", "Filename", "FixedModifications", "VariableModifications", "Label",
open_ms_search_settings_header = ["URI", "Filename", "FixedModifications", "VariableModifications",
"Proteomics Data Acquisition Method", "Label",
"PrecursorMassTolerance", "PrecursorMassToleranceUnit",
"FragmentMassTolerance",
"FragmentMassToleranceUnit", "DissociationMethod", "Enzyme"]
Expand All @@ -722,6 +723,15 @@ def save_search_settings_to_file(self, output_filename, sdrf, f2c):
for _0, row in sdrf.iterrows():
URI = row["comment[file uri]"]
raw = row["comment[data file]"]
if "comment[proteomics data acquisition method]" not in row:
warning_message = "The comment[proteomics data acquisition method] column is missing, " \
"default Data-Dependent Acquisition"
self.warnings[warning_message] = self.warnings.get(warning_message, 0) + 1
acquisition_method = "Data-Dependent Acquisition"
else:
acquisition_method = row["comment[proteomics data acquisition method]"]
acquisition_method = acquisition_method.split(";")[0].split("=")[1]

if raw in raws:
continue
raws.append(raw)
Expand Down Expand Up @@ -768,7 +778,8 @@ def save_search_settings_to_file(self, output_filename, sdrf, f2c):
"sample', 'ITRAQ', and tmt labels in the format 'TMT131C'")

f.write(
URI + "\t" + raw + "\t" + f2c.file2mods[raw][0] + "\t" + f2c.file2mods[raw][1] + "\t" + label + "\t" +
URI + "\t" + raw + "\t" + f2c.file2mods[raw][0] + "\t" + f2c.file2mods[raw][1] + "\t" +
acquisition_method + "\t" + label + "\t" +
f2c.file2pctol[
raw] + "\t" + f2c.file2pctolunit[raw] + "\t" + f2c.file2fragtol[raw] + "\t" + f2c.file2fragtolunit[
raw] + "\t" +
Expand Down
56 changes: 28 additions & 28 deletions sdrf_pipelines/testdata/PXD001819/expected_openms.tsv
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Original file line number Diff line number Diff line change
@@ -1,28 +1,28 @@
URI Filename FixedModifications VariableModifications Label PrecursorMassTolerance PrecursorMassToleranceUnit FragmentMassTolerance FragmentMassToleranceUnit DissociationMethod Enzyme
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R1.raw UPS1_12500amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R2.raw UPS1_12500amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R3.raw UPS1_12500amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R1.raw UPS1_125amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R2.raw UPS1_125amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R3.raw UPS1_125amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R1.raw UPS1_25000amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R2.raw UPS1_25000amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R3.raw UPS1_25000amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R1.raw UPS1_2500amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R2.raw UPS1_2500amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R3.raw UPS1_2500amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R1.raw UPS1_250amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R2.raw UPS1_250amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R3.raw UPS1_250amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R1.raw UPS1_50000amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R2.raw UPS1_50000amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R3.raw UPS1_50000amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R1.raw UPS1_5000amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R2.raw UPS1_5000amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R3.raw UPS1_5000amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R1.raw UPS1_500amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R2.raw UPS1_500amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R3.raw UPS1_500amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R1.raw UPS1_50amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R2.raw UPS1_50amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R3.raw UPS1_50amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) label free sample 5 ppm 0.8 Da HCD Trypsin/P
URI Filename FixedModifications VariableModifications Proteomics Data Acquisition Method Label PrecursorMassTolerance PrecursorMassToleranceUnit FragmentMassTolerance FragmentMassToleranceUnit DissociationMethod Enzyme
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R1.raw UPS1_12500amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R2.raw UPS1_12500amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_12500amol_R3.raw UPS1_12500amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R1.raw UPS1_125amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R2.raw UPS1_125amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_125amol_R3.raw UPS1_125amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R1.raw UPS1_25000amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R2.raw UPS1_25000amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_25000amol_R3.raw UPS1_25000amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R1.raw UPS1_2500amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R2.raw UPS1_2500amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_2500amol_R3.raw UPS1_2500amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R1.raw UPS1_250amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R2.raw UPS1_250amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_250amol_R3.raw UPS1_250amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R1.raw UPS1_50000amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R2.raw UPS1_50000amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50000amol_R3.raw UPS1_50000amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R1.raw UPS1_5000amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R2.raw UPS1_5000amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_5000amol_R3.raw UPS1_5000amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R1.raw UPS1_500amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R2.raw UPS1_500amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_500amol_R3.raw UPS1_500amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R1.raw UPS1_50amol_R1.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R2.raw UPS1_50amol_R2.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/12/PXD001819/UPS1_50amol_R3.raw UPS1_50amol_R3.raw Carbamidomethyl (C) Acetyl (Protein N-term),Oxidation (M) Data-Dependent Acquisition label free sample 5 ppm 0.8 Da HCD Trypsin/P
2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

setup(
name="sdrf-pipelines",
version="0.0.20",
version="0.0.21",
author="BigBio Team",
author_email="[email protected]",
description="Translate, convert SDRF to configuration pipelines",
Expand Down

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