Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fixed error #124

Merged
merged 2 commits into from
Mar 16, 2022
Merged

fixed error #124

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
b459508
fixed error
daichengxin Mar 16, 2022
53e20e3
fixed thermorawfileparser
daichengxin Mar 16, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 0 additions & 1 deletion assets/PXD026600.sdrf.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
Source Name Characteristics[organism] Characteristics[organism part] Characteristics[age] Characteristics[strain] Characteristics[developmental stage] Characteristics[cell line] Characteristics[cell type] Characteristics[sex] Characteristics[disease] characteristics[mass] characteristics[spiked compound] Characteristics[biological replicate] Material Type assay name technology type comment[data file] comment[file uri] comment[technical replicate] comment[fraction identifier] comment[proteomics data acquisition method] comment[label] comment[instrument] comment[modification parameters] comment[modification parameters] comment[cleavage agent details] comment[dissociation method] comment[collision energy] comment[precursor mass tolerance] comment[fragment mass tolerance] factor value[spiked compound]
Sample 1 Escherichia coli K-12 whole plant not available K12 not available not applicable not available not available not available 1 ug CT=Mixture;CN=UPS1;QY=0.1 fmol 1 whole organism run 1 proteomic profiling by mass spectrometry RD139_Narrow_UPS1_0_1fmol_inj1.raw ftp://massive.ucsd.edu/MSV000087597/raw/RD139_Raw_files_DIA_Narrow/RD139_Narrow_UPS1_0_1fmol_inj1.raw 1 1 NT=Data-Independent Acquisition;AC=NCIT:C161786 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion;AC=MS:1002416 NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 AC=MS:1001313;NT=Trypsin NT=HCD;AC=PRIDE:0000590 35% CE 10 ppm 20 mmu CT=Mixture;CN=UPS1;QY=0.1 fmol
Sample 1 Escherichia coli K-12 whole plant not available K12 not available not applicable not available not available not available 1 ug CT=Mixture;CN=UPS1;QY=0.1 fmol 1 whole organism run 2 proteomic profiling by mass spectrometry RD139_Narrow_UPS1_0_1fmol_inj2.raw ftp://massive.ucsd.edu/MSV000087597/raw/RD139_Raw_files_DIA_Narrow/RD139_Narrow_UPS1_0_1fmol_inj2.raw 2 1 NT=Data-Independent Acquisition;AC=NCIT:C161786 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion;AC=MS:1002416 NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 AC=MS:1001313;NT=Trypsin NT=HCD;AC=PRIDE:0000590 35% CE 10 ppm 20 mmu CT=Mixture;CN=UPS1;QY=0.1 fmol
Sample 1 Escherichia coli K-12 whole plant not available K12 not available not applicable not available not available not available 1 ug CT=Mixture;CN=UPS1;QY=0.1 fmol 1 whole organism run 3 proteomic profiling by mass spectrometry RD139_Narrow_UPS1_0_1fmol_inj3.raw ftp://massive.ucsd.edu/MSV000087597/raw/RD139_Raw_files_DIA_Narrow/RD139_Narrow_UPS1_0_1fmol_inj3.raw 3 1 NT=Data-Independent Acquisition;AC=NCIT:C161786 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion;AC=MS:1002416 NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35 NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4 AC=MS:1001313;NT=Trypsin NT=HCD;AC=PRIDE:0000590 35% CE 10 ppm 20 mmu CT=Mixture;CN=UPS1;QY=0.1 fmol
52 changes: 27 additions & 25 deletions bin/prepare_diann_parameters.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,31 +44,33 @@ def convert_mod(unimod_csv, fix_mod, var_mod):
var_ptm = []
fix_ptm = []
unimod = pd.read_csv(unimod_csv, header=0, sep=",")
for mod in fix_mod.split(","):
diann_mod = unimod[unimod['name'] == mod.split(" ")[0]]["params"].values[0]
site = re.findall(pattern, " ".join(mod.split(" ")[1:]))[0]
if site == "Protein N-term":
site = "*n"
elif site == "N-term":
site = "n"

if "TMT" in diann_mod or "Label" in diann_mod or "iTRAQ" in diann_mod or "mTRAQ" in diann_mod:
fix_ptm.append(diann_mod + "," + site + "," + "label")
else:
fix_ptm.append(diann_mod + "," + site)

for mod in var_mod.split(","):
diann_mod = unimod[unimod['name'] == mod.split(" ")[0]]["params"].values[0]
site = re.findall(pattern, " ".join(mod.split(" ")[1:]))[0]
if site == "Protein N-term":
site = "*n"
elif site == "N-term":
site = "n"

if "TMT" in diann_mod or "Label" in diann_mod or "iTRAQ" in diann_mod or "mTRAQ" in diann_mod:
var_ptm.append(diann_mod + "," + site + "," + "label")
else:
var_ptm.append(diann_mod + "," + site)
if fix_mod != "":
for mod in fix_mod.split(","):
diann_mod = unimod[unimod['name'] == mod.split(" ")[0]]["params"].values[0]
site = re.findall(pattern, " ".join(mod.split(" ")[1:]))[0]
if site == "Protein N-term":
site = "*n"
elif site == "N-term":
site = "n"

if "TMT" in diann_mod or "Label" in diann_mod or "iTRAQ" in diann_mod or "mTRAQ" in diann_mod:
fix_ptm.append(diann_mod + "," + site + "," + "label")
else:
fix_ptm.append(diann_mod + "," + site)

if var_mod != "":
for mod in var_mod.split(","):
diann_mod = unimod[unimod['name'] == mod.split(" ")[0]]["params"].values[0]
site = re.findall(pattern, " ".join(mod.split(" ")[1:]))[0]
if site == "Protein N-term":
site = "*n"
elif site == "N-term":
site = "n"

if "TMT" in diann_mod or "Label" in diann_mod or "iTRAQ" in diann_mod or "mTRAQ" in diann_mod:
var_ptm.append(diann_mod + "," + site + "," + "label")
else:
var_ptm.append(diann_mod + "," + site)

return fix_ptm, var_ptm

Expand Down
2 changes: 2 additions & 0 deletions modules/local/thermorawfileparser/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,8 @@ process THERMORAWFILEPARSER {
'https://depot.galaxyproject.org/singularity/thermorawfileparser:1.3.4--ha8f3691_0' :
'quay.io/biocontainers/thermorawfileparser:1.3.4--ha8f3691_0' }"

stageInMode {task.attempt == 1 ? 'link' : (task.attempt == 2 ? 'symlink' : 'copy')}

input:
tuple val(meta), path(rawfile)

Expand Down