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statisticalbiotechnology / quandenser

QUANtification by Distillation for ENhanced Signals with Error Regulation
Apache License 2.0
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Issue running Example #25

Open Alexander-Sol opened 1 month ago

Alexander-Sol commented 1 month ago

I'm trying to run the example you've uploaded, but I encountered some difficulties running Triqler. Specifically, line 1 of the Triqler.sh script is throwing an error

I'm running Windows 11 with Crux v4.2.

I've included the error message below.

Traceback (most recent call last): File "C:\Users\Alex\AppData\Local\Programs\Python\Python310\lib\runpy.py", line 196, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\Alex\AppData\Local\Programs\Python\Python310\lib\runpy.py", line 86, in _run_code exec(code, run_globals) File "C:\Users\Alex\AppData\Local\Programs\Python\Python310\lib\site-packages\triqler\convert\quandenser.py", line 232, in <module> main() File "C:\Users\Alex\AppData\Local\Programs\Python\Python310\lib\site-packages\triqler\convert\quandenser.py", line 38, in main convertQuandenserToTriqler( File "C:\Users\Alex\AppData\Local\Programs\Python\Python310\lib\site-packages\triqler\convert\quandenser.py", line 142, in convertQuandenserToTriqler specToPeptideMap = helpers.parsePsmsPoutFiles(psmsOutputFiles) File "C:\Users\Alex\AppData\Local\Programs\Python\Python310\lib\site-packages\triqler\convert\helpers.py", line 40, in parsePsmsPoutFiles for psm in percolator.parsePsmsPout(psmsOutputFile): File "C:\Users\Alex\AppData\Local\Programs\Python\Python310\lib\site-packages\triqler\convert\percolator.py", line 95, in parsePsmsPout float(row[1]), ValueError: could not convert string to float: './Quandenser_output/consensus_spectra/MaRaCluster.consensus.part1.ms2'

MatthewThe commented 1 month ago

I suspect that the problem is that Crux changed its output format, could you post the first 5 lines of crux_output/percolator.target.psms.txt

Alexander-Sol commented 1 month ago

PSMId filename score q-value posterior_error_prob peptide proteinIds target_0_1681601_4_1 ./Quandenser_output/consensus_spectra/MaRaCluster.consensus.part1.ms2 3.36331 0.000339213 6.11202e-11 K.RGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIK.G HPRR4280170_poolB target_0_1609101_3_1 ./Quandenser_output/consensus_spectra/MaRaCluster.consensus.part1.ms2 3.17684 0.000339213 2.04056e-10 K.KADCPIAWANLMLFDYKDQLK.T HPRR4040265_poolB target_0_1764801_3_1 ./Quandenser_output/consensus_spectra/MaRaCluster.consensus.part1.ms2 3.02753 0.000339213 5.35748e-10 R.FPGNLLLNPFGISITSQSLNPGPFRTPK.A HPRR4030528_poolB target_0_1726301_3_1 ./Quandenser_output/consensus_spectra/MaRaCluster.consensus.part1.ms2 2.99247 0.000339213 6.72044e-10 R.ATTNIIQPLLHAQWVLGDWSECSSTCGAGWQR.R HPRR2700128_poolA

MatthewThe commented 1 month ago

Yes, Crux indeed switched their output format in 4.2. I created a fix in the Triqler repo, you can reinstall it from GitHub:

git clone https://github.com/statisticalbiotechnology/triqler.git
cd triqler
pip install .

I will release a patch version for Triqler if this works for you.

Alexander-Sol commented 1 month ago

Yes, that fixed the issue! Thanks a bunch