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compomics / DeepLC

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
https://iomics.ugent.be/deeplc
Apache License 2.0
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error using GUI to predict rt #53

Closed sehooni closed 1 year ago

sehooni commented 1 year ago

Hi

I want to use deeplc to predict retention times for some peptides so I just use deeplc from GUI. However, there are some problem like below.

2023-05-28 22:43:39 - INFO - Using DeepLC version 2.0.4 Traceback (most recent call last): File "deeplc\gui.py", line 38, in start_gui() File "gooey\python_bindings\gooey_decorator.py", line 134, in return lambda *args, kwargs: func(args, kwargs) File "deeplc\gui.py", line 35, in start_gui main(gui=True) File "deeplc__main__.py", line 70, in main run(vars(argu)) File "deeplc__main__.py", line 130, in run list_of_psms.append(PSM(peptidoform=peprec_to_proforma(seq,mod),spectrum_id=ident)) File "psm_utils\io\peptide_record.py", line 398, in peprec_to_proforma peptide[int(position)] += f"[{label}]" IndexError: list index out of range 2023-05-28 22:44:05 - INFO - Using DeepLC version 2.0.4 Traceback (most recent call last): File "deeplc\gui.py", line 38, in start_gui() File "gooey\python_bindings\gooey_decorator.py", line 134, in return lambda args, kwargs: func(args, kwargs) File "deeplc\gui.py", line 35, in start_gui main(gui=True) File "deeplc__main__.py", line 70, in main run(vars(argu)) File "deeplc__main__.py", line 134, in run psm_list_pred = read_file(file_pred) File "psm_utils\io__init.py", line 125, in read_file filetype = _infer_filetype(filename) File "psm_utils\io\init__.py", line 86, in _infer_filetype raise PSMUtilsIOException("Could not infer filetype.") psm_utils.io.exceptions.PSMUtilsIOException: Could not infer filetype. 2023-05-28 22:48:35 - INFO - Using DeepLC version 2.0.4 Traceback (most recent call last): File "deeplc\gui.py", line 38, in start_gui() File "gooey\python_bindings\gooey_decorator.py", line 134, in return lambda args, kwargs: func(args, kwargs) File "deeplc\gui.py", line 35, in start_gui main(gui=True) File "deeplc__main__.py", line 70, in main run(vars(argu)) File "deeplc__main__.py", line 134, in run psm_list_pred = read_file(file_pred) File "psm_utils\io__init.py", line 125, in read_file filetype = _infer_filetype(filename) File "psm_utils\io\init__.py", line 86, in _infer_filetype raise PSMUtilsIOException("Could not infer filetype.") psm_utils.io.exceptions.PSMUtilsIOException: Could not infer filetype. 2023-05-28 22:49:11 - INFO - Using DeepLC version 2.0.4 Traceback (most recent call last): File "deeplc\gui.py", line 38, in start_gui() File "gooey\python_bindings\gooey_decorator.py", line 134, in return lambda args, kwargs: func(args, kwargs) File "deeplc\gui.py", line 35, in start_gui main(gui=True) File "deeplc__main__.py", line 70, in main run(vars(argu)) File "deeplc__main__.py", line 134, in run psm_list_pred = read_file(file_pred) File "psm_utils\io__init.py", line 125, in read_file filetype = _infer_filetype(filename) File "psm_utils\io\init__.py", line 86, in _infer_filetype raise PSMUtilsIOException("Could not infer filetype.") psm_utils.io.exceptions.PSMUtilsIOException: Could not infer filetype. 2023-05-28 23:19:30 - INFO - Using DeepLC version 2.0.4 Traceback (most recent call last): File "deeplc\gui.py", line 38, in start_gui() File "gooey\python_bindings\gooey_decorator.py", line 134, in return lambda args, *kwargs: func(args, kwargs) File "deeplc\gui.py", line 35, in start_gui main(gui=True) File "deeplc__main__.py", line 70, in main run(vars(argu)) File "deeplc__main__.py", line 134, in run psm_list_pred = read_file(file_pred) File "psm_utils\io__init.py", line 125, in read_file filetype = _infer_filetype(filename) File "psm_utils\io\init__.py", line 86, in _infer_filetype raise PSMUtilsIOException("Could not infer filetype.") psm_utils.io.exceptions.PSMUtilsIOException: Could not infer filetype.

And my CSV file are like below. sequence_information.csv seq,modifications KPVGAAK, KPAVQK, KPLQGK, VPKQAK, QVAPKK, GQLPKK, AAGVPKK, PVVLDK, VPVIDK, QPKIGK, KPAAAAGAK, KPQVNAK, KPSPEVK, KPMLPAK, EPVIAQK, APLMPKK, PLDLGAAK, PKPPAFK, LPLDQAK, PKQGINK, SIHHAR, SLHAHR, ISEPFK, LSIMEK, LSMIEK, SLEIMK, SLEPFK, SLLEMK, SLMLEK, ISFPEK, KPMLPAK,3|Oxidation LVWPSAK, QSVELPK, GVIEPSAK, PSLTGLGR, LGDLGLGR, AEVVGAVR, WVLVQR, APPPPPPK, DTLINPK, GQQIGK, QAGGIGK, QGQIGK, QNALGK, GIVWR, GLVGER, GVIDAR, LGVEGR, LVGWR, VGLWR, QMIQQYEMYCK,10|Carbamidomethyl TEEMPNDSVLENK,4|Oxidation KPATAAGTK, AIHLNK, ....

How can I use deeplc to predict retention time?

RobbinBouwmeester commented 1 year ago

Dear sehooni,

I think I have identified the problem. To be sure, could you also share the input file?

Will make a release fixing this issue ASAP.

Kind regards,

Robbin

sehooni commented 1 year ago

Thank you for reply,

File size is too big to upload. so I'll send you by email!

RobbinBouwmeester commented 1 year ago

The latest release v2.1.9 should fix your issue, please feel free to re-open this issue if it did not.