-
Notifications
You must be signed in to change notification settings - Fork 6
Description
Hi,
Thank you for this bioinformatic tools it looks very interesting.
I would like to use it on peptides longer than 20 amino acids.
Is this currenlty supported?
I am obtaining this error when I try to use it on my data that makes me think the maximum length is 20aa:
Apologies if this was explained in the paper or documentation and I missed it.
Thank you for your support
ARNYLQSLPSKTKVAWAKLFSKSD,DRB1*01:02,"Error: 2025-06-24 14:55:47.291258: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: SSE4.1 SSE4.2 AVX AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
Traceback (most recent call last):
File ""/data/fsluma/pipelines/RStudio-docker/home/immunogeneicity_score_snakemake/tools/TLimmuno2/Python/TLimmuno2.py"", line 122, in
main(args)
File ""/data/fsluma/pipelines/RStudio-docker/home/immunogeneicity_score_snakemake/tools/TLimmuno2/Python/TLimmuno2.py"", line 99, in main
peptide = peptide_code(Data)
^^^^^^^^^^^^^^^^^^
File ""/data/fsluma/pipelines/RStudio-docker/home/immunogeneicity_score_snakemake/tools/TLimmuno2/Python/TLimmuno2.py"", line 40, in peptide_code
Data[""pep_blosum""] = Data[""pep""].apply(blosum62,args=(21,))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ""/data/fsluma/pipelines/RStudio-docker/home/immunogeneicity_score_snakemake/.snakemake/conda/572d1311ff8ad9c7652978bf1897c6bb_/lib/python3.11/site-packages/pandas/core/series.py"", line 4935, in apply
).apply()
^^^^^^^
File ""/data/fsluma/pipelines/RStudio-docker/home/immunogeneicity_score_snakemake/.snakemake/conda/572d1311ff8ad9c7652978bf1897c6bb_/lib/python3.11/site-packages/pandas/core/apply.py"", line 1422, in apply
return self.apply_standard()
^^^^^^^^^^^^^^^^^^^^^
File ""/data/fsluma/pipelines/RStudio-docker/home/immunogeneicity_score_snakemake/.snakemake/conda/572d1311ff8ad9c7652978bf1897c6bb_/lib/python3.11/site-packages/pandas/core/apply.py"", line 1502, in apply_standard
mapped = obj.map_values(
^^^^^^^^^^^^^^^^
File ""/data/fsluma/pipelines/RStudio-docker/home/immunogeneicity_score_snakemake/.snakemake/conda/572d1311ff8ad9c7652978bf1897c6bb/lib/python3.11/site-packages/pandas/core/base.py"", line 925, in map_values
return algorithms.map_array(arr, mapper, na_action=na_action, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ""/data/fsluma/pipelines/RStudio-docker/home/immunogeneicity_score_snakemake/.snakemake/conda/572d1311ff8ad9c7652978bf1897c6bb/lib/python3.11/site-packages/pandas/core/algorithms.py"", line 1743, in map_array
return lib.map_infer(values, mapper, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ""pandas/_libs/lib.pyx"", line 2999, in pandas.libs.lib.map_infer
File ""/data/fsluma/pipelines/RStudio-docker/home/immunogeneicity_score_snakemake/.snakemake/conda/572d1311ff8ad9c7652978bf1897c6bb/lib/python3.11/site-packages/pandas/core/apply.py"", line 1491, in curried
return func(x, *self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File ""/data/fsluma/pipelines/RStudio-docker/home/immunogeneicity_score_snakemake/tools/TLimmuno2/Python/TLimmuno2.py"", line 27, in blosum62
encoder[i] = coder
~~~~~~~^^^