code error

[lijunyuan]

Hi,
I installed toxinPred3 with pip and tested the installment with" toxinpred3 -h", everything seemed ok, with the following information shown"

usage: toxinpred3 [-h] -i INPUT [-o OUTPUT] [-t THRESHOLD] [-m {1,2}] [-d {1,2}]

Please provide following arguments. Please make the suitable changes in the envfile provided in the
folder.

options:
-h, --help show this help message and exit
-i, --input INPUT Input: protein or peptide sequence in FASTA format or single sequence per
line in single letter code
-o, --output OUTPUT Output: File for saving results by default outfile.csv
-t, --threshold THRESHOLD
Threshold: Value between 0 to 1 by default 0.38
-m, --model {1,2} Model: 1: AAC & DPC based ET, 2: Hybrid, by default 1
-d, --display {1,2} Display: 1:Toxin, 2: All peptides, by default 2

"
Then I built a test file, test1.fa:

Psin_g1_t1
MRHPGNCVARLLRELFADAATGAKLTSERKKLIRQLEKNTRRCGRAIEAIKTLEKMIKRR
IPIMDIMAGYINPGTEKYGNQGSTIEIYQHNGHAWCEVKKEKKVVV
I tried to predict toxin with the command "toxinpred3 -i test1.fa", but bugs appears as follows"
##############################################################################

The program ToxinPred3.0 is developed for predicting Toxin and non toxin

peptides from their primary sequence, developed by Prof G. P. S. Raghava's group.

Summary of Parameters:
Input File: test1.fa ; Model: 2 ; Threshold: 0.38
Output File: outfile.csv ; Display: 2
Traceback (most recent call last):
File "/public/home/lijunyuan/anaconda3/envs/ToxinPred3/bin/toxinpred3", line 8, in
sys.exit(main())
~~~~^^
File "/public/home/lijunyuan/anaconda3/envs/ToxinPred3/lib/python3.13/site-packages/toxinpred3/python_scripts/toxinpred3.py", line 327, in main
CM.to_csv("Sequence_1",header=False,index=None,sep="\n")
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/lijunyuan/anaconda3/envs/ToxinPred3/lib/python3.13/site-packages/pandas/util/_decorators.py", line 333, in wrapper
return func(*args, **kwargs)
File "/public/home/lijunyuan/anaconda3/envs/ToxinPred3/lib/python3.13/site-packages/pandas/core/generic.py", line 3967, in to_csv
return DataFrameRenderer(formatter).to_csv(
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
path_or_buf,
^^^^^^^^^^^^
...<14 lines>...
storage_options=storage_options,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/public/home/lijunyuan/anaconda3/envs/ToxinPred3/lib/python3.13/site-packages/pandas/io/formats/format.py", line 1014, in to_csv
csv_formatter.save()
~~~~~~~~~~~~~~~~~~^^
File "/public/home/lijunyuan/anaconda3/envs/ToxinPred3/lib/python3.13/site-packages/pandas/io/formats/csvs.py", line 260, in save
self.writer = csvlib.writer(
~~~~~~~~~~~~~^
handles.handle,
^^^^^^^^^^^^^^^
...<5 lines>...
quotechar=self.quotechar,
^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
ValueError: bad delimiter value

"
Please help check, thanks a lot!