I am interested in plotting the quality-score vs sequence-length, and I tried marginplot after installing the software in conda, and it produced me an error.
I followed the code, mine was:
pauvre marginplot --fastq Ju760.Lig.P-1.fastq
I got the stats back but then I got the error:
Traceback (most recent call last):
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/matplotlib/init.py", line 732, in setitem
cval = self.validatekey
KeyError: 'text.latex.unicode'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/juaguila/miniconda3/envs/NGS-manip/bin/pauvre", line 10, in
sys.exit(main())
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/pauvre/pauvre_main.py", line 630, in main
args.func(parser, args)
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/pauvre/pauvre_main.py", line 64, in run_subtool
submodule.run(args)
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/pauvre/marginplot.py", line 403, in run
margin_plot(df=df.dropna(), **vars(args))
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/pauvre/marginplot.py", line 197, in margin_plot
rc.update_rcParams()
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/pauvre/rcparams.py", line 7, in update_rcParams
rcParams.update({
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/_collections_abc.py", line 999, in update
self[key] = other[key]
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/matplotlib/init.py", line 737, in setitem
raise KeyError(
KeyError: 'text.latex.unicode is not a valid rc parameter (see rcParams.keys() for a list of valid parameters)'
I check the environment, and I have all the required apps in the conda environment.
Could you tell what happened or caused it?
The file I wanted to check is basically a fastq file with about 2.3 GB of data, average length of 5.1 kb and max 240kb.
hempelc
commented
3 months ago
Hi,
I am interested in plotting the quality-score vs sequence-length, and I tried marginplot after installing the software in conda, and it produced me an error. I followed the code, mine was:
pauvre marginplot --fastq Ju760.Lig.P-1.fastqI got the stats back but then I got the error: Traceback (most recent call last): File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/matplotlib/init.py", line 732, in setitem cval = self.validatekey KeyError: 'text.latex.unicode'
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/juaguila/miniconda3/envs/NGS-manip/bin/pauvre", line 10, in
sys.exit(main())
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/pauvre/pauvre_main.py", line 630, in main
args.func(parser, args)
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/pauvre/pauvre_main.py", line 64, in run_subtool
submodule.run(args)
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/pauvre/marginplot.py", line 403, in run
margin_plot(df=df.dropna(), **vars(args))
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/pauvre/marginplot.py", line 197, in margin_plot
rc.update_rcParams()
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/pauvre/rcparams.py", line 7, in update_rcParams
rcParams.update({
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/_collections_abc.py", line 999, in update
self[key] = other[key]
File "/home/juaguila/miniconda3/envs/NGS-manip/lib/python3.10/site-packages/matplotlib/init.py", line 737, in setitem
raise KeyError(
KeyError: 'text.latex.unicode is not a valid rc parameter (see rcParams.keys() for a list of valid parameters)'
I check the environment, and I have all the required apps in the conda environment.
Could you tell what happened or caused it? The file I wanted to check is basically a fastq file with about 2.3 GB of data, average length of 5.1 kb and max 240kb.
Thanks;
Juan Pablo