souradiptoc/codonu

A python project for analysis of codon usage for gene or genome analysis

Hi there 👋 I'm Souradipto Choudhuri

• 🔭 I’m currently working on Bioinformatics tool development
• 🌱 I’m currently learning python
• 👯 I’m looking to collaborate on various bioinformatic tool development
• 📫 How to reach me: [email protected]

codonu's Issues

Not identical Output

Hello sir,
I am new user CodonU .I have one question about output.
I am run Staphylococcus_aureus.fasta file but my output not to same your output.
why.. if you want I will share my output screenshot ............

Originally posted by @Hasanzahid10 in #4 (comment)

Save image issue

When i am neutrality and partty rule2 plot function given save_image = True
FileNotFoundError :[Errno 2] no such file or director show
I am share some image



How to solve this problem .... #Help me

Unable to import CodonU.analyzer

from CodonU import analyzer as an

leads to

ModuleNotFoundError Traceback (most recent call last)
Cell In[1], line 1
----> 1 from CodonU import analyzer as an

File ~/conda/lib/python3.10/site-packages/CodonU/analyzer/init.py:1
----> 1 from .cai_comp import calculate_cai
2 from .rscu_comp import calculate_rscu
3 from .cbi_comp import calculate_cbi

File ~/conda/lib/python3.10/site-packages/CodonU/analyzer/cai_comp.py:1
----> 1 from cai2 import CAI
2 from warnings import filterwarnings
3 from Bio.Data.CodonTable import unambiguous_dna_by_id

ModuleNotFoundError: No module named 'cai2'

Python 3.10.11
CodonU 1.0.4

All MCA Plotting functions not working.

command: viz.plot_mca_aa_aroma(in_file, 11)
error: AttributeError: module 'CodonU.vizualizer' has no attribute 'plot_mca_aa_aroma'

command: viz.plot_mca_aa_gravy(in_file, 11)
error: AttributeError: module 'CodonU.vizualizer' has no attribute 'plot_mca_aa_gravy'

Same for:
viz.plot_mca_rscu(in_file, 11)
viz.plot_mca_codon_freq(in_file, 11)

I have query about cai2

ModuleNotFoundError: No module named 'cai2'

Javascript Error: too much recursion

python 3.11
latest version of codonU

Any thing I try within the examples for my file I get "Javascript Error: too much recursion"

any thoughts?

Error In Installing CodonU

hello i am trying to install CodonU (pip install CodonU) package for my project. I have tried my best to install but i am facing error while installing CodonU. moreover i had tried to sort out this error but i can't. i have attached a screenshot of error that I am facing.
waiting for a nice positive response.
regards Abdul Majeed