ids does not correspond to any enzyme

[Javi-Rop]

I hope this message finds you well. First and foremost, I wanted to express my deepest gratitude for the incredible work you've put into developing [nombre del proyecto]. It's been an invaluable tool for my research, and I've truly appreciated the effort and dedication you've poured into it.

I wanted to share my experience using the tool and provide some feedback on the process. I recently downloaded the genome of a bacterium in .fna format and a substrate with the proteome in .faa format. Following the instructions provided in the repository, I executed the script with the following command: python feeds.py -t 4 -k bacteria -f_length 100 -d s

However, during execution, I encountered some errors related to enzyme IDs. Specifically, I received an "Entry Error" message indicating that certain IDs did not correspond to any enzyme. Upon further investigation, I noticed that IDs '48', '49' and '51' were causing problems.

Despite facing these challenges, I remain excited about the potential of this project and eager to continue exploring its capabilities. If there are any additional troubleshooting steps or suggestions you can provide to fix these errors, I would greatly appreciate it.

Once again, thank you for your hard work and dedication to the advancement of scientific research. Your contributions have had a significant impact and I am truly grateful for the opportunity to use such a valuable tool.

[vborincenturion]

Dear Javi-Rop,

Thank you for your message and kind words regarding FEEDS. I'm glad to hear that the tool has been valuable for your research, and I appreciate your feedback.

To better assist you, could you provide more information about the specific error message you received? Additionally, if possible, could you share the FEEDS output, genome and the substrate files? This would help me to replicate the issue and provide more targeted troubleshooting steps.

[Javi-Rop]

¡Thank you for your prompt response and willingness to help! I really appreciate your interest in addressing the issues I've encountered with FEEDS.

The input genome and substrate files I've used are as follows:

Genome: Pseudomonas putida, GCA_000412675.1_ASM41267v1_genomic.fna
Substrate: Sus scrofa, protein.faa
The error I've been encountering is related to enzyme IDs during script execution:

I've noticed that the RPG library has 46 available enzymes (https://rapid-peptide-generator.readthedocs.io/en/latest/enzymes.html#enzymes). New enzymes can be added using the "rpg -a" command (I still need to investigate this).

For now, I've managed to solve the problem by removing IDs greater than 46 in the extract_rpg_cs_values function, although I don't believe this is the correct approach.

I greatly appreciate your assistance and guidance.

[vborincenturion]

Hi Javi,

Did you locate and replace the "rpg_user.py" file in your RapidPeptideGenerator tool with the one in the db folder of this GitHub repository? I added other enzymes to the RapidPeptideGenerator tool, so I think this might be why you encountered errors.

Let me know if the error persists.

All the best.

[Javi-Rop]

Hi there,

Thank you for your prompt response and suggestion. I've been checking my directory ./miniforge3/envs/feeds/lib/python3.9/site-packages/rpg, but I couldn't find a file named "rpg_user.py". However, I've noticed the presence of a very similar file called "enzymes_definition.py". It seems like it could be an updated or renamed version of the file you mentioned. I'll go ahead and replace it with the file from the "db" folder of your repository and will let you know about any relevant results or changes.

Additionally, I'd like to bring to your attention another error I've encountered. It seems to be related to the BioPython library, specifically in the molecular_weight function where an invalid unambiguous letter for protein, 'X', is encountered. I'm hopeful that updating the enzyme definitions might address this issue as well.

Thanks again for your help and guidance.

Best regards.

[mfrand-7]

Hi everyone,

I've encountered a similar issue where I can't locate a file named "rpg_user.py" in my rpg directory. I've read @Javi-Rop suggestion and am curious if updating the "enzymes_definition.py" file within the rpg directory yielded any results (In my case, it didn't work). Any advice from either of you would be greatly appreciated, as this tool seems incredibly useful, and I’d love to get it running successfully.

As a suggestion, it might be beneficial to include some testing files in the repository. These would help users verify if the program is correctly installed and functional, which could be especially useful for troubleshooting setup issues like this one.

Thank you again for your time and assistance!

Best regards,
Marta

[vborincenturion]

Dear FEEDS tool users,

Thank you for your feedback and considerations. I have added a folder named "test" to the GitHub repository for you to use when testing the tool. Specifically, I included two genomes: one bacterial and one yeast, along with the substrate glutelin from different origins (Barley and Grape). Simply place the files in their respective folders as described in the tool’s instructions on GitHub.

Regarding the file rpg_user.py, as described by the tool’s author (documentation link), enzymes are stored in this file. To locate it, you can run the command:
nano ~/rpg_user.py

At the top of the nano editor, you will see the path to the rpg_user.py file. Usually, it is located at /root/rpg_user.py if the tool was installed using root permissions. Keep in mind that each user might install the tool differently, so it is crucial to locate the correct rpg_user.py file and replace it with the one provided in this repository.

To verify that you replaced the correct file, you can run the following command:
rpg -l

Let me know if you have any questions. Best of luck testing the tool!

Best regards

[mfrand-7]

Thank you very much for your detailed response and the support provided. Thanks to your clear instructions and the new test folder you added to the repository, I was able to solve the issues I was facing, and the tool is now working perfectly.
I truly appreciate the time and effort you put into helping users like me.

Thank you again for your excellent work and support!

Best,