Comments on: Tutorial: Analysis with paprica

By: Nathan

Nathan — Sun, 14 Jan 2024 23:34:22 +0000

Hi Jeff,

Great program, and I’m excited to see my results. I successfully ran my own samples, but when I try to run the combine_results code, I end up with an error — specifically, it flags a nan value and throws a KeyError, which should be handled by the exception line in the code (see the copied source code below, line 256). However, it throws another error on line 248: “ValueError: cannot reindex on an axis with duplicate labels.” Any ideas on what could be going wrong? I didn’t want to try debug the source code without seeing if you had any ideas first. Thanks!

try:
unique_edge_abund.loc[seq, temp_unique.loc[seq, ‘global_edge_num’]] += temp_unique.loc[seq, ‘abundance_corrected’]
except KeyError:
unique_edge_abund.loc[seq, temp_unique.loc[seq, ‘global_edge_num’]] = temp_unique.loc[seq, ‘abundance_corrected’]

By: Jeff

Jeff — Fri, 14 Sep 2018 12:25:42 +0000

In reply to Roman.

Roman,
I just replied on GitHub but including comment here. We don’t have a built-in way to do this as it gets a bit arbitrary; pathways are typically involved in multiple higher-order processes. The best thing to do is to explore BioCyc to create a hierarchy that makes the most sense for your data and project.

Jeff

By: Roman

Roman — Thu, 13 Sep 2018 12:27:46 +0000

Dear Jeff,
thank you very much for Paprica, it is a great software.
May I ask you, I was wondering if there is an easy (semi/automated) way how to group identified pathways into a higher level. I mean in your paper Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula you have a nice figure 6. Metabolic pathways differentially present between summer surface samples and winter and deep samples. where you did group pathways into higher taxonomic level – e.g. Anaerobic metabolism, Nitrogen degradation etc.

Thank you very much.

Roman

By: Jeff

Jeff — Thu, 03 Aug 2017 23:23:14 +0000

In reply to Garima Raj.

This discussion ended up taking place on GitHub, you can check it out here: https://github.com/bowmanjeffs/paprica/issues/52. The next time I’m inside paprica I’ll try to tweak things so that the output contains enzyme names, as this is clearly useful!

By: Garima Raj

Garima Raj — Sun, 18 Jun 2017 07:02:11 +0000

Hi Jeff,
Can you suggest how do i assign names to each E.C number? Its taxing to go through each number in enzyme database. I am sure there is a method, but I am fairly new to bioinformatics. Any suggestion will be very helpful.
Thank you

By: garima raj

garima raj — Fri, 16 Jun 2017 14:35:31 +0000

Hi Jeff, i have used the pathways result to build heatmap and i want to do analysis using the enzyme data, can you please tell how to assign enzyme names to the E.C numbers, there is a huge data and individually looking into each number is very time consuming.
Thank you,
Garima Raj

By: Jeff

Jeff — Mon, 19 Sep 2016 13:02:43 +0000

I’ve made some long overdue updates to this tutorial to get it inline with the latest paprica features and command structure. If you’re working through it and you run into any problems please let me know!

By: Jeff

Jeff — Mon, 08 Aug 2016 14:11:49 +0000

In reply to Roman. You are correct! The tutorial is now lagging a few releases behind... I need to get it up to date!

By: Roman

Roman — Mon, 08 Aug 2016 13:45:05 +0000

Thanks for paprica, it is great piece of software I was looking for.

Btw. I believe that the command for aggregating results is not
python combine_edge_results.py my_analysis
but rather
python combine_edge_results.py my_analysis -edge_in [suffix pattern for edges] -path_in [suffix pattern for paths] -ec_in [suffix pattern for ec numbers] -o [prefix for output]
e.g.
python combine_edge_results.py my_analysis -edge_in bacteria.edge_data.csv -path_in bacteria.sum_pathways.csv -ec_in bacteria.sum_ec.csv -o my_analysis

By: Jeff

Jeff — Mon, 02 May 2016 13:02:11 +0000

In reply to Zhijian Jiang. Hmmm... I can't reproduce this problem in the Virtualbox appliance. Can you confirm that you are using that VB appliance exactly as it came, i.e. that you didn't attempt to carry out the installation steps within the VB appliance? Assuming the indicated Python scripts are located in the paprica directory this problem is usually caused by an issue with the shell script startup files.