main script error about keggcharter HOT 8 CLOSED

Hi there!

I see two issues here, one being reported and the other silently failing. "taxon_name" of your data seems to be a column of booleans, but it should be a column of species names. Also, it seems KEGGCharter could not find KOs from your KEGG IDs.

Could you please share the command you are using to run KEGGCharter, and the input file (or a subset of it)?

from keggcharter.

Hello,

thank you for your prompt reply, I highly appreciate it

so my main goal is to be able to visualize KEGG codes of a given genera and determine the number of times each KO occurs.

I understand this is not the main goal of this tool but I think it can work if I introduced the data as RNA transcript count.

an example,
#######
gene_ name | ko | occ
gene_1 | K01923 | 43
#######
gene_name: gene name - place holder
ko = kegg codes,
occurances: the number of times the KO was detected.

the way I get the data is using eggnog-mapper then merge all annotation output and count the number of times each gene was detected.

I am more than happy to supply the full file if needed.

from keggcharter.

Supplying the full file AND the command used will allow me to understand what is going wrong. KEGGCharter is still very limited in what KEGG IDs it can handle, and it seems it can't handle yours. Also, seems to be some pickle on your taxonomy information. Therefore, to reproduce the error and diagnose it, I need to reproduce what you have done.

If KEGGCharter runs fine with the example data, it is failing to interpret your particular data, and I require it to understand what is going on.

from keggcharter.

test.xlsx

of course,
please find the attached file and here is the command I used
keggcharter.py -f test.xlsx -tcol occ -gcol gene_name -it -keggc ko -o KEGG_Test

thank you

from keggcharter.

What is the purpose of the occ column in this data?

from keggcharter.

occ stands for occurrence and it should reflect the number of times a given ko is detected, like in a pan-genome

example: out of 50 species within genera, how many of them had glucokinase. lets assume the answer is 40.
so for glucokinase within genus x, the occurrence is 40

from keggcharter.

A couple of things here, first you should update KEGGCharter to version 0.4.1 (the latest) as with your example I found some problems I hadn't yet tackled. This version will be available soon, so please wait a bit until it is released (likely today). About your command, it should be set as

keggcharter.py -f test.xlsx -it "My taxonomy" -gcol occ -tcol occ -koc ko

• -it parameter takes as input a value, a string, which will be used to represent the taxonomy in the maps.
• since you are inputting KOs, you should input them with the -koc parameter, instead of the -keggc one
• the columns parameters in KEGGCharter do have weird names, but the same value should be inputted to -gcol and -tcol parameters here because those parameters concern quantification, and the only quantification here is in the "occ" column

from keggcharter.

Closing this as fixed by the two commits today, if version 0.4.1 doesn't meet your needs please do inform here.

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