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Dear Andreas,
I am trying to use MetQy following the manual provided, but I am a little bit lost because I am not very good in using R. The software is properly installed in my computer, I followed examples and they provide results (except some figures e.g. sunburst are missing the text).
Basically I have some genomes annotated using KEGG and I would simply perform the “query_genomes_to_modules” with the “user-specified gene sets”.
My input file has header and is organized as you suggests in the example:

ID ORG_ID ORGANISM KOs ECs
T09999 aaa A K00013;K00014;K00018;… “empty field”

Tabular values separate the different fields (ID ORG_ID ORGANISM KOs ECs) in the header and also in the first line. Is this correct? I do not have EC numbers (empty field), only KEGG IDs for genes.
Could you please report some minimal command lines to do the following:
1-Import the file in R in order to be usable from your software;
2- Calculate the module completion fraction (mcf) for all the modules;
3-Export to a text file the mcf values obtained for all the pathways.
Thanks a lot in advance for your help.
Sincerely

Hi, I have some bacteria genomes (Vibrio vulnificus strains), it was assembled using Spades, and then I use the generated contigs to generate a file.faa using prokka, an then I used it to generate a list of KO in blastKOALA.

my question is, it is possible to analyze those data with MetQy ? does anyone have a pipeline ??? or an example for bacteria genomes ??

Thanks so much

Original message

I have a couple of questions, and I was wondering if you could provide some clues. I couldn't find detailed information about the module completeness fraction calculation. Do you have any specification available? I surfed your code but got lost. For instance, what happens when a module which is defined as (say) K0001+K0002, only one of the genes is found. mcf = 0.5 or mcf = 0? I have doubts about how to interpret the index in different scenarios. I have a case where I can find either one or both genes in all my genomes, but still I get a mcf = 0 for some of them. I was expecting 0.5 for those which only have 1 of them. How is this fraction calculated?

Hello.
I have metagenome fsatq files.
How can I analyze files by converting them?

thanks.

Kohei

Dear Andreas,
I would like to use your tool to analyse the metabolic potential of MAGs. I have tested it already and found out that a few modules are missing. Unfortunately, I do not have access to the KEGG ftp but I wonder if I could make manual modifications (adding modules) to the existing KEGG database file that is used in the package.
Do you think that is possible?

Many thanks
Julia

I have come across a problem in the way this package evaluates the completeness of KEGG pathway modules, given a number KOs, or something comparable. Specifically, this is referring to the function query_missingGenes_from_module.R, but might be present in some of the other KEGG-module related functions?

The issue arrises from how the functions splits modules into blocks, based on spaces:

### SEARCH BLOCKS ----
  block_defs  <- strsplit(DEFINITION[index], split = " ")[[1]]
  nBlocks     <- length(block_defs)

This problem does not arise with every module, instead, it only occurs in more complicates modules which have "nested" blocks (for lack of a better word). For example, module 2 (https://www.genome.jp/kegg-bin/show_module?M00002) leads to this issue. The function in this package comes up with 6 blocks, (nBlocks), while there is only 5 blocks, as to my understanding of KEGG module definitions. This also matches the 5 blocks assumed in KEGGmapper. It must have something to do with the above chunk ignoring the presence of "(" or ")", ie when spaces occur WITHIN a block, instead of separating a block.

This problem should lead to a systematic underestimation of the completeness of pathways, when it inflates the number of blocks in a module. Adjusting the way the blocks are split to only split actual blocks (spaces outside of any "(" or ")"; something that can be done with regex I guess) should solve this issue.

Dear Andreas,
I am trying to use your script query_missingGenes_from_module to spot missing genes from module but I need to do it recursively on multiple modules (a list provided) and then write the result in a file. When I do it on one module only I have no problem but when I put my list in a vector and call with a loop the elements of the vector to be my "ID_MODULE" I don't manage to format the output correctly.

Any hint? Thank you in advantage and for having provided this amazing resource.
Sincerely,
Arianna