sqmitols.py erro

[Panda-smile]

1. Hello professor, I encountered an error when using itols drawing bin, but I don't know where the problem occurred? At the same time, I would like to ask if I want to check the pathways related to starch degradation under metcyc. How can I filter them out for input into the functions file?
2. How to specifically screen the generated fungal bins and perform taxonomy-related drawing methods is not found in the manual.

functionlist.txt

[fpusan]

@jtamames can you help with this?

[jtamames]

Do the following changes to sqm2itol.pl (in the directory utils in the SqueezeMeta installation):

Comment line 105: # next if($k[1] ne "DASTool"); Change line 145 to: my $funfile="$resultpath/20.$project.$funclass.pathways";

[Panda-smile]

First of all, thank you very much for your suggestions, but there are still some confusions: 1. According to the output results, no results related to the function metacycl and abudance were found. 2. Whether the results of the bin can be given to the species level? （default：The result output is based on the statistics of the genus level？）

114，$binname=~s/\s+/_/g; 115，$binname=~s/sp./sp/g;

[jtamames]

The bins are given the taxonomy resulting from the analysis. It is not possible to go to species level if the bin couldn´t be classified at species rank. Regarding the functions, I understand that no pathways are present in the heatmap_pathways.txt file? If so, what happens if you run sqm2itol.pl not specifying a function list (not using the -functions option)?

[Panda-smile]

Hello Professor~ The output result after not running the function is as follows. It is found that there is no value in the heatmap_abund.txt file;（add -function files not generate “heatmap_pathways.txt”，while no add will generate ）

heatmap_pathways.txt heatmap_abund.txt

[jtamames]

The issue on heatmap_abund.txt file is occurring because by default, sqm2itol tries to read RPKM values, but these are no longer present in the bin table. Try specifying -abundances coverage when running sqm2itol.pl Regarding the list of functions, there is a small mistake in line 169 preventing reading some functions with odd characters. That line should be changed to: if($fullfun=~/\Q$u\E\b/i) {

But nevertheless, you also need to check your functionlist.txt file because some items there do not match the name of metacyc pathways. For instance, you should remove all quotes (") and check the spelling, I can spot several typos in the file. I am unsure if these mistakes are breaking the parser, but it could be. Best, J

[fpusan]

Closing due to lack of activity, feel free to reopen