Initially forked from here. Thank you to the awesome binder team!
Part of the Bioinformatics Virtual Coordination Network :)
Vist the KEGG-Decoder GitHub page for more information
There are 4 example files from the various KEGG KOALA outputs, blastkoala.txt, ghostkoala.txt, kofamkoala.txt, and NORP_subset.txt. Each one has the data formatted in a specific way that may (or may not) work with KEGG-Decoder.
blastkoala.txt is a single genome formated correctly
BAFMBKGE_00001 K03596
BAFMBKGE_00002 K03100
BAFMBKGE_00003 K03685
As a single genome, KEGG-Decoder can only produce a static visualization output - interactive visualization requires at least 3 genomes.
KEGG-decoder -i blastkoala.txt -o blastkoala.ko -v static
The blastkoala.svg file contains a heatmap comparing the genome results to the KEGG-Decoder pathways. The more red the cell of the heatmap, the more complete the pathway
ghostkoala.txt has a single genome that is formatted incorrectly
NC_015736.1_1 K01703
NC_015736.1_2 K01704
KEGG-Decoder can only accept gene IDs with a single _. KEGG-Decoder uses all of the string prior to the first _ as the name to associate with each row of the output and heatmap. Identical strings would result in the merging of multiple genomes together
sed 's/NC_/NC/g' ghostkoala.txt > ghostkoala-mod.txt
KEGG-decoder -i ghostkoala-mod.txt -o ghostkoala.ko -v static
kofamkoala.txt is a complex table that requires some pre-processing
sed 's/ \+ /\t/g' kofamkoala.txt | cut -f1,2 | sed 's/\* //g' | grep -v "#" > kofamkoala-mod.txt
KEGG-decoder -i kofamkoala-mod.txt -o kofamkoala.ko -v static
The genome name for the output will be WP as it is the string prior to the first _.
NORP_subset.txt contains KOALA results for 4 genomes. The NORP.ko file will be created after each KEGG-Decoder run, but will contain identical contents. It is the numerical values used to the create the heatmap. Because there are 3+ genomes, we can make an interative visualization as well as a static visualization.
KEGG-decoder -i NORP_subset.txt -o NORP.ko -v static
KEGG-decoder -i NORP_subset.txt -o NORP.ko -v interactive