KEGGCharter as a proper tool of science
Implemented COG2KO
This idea belongs to Lovro Grum. For each KO, COGs are extracted from their KEGG HTML page. This information is reversed, and becomes COG to KO conversion.
New database, making KEGGCharter far more powerful! Makes for a great synergy with reCOGnizer.
Because this is webscrapping, 403 - Forbidden and Timeouts may often occur.
KEGGCharter gives some time between failed tries, and at the end checks for any KOs whose HTMLs were not retrieved. It tries to retrieve those as well.
Sanitization of input file
Checks if:
- inputted columns exist in the input file
- if
--kegg-column,--ko-column,--ec-column,--cog-columncolumns don't have invalid values / bad characters (" " and ";").
Added parameter for dividing quantification of each enzyme by the KOs assigned to it
When set, the --distribute-quantification parameter will instruct KEGGCharter to split the quantification of each enzyme by all the KOs that were assigned to it.
This information is outputted in data_for_charting.tsv.
New tests for several different parameters' combinations
show-available-maps for --show-available-maps parameter.
input-quantification-and-taxonomy for --input-taxonomy and --input-quantification parameters.
include-missing-genomes for --include-missing-genomes parameter.
map-all for --map-all parameter.
New output folders and writting of JSON information
KEGGCharter now stores metabolic maps representations in a maps folder. No brainer.
KEGGCharter additionally stores the information concerning the maps into a json folder. This folder will contain the dictionaries used for generating both the potential and differential maps.
"Potential" JSONs come in the form {box_id: [tax1, tax2, ...]}.
"Differential" JSONs come in the form {box_id: [col1, col2, ...]}. In the future, these should include the quantification value instead.