KEGGCharter symbolic link changed

KEGGCharter is now called as keggcharter, instead of the old keggcharter.py.

Bug fix on checking for functions in taxonomic KGMLs

Organisms that should not be represented - because their KGMLs lacked the boxes in question - were being represented, if they were the first ones for a certain box.

Fixes #8

Now uses inputted KOs directly

KOs are still converted to EC numbers and back to KOs, but the ones used in the metabolic maps are those inputted with the -koc parameter.

Users can still use the newly obtained KOs by reformatting the command to accept those in the "KO (KEGGCharter)" column, ideally using the --resume parameter.

Also, some fixes on adding boxes to grey taxonomy.

Several improvements to taxonomy representation

• Changed font color to white for grey boxes
• Grey adds to already present taxonomies - when a box already has one or more taxonomies, it will be added the grey (other) colour if other taxon is there
• Boxes labels written without prefixes ("ec:" and "ko:")

Several fixes

• checks correctly the taxonomies most abundant, by only considering KOs of the map being represented
• on the path when searching for downloaded KGMLs if downloading resources
• correctly assumes manually set "input-taxonomy"
• if "input-taxonomy", handles correctly the taxon_to_mmap_to_orthologs and mmaps2taxa objects
  Removed map00072

Better help on --genomic-columns

When no parameter is set for --genomic-columns, KEGGCharter will ask if the user wants to input quantification - the same could be accomplished with the --input-quantification parameter.

Helps in handling the absence of genomic quantification.

Resources moved to their own folders

KEGGCharter now downloads resources to proper folders, instead of dumping everything in rd

• kgmls moved to rd/kc_kgmls
• csvs moved to rd/kc_csvs

Implemented CI

CI includes full analysis of KEGGCharter

Also fixed preparation of data for charting

Was happening before transcriptomic_columns was split

MT columns quantification now normalized by number of KOs

For each protein, MT columns quantification is now divided by the number of KOs that were detected for that protein.

Fix

"--number-of-taxa" input working again

Maps tailored for taxonomies

Genomic maps now don't include orthologs that are not associated with the analyzed taxa:

• KGMLs specific for different taxa are obtained
• Allows to know which pathways each organism can participate in
• Also allows to know which orthologs are available

Better imports and progress bars

• Moved progress bars to tqdm
• Simplified imports, became more explicit
• Added openpyxl dependency because of updates on pandas
• Added poppler dependency because I'm dumb sometimes
• Added mscorefonts dependency: fixes pdftoppm error Syntax Error: Couldn't find a font for 'Helvetica'