Bug fix in genomic maps to transcriptomic

Genomic information was presented in transcriptomic maps. It's fixed now

Fix on not using genomic columns

When not specifying genomic columns, still tried to estimate most abundant taxa from genomic column

KGMLs and ECs check, and handling of exception in PDF generation

KGMLs and ECs check

• number of orthologs in KGML is now compared with number of lines in EC list (CSV)
• if they don't match, both will be downloaded again

Handling of exception in PDF generation

• to_pdf started to fail with timeout exception
• a try except now handles that

Fixed bugs in new functionalities

Taxonomy inputting was always happening

KGML loading always read from sys.path, now reads from --resources-directory

Compatibility options for other tools

Two new parameters provide quantification and taxonomy inputation

--input-quantification provides quantification

• creates new column, named Quantification (KEGGCharter), with 1 in every cell
• new column serves as single value --genomic-columns

--input-taxonomy provides taxonomy

• takes string as input
• parameter serves as single value --taxa-list
• creates new column, named Taxonomy (KEGGCharter), with the parameter in every cell

This options allow KEGGCharter to take directly as input the output of UPIMAPI or reCOGnizer

An even faster KEGGCharter

kegg_link access was moved out of the main map generation loop

• intermediate step to allow multiprocessing
• added --resources_directory parameter to allow customization of the KGMLs and CSVs folder

KGMLs handled locally

KEGGCharter now downloads KGMLs, and charts information directly from them

• Significantly speeds KEGGCharter workflow
• Pathway object is created from KGML with KGML_parser.read
• Circumvents BioPython problem of forcing 0.7.1 DTD guidelines on the XML schema

Major improvements in visualization

• KOs now converted to EC numbers directly to the maps
• No more gray outline boxes
• Exception for loading metabolic map improved

New input options and improved handling

Can now be resumed after running it the first time

• to retry failed maps, or if something failed in the latter steps

Also, accepts more diversified input

• allows to set different column names for taxonomy, KEGG IDs and KOs

Changes for bioconda

KEGGCharter files now go to share folder
Also created try/except for maps that fail to download