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K-mer classification method improvement

Jonkheer, Eef requested to merge phenotype_parsing into master

New k-mer classification method with improved scaling

The output file names and locations have been changed for some functionalities (Sorry DJ).

kmer_classification

  • kmer_distance_tree.R -> genome_kmer_distance_tree.R

  • distance_inf_distinct_kmers.csv -> removed

  • mash_distance.csv -> distances_for_tree/genome_mash_distance.csv

  • distance_distinct_kmers.csv -> distances_for_tree/genome_distance_distinct_kmers.csv

  • distance_all_kmers.csv -> distances_for_tree/genome_distance_all_kmers.csv

  • core_kmers.csv -> kmer_identifiers/core_kmers.csv

  • accessory_kmers.csv -> kmer_identifiers/accessory_kmers.csv

  • unique_kmers.csv -> kmer_identifiers/unique_kmers.csv

  • phenotype_shared_kmers.csv -> kmer_identifiers/phenotype_shared_kmers.csv

  • phenotype_specific_kmers.csv -> kmer_identifiers/phenotype_specific_kmers.csv

  • phenotype_exclusive_kmers.csv -> kmer_identifiers/phenotype_exclusive_kmers.csv

function_overview

  • function_overview_per_group.csv -> removed
  • go_overview.txt -> go_overview.csv
  • pfam_overview.txt -> pfam_overview.csv
  • tigrfam_overview.txt -> tigrfam_overview.csv
  • interpro_overview.txt -> interpro_overview.csv
  • bgc_overview.txt -> bgc_overview.csv
  • phobius_overview.txt -> phobius_signalp_overview.txt
  • cog_overview.txt -> cog_overview.csv

rename_phylogeny

  • tree.newick_RENAMED -> tree_RENAMED.newick

msa_of_group

  • informative/variable_sites.csv -> informative/variable_site_counts.csv

calculate_ANI

  • ani.tree -> ANI.newick

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