CONFIG_rbh_to_ribbon.yaml

#
# Example config.yaml file for: odp_rbh_to_ribbon
# Author: dts
# github account: @conchoecia
# link to github repo: https://github.com/conchoecia/odp
# date: 2022-2023
# license: GNU GPL https://github.com/conchoecia/odp/blob/main/LICENSE
#
# Goal: This script creates ribbon plots of genome synteny.
#
# First select which plotting order is desired for the chromosomes
#  chr_sort_order < custom | optimal-top | optimal-size | optimal-random >
#    custom         - use the custom sorting order for EVERY species in chromorder
#    optimal-top    - use the custom order for the topmost species, then optimizes everything else
#    optimal-size   - sort the top species' chromosomes by number of genes, optimize everything else
#    optimal-chr-or - use `chromorder` when possible, optimize everything else
#    optimal-random - randomly sort the chromosomes of the top species, optimize everything else
chr_sort_order: optimal-chr-or

# - If you only want to plot the significant relationships, set to False
#   - the significant lines will be 0.8
# - If you want to plot everything, set to True
#   - the significant lines will be 0.8, the faint lines will be 0.15
plot_all: True

# - First type in the list of species to plot
# - In this example we plot the relationships between
#   three species with the codes "EMU", "RES", and "HCA".
#   These three species must also be present in the "species"
#   entry of the config file below.
species_order:
  - EMU
  - RES
  - HCA

# - If there are any organisms for which you would like to specify the
#   chromosome order, then this is the place to do it. The species name
#   here must match the species name in the "species" part of the config
#   file.
# - Only the chromosomes here will be plotted for this species. This is an
#   easy way to just plot a subset of chromosomes that you are interested in.
chromorder:
  EMU:
    - EMU1
    - EMU6
    - EMU5
    - EMU4
    - EMU2
    - EMU3

# NOTE : YOU CAN ONLY SPECIFY ONE OF THE FOLLOWING:
#        COMMENT OUT THE ONE YOU DO NOT USE
#  - rbh_files_in_order
#  - rbh_directory

# - This is the list of RBH files output from odp2 or another source.
# - Each RBH file contains the orthologs between species that should be
#   plotted.
# - The number of files will always be the number of species minus one.
# - Currently, only relationships that are significant with Fisher's exact
#   test will be plotted here.
rbh_files_in_order:
  - /path/to/EMU_RES_xy_reciprocal_best_hits.coloredby_BCnS_LGs.plotted.rbh
  - /path/to/HCA_RES_xy_reciprocal_best_hits.coloredby_BCnS_LGs.plotted.rbh

# If your rbh files were generated with odp, you can just supply the
#  path to the
rbh_directory: /path/to/odp/step2-figures/synteny_coloredby_BCnS_LGs/

# - All of the species that are in "species_order" above should be here
# - This information is important for calculating some stats that are used
#   for plotting.
# - The necessary fields are:
#   - proteins
#   - chrom
#   - genome
# - If you specify "minscafsize", then only scaffolds >= this size are
#   included in the ribbon plot.
species:
  HCA:
    genus:    "Hormiphora"
    species:  "californensis"
    proteins: "/path/to/HCA.pep"
    chrom:    "/path/to/HCA.chrom"
    genome:   "/path/to/HCA.fasta"
    minscafsize: 5000000

  RES:
    # as you can see in this example, it doesn't matter if the file
    # prefixes match the species name (RES) specified above
    proteins:    "/path/to/rhopilema_chromosome_v1.pep"
    chrom:       "/path/to/rhopilema_chromosome_v1.chrom"
    genome:      "/path/to/rhopilema_chromosome_v1.fasta"
    genus:       "Rhopilema"
    species:     "esculentum"
    minscafsize: 4000000

  EMU:
    genus:     "Ephydatia"
    species:   "muelleri"
    proteins:  "/path/to/EMU.pep"
    chrom:     "/path/to/EMU.chrom"
    genome:    "/path/to/EMU.fasta"
    minscafsize: 1000000