#!/bin/bash

# Setup the project
dape init
dape add Rm1021 -c red
dape add BL225C -c green
dape add AK83 -c blue
dape add AK58 -c orange

# Add the genomic data and KAAS outputs
dgenome add-dir genome/
dgenome add-ko kegg/AK58.tab kegg/AK83.tab kegg/Rm1021.tab kegg/BL225C.tab

# Pangenome estimation/KEGG mapping
dgenome start -n 4 -x SinMel_

# Annotate the orthologs w/o KEGG IDs
dgenome annotate

# Statistics and exports
dgenome stats
dgenome export

# Add the phenomic data
dphenome add-dir phenome

# Control signal subtraction
dphenome zero

# Parameters calculation and Elbow test to decide the value of k
dphenome start -e -g
# AV/parameters calculation (k=5)
dphenome start -f -n 5

# Curve plots
dphenome plot

# Activity rings
dphenome rings
mv ActivityRing.png ActivityOverall.png
dphenome rings -o Rm1021 -d 2

# Statistics and exports (including YAML files) 
dphenome stats -a 3 -d 2
dphenome export

# Pathway maps
dape map -d 2
dape map -a

# Combined genomic/phenomic analysis
dape start -s -t 2
dape start -a -s -t 2