LANGUAGE=python
VARS= $^
EXE =$(LANGUAGE) $(VARS)
ROOT_DIR := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
DATA_DIR = Data
CODE_DIR = Code





all:Data/derived/combined_fungi_fasta.fasta\
Data/derived/mmseqs2_results/combined_fungi_fasta_SST100_rep_seq.fasta\
Data/derived/mmseqs2_results/combined_fungi_fasta_SST75_rep_seq.fasta\
Data/derived/mmseqs2_results/combined_fungi_fasta_SST50_rep_seq.fasta\
Data/derived/mmseqs2_results/combined_fungi_fasta_SST25_rep_seq.fasta\
Data/derived/length_output_fungal.csv\
Figures/shared_lengths_fungi.png\
Data/derived/forLogoMaker/fungal_toxins_animal_toxins_LogoMaker.csv\
Data/derived/forLogoMaker/fungal_toxins_bacterial_toxins_LogoMaker.csv\
Figures/shared_aromaticity_0.1.png


# Step 1: Combine the raw files containing fungi toxins to one large fasta file. 
Data/derived/combined_fungi_fasta.fasta: Code/python/process_fasta.py Data/derived/fungi/ 
		python Code/python/process_fasta.py Data/derived/fungi/ Data/derived/combined_fungi_fasta.fasta Data/derived/combined_fungi_fasta_data.csv

# Step 2: Redundancy reduce this file to separate levels off redundancy 100, 75,50, 25 
Data/derived/mmseqs2_results/combined_fungi_fasta_SST100_rep_seq.fasta: Data/derived/combined_fungi_fasta.fasta
		mmseqs easy-cluster Data/derived/combined_fungi_fasta.fasta Data/derived/mmseqs2_results/combined_fungi_fasta_SST100 Data/derived/mmseqs2_results/temporary_files --min-seq-id 1 --cov-mode 0

Data/derived/mmseqs2_results/combined_fungi_fasta_SST75_rep_seq.fasta: Data/derived/combined_fungi_fasta.fasta
		mmseqs easy-cluster Data/derived/combined_fungi_fasta.fasta Data/derived/mmseqs2_results/combined_fungi_fasta_SST75 Data/derived/mmseqs2_results/temporary_files --min-seq-id 0.75 --cov-mode 0

Data/derived/mmseqs2_results/combined_fungi_fasta_SST50_rep_seq.fasta: Data/derived/combined_fungi_fasta.fasta
		mmseqs easy-cluster Data/derived/combined_fungi_fasta.fasta Data/derived/mmseqs2_results/combined_fungi_fasta_SST50 Data/derived/mmseqs2_results/temporary_files --min-seq-id 0.5 --cov-mode 0

Data/derived/mmseqs2_results/combined_fungi_fasta_SST25_rep_seq.fasta: Data/derived/combined_fungi_fasta.fasta
		mmseqs easy-cluster Data/derived/combined_fungi_fasta.fasta Data/derived/mmseqs2_results/combined_fungi_fasta_SST25 Data/derived/mmseqs2_results/temporary_files --min-seq-id 0.25 --cov-mode 0

# Step 3: visualize the length of the fungi protein in connection to the other proteins

Data/derived/length_output_fungal.csv: Code/python/len_analysis_part1.py Data/derived/mmseqs2_results/mode0_clu_rep_animal_toxins_SST100_rep_seq.fasta Data/derived/mmseqs2_results/combined_fungi_fasta_SST100_rep_seq.fasta Data/derived/mmseqs2_results/mode0_clu_rep_bacterial_toxins_SST100_rep_seq.fasta
		python $^ 
		
Figures/shared_lengths_fungi.png: Code/R/visualization_length2.R Data/derived/length_output_fungal.csv
		Rscript $^
		
# Step 4: visualises the pI, aromaticity and logos 
# Step 4.1: Calculate the surprise matrix for  fungi vs animals toxins and fungi vs bacterial toxins
Data/derived/forLogoMaker/fungal_toxins_animal_toxins_LogoMaker.csv: Code/R/matrix_for_logomaker_fungi.R Data/derived/mmseqs2_results/combined_fungi_fasta_SST100_rep_seq.fasta Data/derived/mmseqs2_results/mode0_clu_rep_animal_toxins_SST100_rep_seq.fasta Data/derived/mmseqs2_results/all_fungiandanimal_toxins.fasta
		Rscript $^

Data/derived/forLogoMaker/fungal_toxins_bacterial_toxins_LogoMaker.csv: Code/R/matrix_for_logomaker_fungi.R Data/derived/mmseqs2_results/combined_fungi_fasta_SST100_rep_seq.fasta Data/derived/mmseqs2_results/mode0_clu_rep_bacterial_toxins_SST100_rep_seq.fasta Data/derived/mmseqs2_results/all_fungiandbacterial_toxins.fasta
		Rscript $^		

# Step 4.2 final visualisation
Figures/shared_aromaticity_0.1.png: Code/python/shared_pI_aromaticity.py Data/derived/mmseqs2_results/mode0_clu_rep_animal_toxins_SST100_rep_seq.fasta Data/derived/mmseqs2_results/combined_fungi_fasta_SST100_rep_seq.fasta Data/derived/mmseqs2_results/mode0_clu_rep_bacterial_toxins_SST100_rep_seq.fasta Data/derived/mmseqs2_results/mode0_clu_rep_bacterial_control_SST100_rep_seq.fasta Data/derived/forLogoMaker/fungi_toxins_animal_toxins_LogoMaker.csv Data/derived/forLogoMaker/fungi_toxins_bacterial_toxins_LogoMaker.csv
		python3 $^
