import pandas as pd

######################################################
# config file
######################################################
configfile: "config.yaml"

######################################################
# read samples.txt to dict
######################################################
SAMPLES = pd.read_csv(config["SAMPLES_FILE"], header=None, sep="\t").set_index(1, drop=False)[0].to_dict()

f = open(config['contrasts'], 'r')
CONTRASTS = [i.strip().replace('\t', '_vs_') for i in f.readlines()]

######################################################
# result files
######################################################
rule all:
    input:
        config["Assembly_Dir"] + "/trinity_out_dir.Trinity.fasta",           										# Trinity.fasta
        config["Assembly_Dir"] + "/trinity_out_dir.Trinity.fasta.txt",       										# Trinity assembly result statistics
        config["Assembly_Dir"] + "/corset.fasta",                            										# corset.fasta  
	    config["Assembly_Dir"] + "/corset.fasta.txt",                        										# corset cluster result statistics
        config["Assembly_Dir"] + "/corset-clusters_trans_map.txt",           										# corset cluster to transcript mapping
        config["Assembly_Dir"] + "/run_busco/short_summary_busco.txt",       										# busco result
        #config["Annotation_Dir"] + "/anno_stat.txt",                         										# annotation statistics
        config["Quantification_Dir"] + "/my.gene.counts.matrix",             										# gene counts matrix
        config["Quantification_Dir"] + "/my.gene.TMM.EXPR.matrix",           										# TMP and TMM normalized matrix
        config["ExprAnalysis_Dir"] + "/sample_cor/my.minRow10.sample_cor.dat",										# sample correlation
        config["ExprAnalysis_Dir"] + "/sample_cor/my.minRow10.sample_cor_matrix.pdf",								# sample correlation plot
        config["ExprAnalysis_Dir"] + "/pca/my.minRow10.PCA.prcomp.scores",											# sample PCA
        config["ExprAnalysis_Dir"] + "/pca/my.minRow10.prcomp.principal_components.pdf",							# sample PCA plot
        expand(config["ExprAnalysis_Dir"] + "/deg/my.gene.counts.matrix.{vs}.DESeq2.DE_results", vs=CONTRASTS)
        #expand(config["ExprAnalysis_Dir"] + "/deg/my.gene.counts.matrix.{vs}.DESeq2.DE_results.ekp_results.txt", vs = CONTRASTS)



######################################################
# Includes
######################################################
include: "Includes/Assembly.snake"
#include: "Includes/Annotation.snake"
include: "Includes/Mapping_Denovo.snake"
include: "Includes/Quantification_Denovo.snake"
include: "Includes/ExprAnalysis.snake"