visualisation works fine

visualize.py

@@ -100,7 +100,6 @@ def make_box_plot(groups_files_names, groups_genes_of_interest, output_directory
 		sorted_genes_of_interest = sorted(genes_of_interest, key = lambda x: np.mean(genes_of_interest[x]))
 
 		for gene in sorted_genes_of_interest:
-			print(genes_of_interest[gene])
 			group_data.extend(genes_of_interest[gene])
 
 		data.append(group_data)
@@ -165,18 +164,20 @@ def read_correlation(correlation_file, groups, variable):
 			if len(genes_family) != 0:
 				logger.info("working with the gene " + gene_name)
 
+				#the score is in [3], the tsl is in [2]
+
 				for genes_line in re.split(r'\n', genes_family):
 					genes_array = re.split(r'\t', genes_line)
 					if genes_array[0] == gene_name:
 						#this is a perfect match <3
-						genes_to_show[gene_name].append(float(genes_array[2])) #append score to the array
+						genes_to_show[gene_name].append(float(genes_array[3])) #append score to the array
 					elif genes_array[0].startswith(gene_name) and len(genes_array[0]) <= len(gene_name) + variable: #the found gene is by default 1 char longer than the gene name
 						if genes_array[0] in genes_to_show.keys():
-							genes_to_show[genes_array[0]].append(float(genes_array[2]))
+							genes_to_show[genes_array[0]].append(float(genes_array[3]))
 						else: #this gene is not yet saved
 							#make a new place in the dictionary for this gene
 							genes_to_show[genes_array[0]] = genes_to_show.get(genes_array[0], [])
-							genes_to_show[genes_array[0]].append(float(genes_array[2]))
+							genes_to_show[genes_array[0]].append(float(genes_array[3]))
 
 			else:
 				logger.info("no similar genes to " + gene_name + " were found")